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Crystal structure of human PD-L1 in complex with high affinity PD-1 mutant

Method: X-RAY DIFFRACTION Dmax: 90.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Programmed cell death protein 1

Homo sapiens

UniProt Q15116

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 26–146 Mutation：V64H, N66V, Y68H, M70E, N74G, K78T, C93A, L122V, A125V, A132I Programmed cell death 1 ligand 1 × 1 （Q9NZQ7） CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；0.1 M bis-TRIS pH 6.4, 17% PEG MME 5000, 2 mM LiCl Resolution 2.89 Å R-free 0.260
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 26–146 Mutation：V64H, N66V, Y68H, M70E, N74G, K78T, C93A, L122V, A125V, A132I Programmed cell death 1 ligand 1 × 1 （Q9NZQ7） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；0.1 M bis-TRIS pH 6.4, 17% PEG MME 5000, 2 mM LiCl Resolution 2.89 Å R-free 0.260

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5IUS Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2M2D Human programmed cell death 1 receptor Deposited 2012-12-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 34–150（117 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.4；298 K；Ionic strength (raw mmCIF value) 0.125；Pressure ambient
NMR sample composition 0.5 mM [U-15N] protein, 25 mM potassium phosphate, 100 mM sodium chloride, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.5 mM [U-13C; U-15N] protein, 25 mM potassium phosphate, 100 mM sodium chloride, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.5 mM protein, 25 mM potassium phosphate, 100 mM sodium chloride, 100% D2O | 100% D2O
Resolution not provided
3RRQ Crystal structure of the extracellular domain of human PD-1 Deposited 2011-04-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–160（129 aa） Fragment：Residues 32-160
Mutation：A132L No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；3.5M Sodium formate, 0.1M Bis-Tris, pH 7.5, Vapor diffusion, Sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP
Resolution 2.10 Å R-free 0.249
4ZQK Structure of the complex of human programmed death-1 (PD-1) and its ligand PD-L1. Deposited 2015-05-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 33–150（118 aa） Fragment：UNP Residues 33-150
Mutation：C93S NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.1 M BIS-Tris pH 5.5, 1.84 M ammonium sulfate
Resolution 2.45 Å R-free 0.253
5B8C High resolution structure of the human PD-1 in complex with pembrolizumab Fv Deposited 2016-06-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 32–160（129 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20 % PEG 3350, 0.2 M KNO3
Resolution 2.15 Å R-free 0.226
5B8C High resolution structure of the human PD-1 in complex with pembrolizumab Fv Deposited 2016-06-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 32–160（129 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20 % PEG 3350, 0.2 M KNO3
Resolution 2.15 Å R-free 0.226
5B8C High resolution structure of the human PD-1 in complex with pembrolizumab Fv Deposited 2016-06-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 32–160（129 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20 % PEG 3350, 0.2 M KNO3
Resolution 2.15 Å R-free 0.226
5B8C High resolution structure of the human PD-1 in complex with pembrolizumab Fv Deposited 2016-06-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 32–160（129 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20 % PEG 3350, 0.2 M KNO3
Resolution 2.15 Å R-free 0.226
5GGR PD-1 in complex with nivolumab Fab Deposited 2016-06-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Y 26–150（125 aa） Fragment：UNP residues 26-150
Mutation：C93S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH 6.5, 12% PEG500 MME, 6% PEG20,000, 50 mM ammonium acetate
Resolution 3.30 Å R-free 0.268
5GGR PD-1 in complex with nivolumab Fab Deposited 2016-06-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Z 26–150（125 aa） Fragment：UNP residues 26-150
Mutation：C93S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH 6.5, 12% PEG500 MME, 6% PEG20,000, 50 mM ammonium acetate
Resolution 3.30 Å R-free 0.268
5GGS PD-1 in complex with pembrolizumab Fab Deposited 2016-06-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Z 26–148（123 aa） Fragment：UNP residues 26-148
Mutation：C93S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH 6.5, 12% PEG500 MME, 6% PEG20,000, 50 mM ammonium acetate
Resolution 2.00 Å R-free 0.228
5GGS PD-1 in complex with pembrolizumab Fab Deposited 2016-06-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Y 26–148（123 aa） Fragment：UNP residues 26-148
Mutation：C93S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES, pH 6.5, 12% PEG500 MME, 6% PEG20,000, 50 mM ammonium acetate
Resolution 2.00 Å R-free 0.228
5JXE Human PD-1 ectodomain complexed with Pembrolizumab Fab Deposited 2016-05-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 33–146（114 aa） Fragment：UNP RESIDUES 34-146
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M sodium citrate pH 5.6, 19 mM n-Decyl-N,N-dimethylglycine, 20% isopropanol and 20% PEG 4000
Resolution 2.90 Å R-free 0.286
5JXE Human PD-1 ectodomain complexed with Pembrolizumab Fab Deposited 2016-05-13 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 33–146（114 aa） Fragment：UNP RESIDUES 34-146
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M sodium citrate pH 5.6, 19 mM n-Decyl-N,N-dimethylglycine, 20% isopropanol and 20% PEG 4000
Resolution 2.90 Å R-free 0.286
5WT9 Complex structure of PD-1 and nivolumab-Fab Deposited 2016-12-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–167（167 aa） Fragment：UNP RESIDUES 1-167
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.2M Ammonium acetate, 0.1 M BIS-TRIS pH5.5, 25% w/v Polyethylene glycol 3350
Resolution 2.40 Å R-free 0.228
6HIG hPD-1/NBO1a Fab complex Deposited 2018-08-29 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 33–150（118 aa）
Mutation：C93S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；0.2 M NH4I 20 % PEG 3.35 K
Resolution 2.20 Å R-free 0.270
6J14 Complex structure of GY-14 and PD-1 Deposited 2018-12-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 33–147（115 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6.5；277 K；0.06 M MgCl2, CaCl2, 0.1 M imidazole-MES (pH 6.5), 18% v/v ethylene glycol and polyethylene glycol 8000
Resolution 1.40 Å R-free 0.215
6J15 Complex structure of GY-5 Fab and PD-1 Deposited 2018-12-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 32–147（116 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；277 K；0.1 M citrate (pH 5.0), 20% w/v polyethylene glycol 6000, 0.2 M ammonium acetate
Resolution 2.60 Å R-free 0.277
6J15 Complex structure of GY-5 Fab and PD-1 Deposited 2018-12-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 32–147（116 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；277 K；0.1 M citrate (pH 5.0), 20% w/v polyethylene glycol 6000, 0.2 M ammonium acetate
Resolution 2.60 Å R-free 0.277
6JBT Complex structure of toripalimab-Fab and PD-1 Deposited 2019-01-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 21–170（150 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；277 K；0.09 M Halogens consisting of NaF, NaBr and NaI additives, 0.1 M Tris-Base (pH8.5), 37.5% (v/v) MPD-P1K-P3350 consisting of MPD (racemic), PEG 1K and PEG 3350
Resolution 2.47 Å R-free 0.252
6JJP Crystal structure of Fab of a PD-1 monoclonal antibody MW11-h317 in complex with PD-1 Deposited 2019-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 21–167（147 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.1 M Bis-Tris (pH 6.5) and 28% polyethylene glycol monomethyl ether 2000
Resolution 2.90 Å R-free 0.247
6JJP Crystal structure of Fab of a PD-1 monoclonal antibody MW11-h317 in complex with PD-1 Deposited 2019-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 21–167（147 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；0.1 M Bis-Tris (pH 6.5) and 28% polyethylene glycol monomethyl ether 2000
Resolution 2.90 Å R-free 0.247
6K0Y Study of the interactions of a novel monoclonal antibody, mAb059c, with the hPD-1 receptor Deposited 2019-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 25–167（143 aa）
Mutation：C93S EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.2M NaCl , 0.1M Tris pH 8, 14% PEG 4K
Resolution 1.70 Å R-free 0.214
6UMT High-affinity human PD-1 PD-L2 complex Deposited 2019-10-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 33–150（118 aa） Fragment：UNP residues 33-150
Mutation：N74G, T76P, A132V MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；200 mM magnesium acetate, 10% w/v PEG8000
Resolution 1.99 Å R-free 0.226
6UMU Human apo PD-1 triple mutant Deposited 2019-10-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 33–150（118 aa） Fragment：UNP residues 33-150
Mutation：N74G, T76P, A132V CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM sodium chloride, 100 mM Tris-HCl, pH 8.0, 27% w/v PEG5000 MME
Resolution 1.18 Å R-free 0.164
6UMV Human apo PD-1 double mutant Deposited 2019-10-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 33–150（118 aa） Fragment：UNP residues 33-150
Mutation：T76P, A132V CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM sodium chloride, 100 mM Tris-HCl, pH 8.0, 36% w/v PEG3350
Resolution 1.42 Å R-free 0.189
6XKR Structure of Sasanlimab Fab in complex with PD-1 Deposited 2020-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain P 32–160（129 aa）
Not recorded GOL GLYCEROL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；298 K；0.5M LiCl, 0.1M Citric Acid, pH 4, 22% w/v PEG 6000, 0.5% w/v ODG
Resolution 2.59 Å R-free 0.271
7BXA Crystal structure of PD-1 in complex with tislelizumab Fab Deposited 2020-04-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 29–150（122 aa）
Mutation：C93S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium sulfate, 30% w/v polyethylene glycol 4000
Resolution 3.32 Å R-free 0.299
7BXA Crystal structure of PD-1 in complex with tislelizumab Fab Deposited 2020-04-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain P 29–150（122 aa）
Mutation：C93S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium sulfate, 30% w/v polyethylene glycol 4000
Resolution 3.32 Å R-free 0.299
7CGW Complex structure of PD-1 and tislelizumab Fab Deposited 2020-07-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 25–169（145 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；0.1M Citric acid, pH4.0, 1M LiCl and 20% PEG6000
Resolution 3.20 Å R-free 0.254
7CGW Complex structure of PD-1 and tislelizumab Fab Deposited 2020-07-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain P 25–169（145 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；0.1M Citric acid, pH4.0, 1M LiCl and 20% PEG6000
Resolution 3.20 Å R-free 0.254
7CU5 N-Glycosylation of PD-1 and glycosylation dependent binding of PD-1 specific monoclonal antibody camrelizumab Deposited 2020-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 30–147（118 aa）
Chain Q 30–147（118 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M cadmium chloride, 0.1M Na acetate, pH4.6, 30 %(v/v) PEG 400 a month later.
Resolution 2.81 Å R-free 0.252
7E9B Structural basis of HLX10 PD-1 receptor recognition, a promising anti-PD-1 antibody clinical candidate for cancer immunotherapy Deposited 2021-03-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 32–146（115 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Tris pH 7.5 containing 23% (w/v) PEG 4000
Resolution 1.78 Å R-free 0.210
7VUX Complex structure of PD1 and 609A-Fab Deposited 2021-11-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 32–160（129 aa）
Not recorded THR THREONINE × 1 GOL GLYCEROL × 7 EDO 1,2-ETHANEDIOL × 7 MG MAGNESIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Ammonium formate, pH 6.6, 20% w/v PEG 3350
Resolution 1.64 Å R-free 0.202
7WSL PD-1 in complex with Dostarlimab Deposited 2022-01-30 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 29–150（122 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2M trimethylamine N-oxide dihydrate, 0.1M Tris pH 8.5, 20% w/v PEG 3350
Resolution 1.53 Å R-free 0.178
7WVM The complex structure of PD-1 and cemiplimab Deposited 2022-02-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 31–147（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Sodium acetate, pH 5.0, 5% w/v PGA (Na+ form, LM), 20% w/v PEG 2000 MME
Resolution 3.40 Å R-free 0.287
7WVM The complex structure of PD-1 and cemiplimab Deposited 2022-02-10 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 31–147（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Sodium acetate, pH 5.0, 5% w/v PGA (Na+ form, LM), 20% w/v PEG 2000 MME
Resolution 3.40 Å R-free 0.287
8AS0 PD-1 extracellular domain in complex with Fab fragment from D12 antibody Deposited 2022-08-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 24–170（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；22% PEG 3350, 250 mM sodium malonate, pH 4.5
Resolution 3.50 Å R-free 0.293
8AS0 PD-1 extracellular domain in complex with Fab fragment from D12 antibody Deposited 2022-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 24–170（147 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；22% PEG 3350, 250 mM sodium malonate, pH 4.5
Resolution 3.50 Å R-free 0.293
8AS0 PD-1 extracellular domain in complex with Fab fragment from D12 antibody Deposited 2022-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 24–170（147 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；22% PEG 3350, 250 mM sodium malonate, pH 4.5
Resolution 3.50 Å R-free 0.293
8AS0 PD-1 extracellular domain in complex with Fab fragment from D12 antibody Deposited 2022-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 24–170（147 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；22% PEG 3350, 250 mM sodium malonate, pH 4.5
Resolution 3.50 Å R-free 0.293
8AS0 PD-1 extracellular domain in complex with Fab fragment from D12 antibody Deposited 2022-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain O 24–170（147 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；22% PEG 3350, 250 mM sodium malonate, pH 4.5
Resolution 3.50 Å R-free 0.293
8AS0 PD-1 extracellular domain in complex with Fab fragment from D12 antibody Deposited 2022-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain R 24–170（147 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；22% PEG 3350, 250 mM sodium malonate, pH 4.5
Resolution 3.50 Å R-free 0.293
8AS0 PD-1 extracellular domain in complex with Fab fragment from D12 antibody Deposited 2022-08-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 7 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain X 24–170（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；22% PEG 3350, 250 mM sodium malonate, pH 4.5
Resolution 3.50 Å R-free 0.293
8AS0 PD-1 extracellular domain in complex with Fab fragment from D12 antibody Deposited 2022-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain Y 24–170（147 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；22% PEG 3350, 250 mM sodium malonate, pH 4.5
Resolution 3.50 Å R-free 0.293
8EQ6 PD1 signaling receptor bound to FAB Complex Deposited 2022-10-07 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–148（124 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；20.5% PEG 3350, 0.4M MgCl2, 0.1M Bis-Tris pH 5.5
Resolution 1.65 Å R-free 0.257
8GY5 High-resolution structure of the cemiplimab Fab in complex with PD-1 Deposited 2022-09-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Q 26–150（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium formate, 20% PEG 3350
Resolution 1.98 Å R-free 0.235
8GY5 High-resolution structure of the cemiplimab Fab in complex with PD-1 Deposited 2022-09-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain P 26–150（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium formate, 20% PEG 3350
Resolution 1.98 Å R-free 0.235
8U31 Crystal structure of PD-1 in complex with a Fab Deposited 2023-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–146（122 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 20% w/v PEG 3,350
Resolution 2.73 Å R-free 0.237
8U32 Crystal structure of PD-1 in complex with a Fab Deposited 2023-09-07 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–146（122 aa）
Mutation：C93S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 %w/v PEG 3350, 0.2 M Na2 Malon, 0.1 M BIS-TRIS prop pH 8.5
Resolution 2.51 Å R-free 0.230
8U32 Crystal structure of PD-1 in complex with a Fab Deposited 2023-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 25–146（122 aa）
Mutation：C93S NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 %w/v PEG 3350, 0.2 M Na2 Malon, 0.1 M BIS-TRIS prop pH 8.5
Resolution 2.51 Å R-free 0.230
9EHT Crystal Structure of PD-1/retifanlimab complex Deposited 2024-11-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 26–150（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；35.00 % (w/v) 2,4-methyl pentanediol, 200 mM Sodium chloride, and 100 mM Tris at pH 7.0
Resolution 1.54 Å R-free 0.208
9EHT Crystal Structure of PD-1/retifanlimab complex Deposited 2024-11-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 26–150（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；35.00 % (w/v) 2,4-methyl pentanediol, 200 mM Sodium chloride, and 100 mM Tris at pH 7.0
Resolution 1.54 Å R-free 0.208
9HK1 PD1 signaling receptor bound to FAB Complex Deposited 2024-12-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 25–148（124 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；20.5% PEG 3350, 0.4M MgCl2, 0.1M Bis-Tris pH 5.5
Resolution 2.03 Å R-free 0.276
9HK1 PD1 signaling receptor bound to FAB Complex Deposited 2024-12-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 25–148（124 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；20.5% PEG 3350, 0.4M MgCl2, 0.1M Bis-Tris pH 5.5
Resolution 2.03 Å R-free 0.276
9Q8L Crystal Structure of 21A08Ap1-Fab in Complex with Human PD-1 at 1.85 angstrom Resolution Deposited 2025-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 24–170（147 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 DMS DIMETHYL SULFOXIDE × 1 PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris pH 8.5, 25% w/v PEG 3,350, 20% w/v MPD
Resolution 1.85 Å R-free 0.216

33 other PDB entries and 55 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PDCD1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–125； UniProt 26–146 Author chain B； PDBConstruct 5–125； UniProt 26–146

Programmed cell death 1 ligand 1

Homo sapiens

UniProt Q9NZQ7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 18–239 Not recorded Programmed cell death protein 1 × 1 （Q15116） CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；0.1 M bis-TRIS pH 6.4, 17% PEG MME 5000, 2 mM LiCl Resolution 2.89 Å R-free 0.260
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 18–239 Not recorded Programmed cell death protein 1 × 1 （Q15116） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.4；293 K；0.1 M bis-TRIS pH 6.4, 17% PEG MME 5000, 2 mM LiCl Resolution 2.89 Å R-free 0.260

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5IUS Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
13FL Structure of FabS1CE2_P2a in complex with the N-terminal domain of PD-L1 Deposited 2026-05-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 19–132（114 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.22 Å R-free 0.239
3BIK Crystal Structure of the PD-1/PD-L1 Complex Deposited 2007-11-30 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 18–239（222 aa） Fragment：EXTRACELLULAR REGION
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；20% PEG 3350, 200MM NH4H2PO4, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.65 Å R-free 0.268
3BIS Crystal Structure of the PD-L1 Deposited 2007-11-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 18–239（222 aa） Fragment：EXTRACELLULAR REGION
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；20% PEG 3350, 0.1 M NaCacodylate, 0.2 M ammonium formate or ammonium fluoride, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.64 Å R-free 0.292
3BIS Crystal Structure of the PD-L1 Deposited 2007-11-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 18–239（222 aa） Fragment：EXTRACELLULAR REGION
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；20% PEG 3350, 0.1 M NaCacodylate, 0.2 M ammonium formate or ammonium fluoride, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.64 Å R-free 0.292
3FN3 Dimeric Structure of PD-L1 Deposited 2008-12-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 19–238（220 aa） Fragment：extracellular domain
Chain B 19–238（220 aa） Fragment：extracellular domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；15% PEG 3350 (w/v), 0.2M ammonium acetate (NH4Ac), 0.1M BIS-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.70 Å R-free 0.296
3SBW Crystal structure of the complex between the extracellular domains of mouse PD-1 mutant and human PD-L1 Deposited 2011-06-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 19–239（221 aa） Fragment：UNP residues 19-239
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；277 K；0.1M Sodium citrate pH 5, 20% PEG 8000, Vapor diffusion, Sitting drop, temperature 277K
Resolution 2.28 Å R-free 0.270
4Z18 CRYSTAL STRUCTURE OF HUMAN PD-L1 Deposited 2015-03-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 19–239（221 aa） Fragment：UNP RESIDUES 19-339
Chain B 19–239（221 aa） Fragment：UNP RESIDUES 19-339
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG 3350, sodium chloride, hepes
Resolution 1.95 Å R-free 0.246
4ZQK Structure of the complex of human programmed death-1 (PD-1) and its ligand PD-L1. Deposited 2015-05-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 18–132（115 aa）
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.1 M BIS-Tris pH 5.5, 1.84 M ammonium sulfate
Resolution 2.45 Å R-free 0.253
5C3T PD-1 binding domain from human PD-L1 Deposited 2015-06-17 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 18–134（117 aa） Fragment：UNP residues 18-134
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.15 K；1.84 Na Formate
Resolution 1.80 Å R-free 0.178
5GGT PD-L1 in complex with BMS-936559 Fab Deposited 2016-06-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 18–134（117 aa） Fragment：UNP residues 18-134
Mutation：Q57E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M imidazole, pH 9.0, 1.2M sodium citrate
Resolution 2.80 Å R-free 0.269
5GRJ Crystal structure of human PD-L1 with monoclonal antibody avelumab Deposited 2016-08-11 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 18–238（221 aa） Fragment：UNP residues 18-238
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.5；291 K；0.2 M magnesium chloride hexahydrate, 0.1 M HEPES-Na, 30%(v/v) iso-Propanol
Resolution 3.21 Å R-free 0.238
5J89 Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor Deposited 2016-04-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 2–134（133 aa）
Chain D 2–134（133 aa）
Not recorded 6GX N-{2-[({2-methoxy-6-[(2-methyl[1,1'-biphenyl]-3-yl)methoxy]pyridin-3-yl}methyl)amino]ethyl}acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.01M Tris pH=8.5, 0.3M sodium chloride, 27% (w/v) PEG 4000
Resolution 2.20 Å R-free 0.256
5J89 Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor Deposited 2016-04-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–134（133 aa）
Chain B 2–134（133 aa）
Not recorded 6GX N-{2-[({2-methoxy-6-[(2-methyl[1,1'-biphenyl]-3-yl)methoxy]pyridin-3-yl}methyl)amino]ethyl}acetamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.01M Tris pH=8.5, 0.3M sodium chloride, 27% (w/v) PEG 4000
Resolution 2.20 Å R-free 0.256
5J8O Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor Deposited 2016-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Not recorded 6GZ (2R)-1-({3-bromo-4-[(2-methyl[1,1'-biphenyl]-3-yl)methoxy]phenyl}methyl)piperidine-2-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.2 M ammonium formate and 20% (w/v) PEG 3350
Resolution 2.30 Å R-free 0.305
5JDR Structure of PD-L1 Deposited 2016-04-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–239（222 aa） Fragment：UNP RESIDUES 18-239
Chain B 18–239（222 aa） Fragment：UNP RESIDUES 18-239
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions LIQUID DIFFUSION；295 K；0.2 M Ammonium Acetate, 20% PEG 3350
Resolution 2.70 Å R-free 0.276
5JDS Crystal structure of PD-L1 complexed with a nanobody at 1.7 Angstron resolution Deposited 2016-04-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 18–132（115 aa） Fragment：UNP RESIDUES 18-132
Not recorded NA SODIUM ION × 2 CL CHLORIDE ION × 3 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIQUID DIFFUSION；295 K；2M NaCl, 1.4M (NH4)2SO4
Resolution 1.70 Å R-free 0.204
5N2D Structure of PD-L1/small-molecule inhibitor complex Deposited 2017-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–134（133 aa）
Chain B 2–134（133 aa）
Chain C 2–134（133 aa）
Chain D 2–134（133 aa）
Not recorded 8J8 ~{N}-[2-[[2,6-dimethoxy-4-[(2-methyl-3-phenyl-phenyl)methoxy]phenyl]methylamino]ethyl]ethanamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris pH 8.5, 0.2 M magnesium chloride, 30% (w/v) PEG 4000
Resolution 2.35 Å R-free 0.267
5N2F Structure of PD-L1/small-molecule inhibitor complex Deposited 2017-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Not recorded 8HW 4-[[4-[[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methyl-phenyl]methoxy]-2,5-bis(fluoranyl)phenyl]methylamino]-3-oxidanylidene-butanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.01 M Tris pH 8.4 , 0.28 M sodium chloride, 27% (w/v) PEG 4000
Resolution 1.70 Å R-free 0.230
5NIU Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor Deposited 2017-03-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Not recorded 8YZ (2~{R})-2-[[2-[(3-cyanophenyl)methoxy]-4-[[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methyl-phenyl]methoxy]-5-methyl-phenyl]methylamino]-3-oxidanyl-propanoic acid × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Tris pH 8.5 containing 0.2 M magnesium chloride and 30% (w/v) PEG 4000
Resolution 2.01 Å R-free 0.262
5NIU Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor Deposited 2017-03-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 18–134（117 aa）
Chain D 18–134（117 aa）
Not recorded 8YZ (2~{R})-2-[[2-[(3-cyanophenyl)methoxy]-4-[[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methyl-phenyl]methoxy]-5-methyl-phenyl]methylamino]-3-oxidanyl-propanoic acid × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M Tris pH 8.5 containing 0.2 M magnesium chloride and 30% (w/v) PEG 4000
Resolution 2.01 Å R-free 0.262
5O45 Structure of human PD-L1 in complex with inhibitor Deposited 2017-05-26 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 17–134（118 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M imidazole malate (pH 8.5) 27% PEG 10000
Resolution 0.99 Å R-free 0.137
5O4Y Structure of human PD-L1 in complex with inhibitor Deposited 2017-05-31 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 18–132（115 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium acetate (pH 5.5), 0.1 M Bis-Tris, 25% PEG 3350
Resolution 2.30 Å R-free 0.262
5O4Y Structure of human PD-L1 in complex with inhibitor Deposited 2017-05-31 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 18–132（115 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium acetate (pH 5.5), 0.1 M Bis-Tris, 25% PEG 3350
Resolution 2.30 Å R-free 0.262
5O4Y Structure of human PD-L1 in complex with inhibitor Deposited 2017-05-31 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 18–132（115 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium acetate (pH 5.5), 0.1 M Bis-Tris, 25% PEG 3350
Resolution 2.30 Å R-free 0.262
5X8L PD-L1 in complex with atezolizumab Deposited 2017-03-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 18–134（117 aa） Fragment：UNP residues 18-134
Mutation：Q47E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Sodium HEPES pH 7.5, 20% w/v PEG8000
Resolution 3.10 Å R-free 0.256
5X8L PD-L1 in complex with atezolizumab Deposited 2017-03-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 18–134（117 aa） Fragment：UNP residues 18-134
Mutation：Q47E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Sodium HEPES pH 7.5, 20% w/v PEG8000
Resolution 3.10 Å R-free 0.256
5X8L PD-L1 in complex with atezolizumab Deposited 2017-03-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 18–134（117 aa） Fragment：UNP residues 18-134
Mutation：Q47E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Sodium HEPES pH 7.5, 20% w/v PEG8000
Resolution 3.10 Å R-free 0.256
5X8L PD-L1 in complex with atezolizumab Deposited 2017-03-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 18–134（117 aa） Fragment：UNP residues 18-134
Mutation：Q47E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Sodium HEPES pH 7.5, 20% w/v PEG8000
Resolution 3.10 Å R-free 0.256
5X8L PD-L1 in complex with atezolizumab Deposited 2017-03-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 18–134（117 aa） Fragment：UNP residues 18-134
Mutation：Q47E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Sodium HEPES pH 7.5, 20% w/v PEG8000
Resolution 3.10 Å R-free 0.256
5X8M PD-L1 in complex with durvalumab Deposited 2017-03-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 18–134（117 aa） Fragment：UNP residues 18-134
Mutation：Q47E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Ammonium sulfate, 0.1M Bis-Tris pH 5.5, 25% w/v PEG 3350
Resolution 2.66 Å R-free 0.219
5XJ4 Complex structure of durvalumab-scFv/PD-L1 Deposited 2017-04-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–238（220 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7；291 K；3.5 M sodium formate, pH 7.0
Resolution 2.30 Å R-free 0.240
5XXY Crystal structure of PD-L1 complexed with atezolizumab fab at 2.9A Deposited 2017-07-05 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 18–133（116 aa） Fragment：IgV domain,UNP residues 18-133
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；2M ammonium sulfate, 0.1M Tris PH 7.0
Resolution 2.90 Å R-free 0.295
6L8R membrane-bound PD-L1-CD Deposited 2019-11-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 260–290（31 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR sample composition 0.5 mM 15N_13C_2H PD-L1-CD, 60 mM DMPG, 85 mM DHPC, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM 15N_13C PD-L1-CD, 60 mM 2H DMPG, 85 mM 2H DHPC, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM 15N_2H PD-L1-CD, 60 mM POPG, 85 mM 2H DHPC, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6NM7 PD-L1 IgV domain bound to fragment Deposited 2019-01-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 19–134（116 aa）
Chain B 19–134（116 aa）
Mutation：V76T Mutation：V76T 22L 5-phenylthieno[2,3-d]pyrimidin-4(3H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.056 M NaH2PO4, 1.344 M K2HPO4
Resolution 2.43 Å R-free 0.269
6NM8 IgV-V76T BMS compound 105 Deposited 2019-01-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 19–134（116 aa）
Chain B 19–134（116 aa）
Mutation：V76T Mutation：V76T KSD N-({2,6-dimethoxy-4-[(2-methyl[1,1'-biphenyl]-3-yl)methoxy]phenyl}methyl)-D-alanine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；29% PEG 4000, 0.28 M NaCl, 0.01 M Tris
Resolution 2.79 Å R-free 0.304
6NNV PD-L1 IgV domain complex with macro-cyclic peptide Deposited 2019-01-15 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa） Fragment：UNP residues 18-134
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.056 M sodium phosphate monobasic, 1.344 M potassium phosphate dibasic
Resolution 1.92 Å R-free 0.253
6NNV PD-L1 IgV domain complex with macro-cyclic peptide Deposited 2019-01-15 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 18–134（117 aa） Fragment：UNP residues 18-134
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.056 M sodium phosphate monobasic, 1.344 M potassium phosphate dibasic
Resolution 1.92 Å R-free 0.253
6NNV PD-L1 IgV domain complex with macro-cyclic peptide Deposited 2019-01-15 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 18–134（117 aa） Fragment：UNP residues 18-134
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.056 M sodium phosphate monobasic, 1.344 M potassium phosphate dibasic
Resolution 1.92 Å R-free 0.253
6NNV PD-L1 IgV domain complex with macro-cyclic peptide Deposited 2019-01-15 Different construct Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 18–134（117 aa） Fragment：UNP residues 18-134
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.056 M sodium phosphate monobasic, 1.344 M potassium phosphate dibasic
Resolution 1.92 Å R-free 0.253
6NOJ PD-L1 IgV domain V76T with fragment Deposited 2019-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa） Fragment：UNP residues 18-134
Chain B 18–134（117 aa） Fragment：UNP residues 18-134
Not recorded KW7 methyl 3-amino-4-(2-fluorophenyl)-1H-pyrrole-2-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.056 M sodium phosphate monobasic, 1.344 M potassium phosphate dibasic
Resolution 2.33 Å R-free 0.245
6NOS PD-L1 IgV domain V76T with fragment Deposited 2019-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa） Fragment：UNP residues 18-134
Chain B 18–134（117 aa） Fragment：UNP residues 18-134
Not recorded KWA 1-[5-(3,5-dichlorophenyl)furan-2-yl]-N-methylmethanamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.056 M sodium phosphate monobasic, 1.344 M potassium phosphate dibasic
Resolution 2.70 Å R-free 0.275
6NP9 PD-L1 IgV domain V76T with fragment Deposited 2019-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Mutation：V76T SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；Ammonium Sulfate
Resolution 1.27 Å R-free 0.218
6PV9 Human PD-L1 bound to a macrocyclic peptide which blocks the PD-1/PD-L1 interaction Deposited 2019-07-19 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–239（221 aa） Fragment：extracellular domain (UNP residues 19-239)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；20% PEG3000, 0.1 M sodium citrate, pH 5.5
Resolution 2.00 Å R-free 0.226
6R3K Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor Deposited 2019-03-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 JQT (2~{S},4~{R})-1-[[5-chloranyl-2-[(3-cyanophenyl)methoxy]-4-[[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methyl-phenyl]methoxy]phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.01 M Tris pH 8.4 containing 0.28 M sodium chloride and 27% (w/v) PEG 4000
Resolution 2.20 Å R-free 0.259
6R3K Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor Deposited 2019-03-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 18–134（117 aa）
Chain D 18–134（117 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 JQT (2~{S},4~{R})-1-[[5-chloranyl-2-[(3-cyanophenyl)methoxy]-4-[[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methyl-phenyl]methoxy]phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.01 M Tris pH 8.4 containing 0.28 M sodium chloride and 27% (w/v) PEG 4000
Resolution 2.20 Å R-free 0.259
6RPG Structure of human Programmed cell death 1 ligand 1 (PD-L1) with inhibitor Deposited 2019-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Not recorded KDW ~{N}-[2-[[4-[[3-[3-[[4-[(2-acetamidoethylamino)methyl]-5-[(5-cyanopyridin-3-yl)methoxy]-2-methyl-phenoxy]methyl]-2-methyl-phenyl]-2-methyl-phenyl]methoxy]-2-[(5-cyanopyridin-3-yl)methoxy]-5-methyl-phenyl]methylamino]ethyl]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M BIS-Tris pH 5.4, 0.2 M ammonium sulfate and 23 % (w/v) PEG 3350
Resolution 2.70 Å R-free 0.281
6VQN Co-crystal structure of human PD-L1 complexed with Compound A Deposited 2020-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Not recorded R81 N,N'-(2,2'-dimethyl[1,1'-biphenyl]-3,3'-diyl)bis(5-{[(2-hydroxyethyl)amino]methyl}pyridine-2-carboxamide) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM NaCitrate, pH 6.5 and 22% (w/v) PEG 3000
Resolution 2.49 Å R-free 0.228
6VQN Co-crystal structure of human PD-L1 complexed with Compound A Deposited 2020-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 18–134（117 aa）
Not recorded R81 N,N'-(2,2'-dimethyl[1,1'-biphenyl]-3,3'-diyl)bis(5-{[(2-hydroxyethyl)amino]methyl}pyridine-2-carboxamide) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM NaCitrate, pH 6.5 and 22% (w/v) PEG 3000
Resolution 2.49 Å R-free 0.228
6YCR Structure of human PD-L1 in complex with inhibitor Deposited 2020-03-18 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.0M succinic acid, 0.1M HEPES pH 7.0, 1% w/v PEG 2000 MME
Resolution 1.54 Å R-free 0.180
7BEA Structure of human Programmed cell death 1 ligand 1 (PD-L1) with inhibitor Deposited 2020-12-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Not recorded TK2 2-(aminomethyl)-6-[(2-methyl-3-phenyl-phenyl)methoxy]-~{N}-(2-phenylethyl)imidazo[1,2-a]pyridin-3-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；1.2 M Sodium citrate tribasic dihydrate 0.01 M Sodium borate, pH 8.5
Resolution 2.45 Å
7C88 Complex structure of JS003 and PD-L1 Deposited 2020-05-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain M 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Na HEPES 7.0, 15% w/v PEG 20000
Resolution 2.00 Å R-free 0.258
7C88 Complex structure of JS003 and PD-L1 Deposited 2020-05-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–136（136 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Na HEPES 7.0, 15% w/v PEG 20000
Resolution 2.00 Å R-free 0.258
7CZD Crystal structure of PD-L1 in complex with a VHH Deposited 2020-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 19–134（116 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350
Resolution 1.64 Å R-free 0.184
7CZD Crystal structure of PD-L1 in complex with a VHH Deposited 2020-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 19–134（116 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350
Resolution 1.64 Å R-free 0.184
7DCV Structure of the transmembrane domain of human PD-L1 Deposited 2020-10-27 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 232–290（59 aa）
Mutation：C250A, M266L, M267L, C272S No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；310 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR sample composition 20 mM MES, 30 mM DMPC, 60 mM DHPC, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 20 mM MES, 30 mM [U-2H] DMPC, 60 mM [U-2H] DHPC, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7DY7 Discovery of Novel Small-molecule Inhibitors of PD-1/PD-L1 Axis that Promotes PD-L1 Internalization and Degradation Deposited 2021-01-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Not recorded HOU 2-[[3-[[5-(2-methyl-3-phenyl-phenyl)-1,3,4-oxadiazol-2-yl]amino]phenyl]methylamino]ethanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；PEG 3350,ammonium acetate
Resolution 2.42 Å R-free 0.240
7NLD Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor Deposited 2021-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 18–134（117 aa）
Chain D 18–134（117 aa）
Not recorded UGZ N-(2-((2'-chloro-3'-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-3-methoxy-[1,1'-biphenyl]-4-yl)(methyl)amino)ethyl)methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M sodium cocdylate pH 6.5; 25% PEG4000
Resolution 2.30 Å R-free 0.294
7NLD Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor Deposited 2021-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Not recorded UGZ N-(2-((2'-chloro-3'-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-3-methoxy-[1,1'-biphenyl]-4-yl)(methyl)amino)ethyl)methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M sodium cocdylate pH 6.5; 25% PEG4000
Resolution 2.30 Å R-free 0.294
7NLD Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor Deposited 2021-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 18–134（117 aa）
Chain F 18–134（117 aa）
Not recorded UGZ N-(2-((2'-chloro-3'-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-3-methoxy-[1,1'-biphenyl]-4-yl)(methyl)amino)ethyl)methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M sodium cocdylate pH 6.5; 25% PEG4000
Resolution 2.30 Å R-free 0.294
7OUN Structure of human PD-L1 in complex with macrocyclic inhibitor Deposited 2021-06-12 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 17–134（118 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.24；298 K；0.1M sodium citrate 1.95M ammonium sulphate
Resolution 1.90 Å R-free 0.246
7SJQ Ex silico engineering of cystine-dense peptides yielding a potent bispecific T-cell engager Deposited 2021-10-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Not recorded GOL GLYCEROL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；300 K；Sodium Citrate pH 7, ammonium sulfate
Resolution 2.00 Å R-free 0.232
7TPS Crystal structure of ALPN-202 (engineered CD80 vIgD) in complex with PD-L1 Deposited 2022-01-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 19–227（209 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.03 M sodium nitrate, 0.03 M sodium phosphate dibasic, 0.03 M ammonium sulfate, 0.1 M sodium HEPES/MOPS (acid), pH 7.5, 20% v/v glycerol, 10% w/v PEG 4000
Resolution 3.15 Å R-free 0.291
7TPS Crystal structure of ALPN-202 (engineered CD80 vIgD) in complex with PD-L1 Deposited 2022-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 19–227（209 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.03 M sodium nitrate, 0.03 M sodium phosphate dibasic, 0.03 M ammonium sulfate, 0.1 M sodium HEPES/MOPS (acid), pH 7.5, 20% v/v glycerol, 10% w/v PEG 4000
Resolution 3.15 Å R-free 0.291
7UX5 Structure of PDL1 in complex with FP28136, a Helicon Polypeptide Deposited 2022-05-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Not recorded WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M TRIS pH 8, 25% v/v PEG 350 MME.
Resolution 3.35 Å R-free 0.301
7UX5 Structure of PDL1 in complex with FP28136, a Helicon Polypeptide Deposited 2022-05-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 18–134（117 aa）
Not recorded WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M TRIS pH 8, 25% v/v PEG 350 MME.
Resolution 3.35 Å R-free 0.301
7UX5 Structure of PDL1 in complex with FP28136, a Helicon Polypeptide Deposited 2022-05-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 18–134（117 aa）
Not recorded WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M TRIS pH 8, 25% v/v PEG 350 MME.
Resolution 3.35 Å R-free 0.301
7UX5 Structure of PDL1 in complex with FP28136, a Helicon Polypeptide Deposited 2022-05-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 18–134（117 aa）
Not recorded WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M TRIS pH 8, 25% v/v PEG 350 MME.
Resolution 3.35 Å R-free 0.301
7UX5 Structure of PDL1 in complex with FP28136, a Helicon Polypeptide Deposited 2022-05-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 18–134（117 aa）
Not recorded WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M TRIS pH 8, 25% v/v PEG 350 MME.
Resolution 3.35 Å R-free 0.301
7UX5 Structure of PDL1 in complex with FP28136, a Helicon Polypeptide Deposited 2022-05-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain K 18–134（117 aa）
Not recorded WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M TRIS pH 8, 25% v/v PEG 350 MME.
Resolution 3.35 Å R-free 0.301
7UXO Structure of PDL1 in complex with FP30790, a Helicon Polypeptide Deposited 2022-05-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Not recorded NH2 AMINO GROUP × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M Sodium acetate pH 4.6, 2.0 M Sodium formate.
Resolution 2.25 Å R-free 0.250
7UXP Structure of PDL1 in complex with FP28132, a Helicon Polypeptide Deposited 2022-05-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Not recorded NH2 AMINO GROUP × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M MES pH 6.5, 1.6 M Magnesium sulfate.
Resolution 2.62 Å R-free 0.286
7UXP Structure of PDL1 in complex with FP28132, a Helicon Polypeptide Deposited 2022-05-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 18–134（117 aa）
Not recorded NH2 AMINO GROUP × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M MES pH 6.5, 1.6 M Magnesium sulfate.
Resolution 2.62 Å R-free 0.286
7UXQ Structure of PDL1 in complex with FP28135, a Helicon Polypeptide Deposited 2022-05-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；1.1 M Sodium Malonate pH 7.0, 0.1 M HEPES pH 7.0, 0.5% v/v Jeffamine ED-2001 Reagent pH 7.0.
Resolution 2.89 Å R-free 0.228
7UXQ Structure of PDL1 in complex with FP28135, a Helicon Polypeptide Deposited 2022-05-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 18–134（117 aa）
Not recorded EDO 1,2-ETHANEDIOL × 6 WHL N,N'-(1,4-phenylene)diacetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；1.1 M Sodium Malonate pH 7.0, 0.1 M HEPES pH 7.0, 0.5% v/v Jeffamine ED-2001 Reagent pH 7.0.
Resolution 2.89 Å R-free 0.228
7VUN Design, modification, evaluation and cocrystal studies of novel phthalimides regulating PD-1/PD-L1 interaction Deposited 2021-11-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Chain C 18–134（117 aa）
Chain D 18–134（117 aa）
Chain E 18–134（117 aa）
Chain F 18–134（117 aa）
Chain G 18–134（117 aa）
Chain H 18–134（117 aa）
Not recorded 8H7 (2~{S},3~{S})-2-[[6-[(3-cyanophenyl)methoxy]-2-(2-methyl-3-phenyl-phenyl)-1,3-bis(oxidanylidene)isoindol-5-yl]methylamino]-3-oxidanyl-butanoic acid × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；PEG 3350, 1,4 - Dioxane, Tris
Resolution 2.70 Å R-free 0.289
7XAD Crystal strucutre of PD-L1 and DBL2_02 designed protein binder Deposited 2022-03-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–238（238 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M potassium/sodium tartrate, 0.1 M Bis Tris propane, pH 6.5 ,20 % w/v PEG 3350
Resolution 3.00 Å R-free 0.294
7XAD Crystal strucutre of PD-L1 and DBL2_02 designed protein binder Deposited 2022-03-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–238（238 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M potassium/sodium tartrate, 0.1 M Bis Tris propane, pH 6.5 ,20 % w/v PEG 3350
Resolution 3.00 Å R-free 0.294
7XAD Crystal strucutre of PD-L1 and DBL2_02 designed protein binder Deposited 2022-03-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–238（238 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M potassium/sodium tartrate, 0.1 M Bis Tris propane, pH 6.5 ,20 % w/v PEG 3350
Resolution 3.00 Å R-free 0.294
7XAD Crystal strucutre of PD-L1 and DBL2_02 designed protein binder Deposited 2022-03-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–238（238 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M potassium/sodium tartrate, 0.1 M Bis Tris propane, pH 6.5 ,20 % w/v PEG 3350
Resolution 3.00 Å R-free 0.294
7XAE Crystal strucutre of PD-L1 and 3ONJA protein Deposited 2022-03-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–238（238 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium citrate tribasic dihydrate pH 5.5, 16% w/v Polyethylene glycol 8,000
Resolution 3.44 Å R-free 0.262
7XAE Crystal strucutre of PD-L1 and 3ONJA protein Deposited 2022-03-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–238（238 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium citrate tribasic dihydrate pH 5.5, 16% w/v Polyethylene glycol 8,000
Resolution 3.44 Å R-free 0.262
7YDS The structure of the bispecific antibody targeted PD-L1 and 4-1BB Deposited 2022-07-04 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–136（136 aa）
Mutation：N35Q No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；18% PEG4000, 0.1M Bis-tris pH 6.2
Resolution 2.30 Å R-free 0.246
8ALX Structure of human PD-L1 in complex with inhibitor Deposited 2022-08-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Not recorded ACT ACETATE ION × 3 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1.4 M sodium acetate trihydrate; 0.1 M sodium cacodylate pH 6.5
Resolution 1.10 Å R-free 0.136
8AOK Complex of PD-L1 with VHH6 Deposited 2022-08-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 3 ACY ACETIC ACID × 1 OXM OXAMIC ACID × 1 EDO 1,2-ETHANEDIOL × 2 FMT FORMIC ACID × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M HEPES:MOPS, pH 7.5, 0.02 M Ammonium acetate, 0.02 M Potassium sodium tartrate tetrahydrate, 0.02 M Sodium citrate tribasic dihydrate, 0.02 M Sodium formate, 0.02M Sodium oxamate, 10% (w/v) PEG 20000 and 20% (v/v) PEG 500-MME.
Resolution 1.60 Å R-free 0.185
8AOM Complex of PD-L1 with VHH1 Deposited 2022-08-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 19–239（221 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M MOPS, pH 7.5, and 12% (w/v) PEG 8000
Resolution 2.20 Å R-free 0.245
8JBA Discovery and Crystallography Study of Novel Oxadiazole Analogs as Small Molecule PD-1/PD-L1 inhibitors Deposited 2023-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Not recorded AU9 (2~{S})-2-[[3-[[5-[(2-methyl-3-phenyl-phenoxy)methyl]-1,3,4-oxadiazol-2-yl]sulfanylmethyl]phenyl]methylamino]-3-oxidanyl-propanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；Tris, Potassium sodium tartrate tetrahydrate
Resolution 2.60 Å R-free 0.257
8K5N Discovery of Novel PD-L1 Inhibitors That Induce Dimerization and Degradation of PD-L1 Based on Fragment Coupling Strategy Deposited 2023-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Not recorded I7M 3-[(1~{S})-1-[6-methoxy-3-methyl-5-[[[(2~{S})-5-oxidanylidenepyrrolidin-2-yl]methylamino]methyl]pyridin-2-yl]oxy-2,3-dihydro-1~{H}-inden-4-yl]-2-methyl-~{N}-[5-[[[(2~{S})-5-oxidanylidenepyrrolidin-2-yl]methylamino]methyl]pyridin-2-yl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；Ammonium acetate, PEG 3350
Resolution 2.20 Å R-free 0.234
8OR1 Co-crystal strucutre of PD-L1 with low molecular weight inhibitor Deposited 2023-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–133（116 aa）
Chain B 18–133（116 aa）
Not recorded VYC 5-[[5-[[2-chloranyl-3-(2-fluorophenyl)phenyl]methoxy]-2-[(~{E})-2-hydroxyethyliminomethyl]phenoxy]methyl]pyridine-3-carbonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.0 M Ammonium sulfate, 0.1 M Sodium acetate pH 5.0
Resolution 3.50 Å R-free 0.296
8P1O Solubilizer tag effect on PD-L1/inhibitor binding properties for m-terphenyl derivatives Deposited 2023-05-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–134（133 aa）
Chain B 2–134（133 aa）
Not recorded WEW (3~{R})-1-[[4-[2-chloranyl-3-(2,3-dihydro-1,4-benzodioxin-6-yl)phenyl]-2-methoxy-phenyl]methyl]-~{N}-(2-hydroxyethyl)pyrrolidine-3-carboxamide × 1 CL CHLORIDE ION × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；27 % w/v PEG 3350, 0.1 M Bis-Tris propane, pH 7.0 and 0.2 M Lithium sulfate
Resolution 2.17 Å R-free 0.289
8P64 Co-crystal structure of PD-L1 with low molecular weight inhibitor Deposited 2023-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Not recorded X1Q ~{N}-[[1-[(~{E})-2-(2-methyl-3-phenyl-phenyl)ethenyl]-1,2,3,4-tetrazol-5-yl]methyl]ethanamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.2 M S38 sodium citrate tribasic dihydrate 0.01 M sodium borate, pH 8.5
Resolution 3.31 Å R-free 0.297
8RPB Structure of S79 Fab in complex with IgV domain of human PD-L1 Deposited 2024-01-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain P 18–133（116 aa）
Not recorded CL CHLORIDE ION × 1 GOL GLYCEROL × 3 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1M Tris pH 8.0, 1.6M Li2SO4
Resolution 2.79 Å R-free 0.251
8XR5 Crystal structure of PD-L1 complexed with small molecule inhibitor X18 Deposited 2024-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 19–134（116 aa）
Chain B 19–134（116 aa）
Not recorded A1LV3 (2~{R})-2-[[2-(2,1,3-benzoxadiazol-5-ylmethoxy)-5-chloranyl-4-[[2-fluoranyl-3-[3-[3-(4-oxidanylpiperidin-1-yl)propoxy]phenyl]phenyl]methoxy]phenyl]methylamino]-3-oxidanyl-propanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；19% PEG3350 and 0.2 M Ammonium tartrate dibasic
Resolution 1.95 Å R-free 0.257
8ZNL PD-L1 de novo designed binder with picomolar binding affinity Deposited 2024-05-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 19–132（114 aa）
Not recorded BR BROMIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；buffer containing 0.03M Sodium fluoride; 0.03M Sodium bromide; 0.03M Sodium iodide; 0.1 M (Imidazole/MES) pH6.5, 12.5% v/v MPD; 12.5% PEG1000; 12.5% w/v PEG 3350.
Resolution 1.77 Å R-free 0.275
8ZNL PD-L1 de novo designed binder with picomolar binding affinity Deposited 2024-05-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 19–132（114 aa）
Not recorded BR BROMIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；buffer containing 0.03M Sodium fluoride; 0.03M Sodium bromide; 0.03M Sodium iodide; 0.1 M (Imidazole/MES) pH6.5, 12.5% v/v MPD; 12.5% PEG1000; 12.5% w/v PEG 3350.
Resolution 1.77 Å R-free 0.275
8ZNL PD-L1 de novo designed binder with picomolar binding affinity Deposited 2024-05-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 19–132（114 aa）
Not recorded BR BROMIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；buffer containing 0.03M Sodium fluoride; 0.03M Sodium bromide; 0.03M Sodium iodide; 0.1 M (Imidazole/MES) pH6.5, 12.5% v/v MPD; 12.5% PEG1000; 12.5% w/v PEG 3350.
Resolution 1.77 Å R-free 0.275
8ZNL PD-L1 de novo designed binder with picomolar binding affinity Deposited 2024-05-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 19–132（114 aa）
Not recorded BR BROMIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；buffer containing 0.03M Sodium fluoride; 0.03M Sodium bromide; 0.03M Sodium iodide; 0.1 M (Imidazole/MES) pH6.5, 12.5% v/v MPD; 12.5% PEG1000; 12.5% w/v PEG 3350.
Resolution 1.77 Å R-free 0.275
9EO0 Small-Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1 Deposited 2024-03-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Not recorded A1H56 ~{N}-[3-[3-[[5-[(2-hydroxyethylamino)methyl]pyridin-2-yl]carbonylamino]-2-methyl-phenyl]-2-methyl-phenyl]-5-[[3-(methylsulfonylamino)propylamino]methyl]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M Sodium HEPES 7.5 25 % w/v PEG 3350
Resolution 2.50 Å R-free 0.302
9EO0 Small-Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1 Deposited 2024-03-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 18–134（117 aa）
Chain F 18–134（117 aa）
Not recorded A1H56 ~{N}-[3-[3-[[5-[(2-hydroxyethylamino)methyl]pyridin-2-yl]carbonylamino]-2-methyl-phenyl]-2-methyl-phenyl]-5-[[3-(methylsulfonylamino)propylamino]methyl]pyridine-2-carboxamide × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M Sodium HEPES 7.5 25 % w/v PEG 3350
Resolution 2.50 Å R-free 0.302
9EO0 Small-Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1 Deposited 2024-03-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain D 18–134（117 aa）
Chain E 18–134（117 aa）
Not recorded A1H56 ~{N}-[3-[3-[[5-[(2-hydroxyethylamino)methyl]pyridin-2-yl]carbonylamino]-2-methyl-phenyl]-2-methyl-phenyl]-5-[[3-(methylsulfonylamino)propylamino]methyl]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M Sodium HEPES 7.5 25 % w/v PEG 3350
Resolution 2.50 Å R-free 0.302
9ERY Co-crystal strucutre of PD-L1 with low molecular weight inhibitor Deposited 2024-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Not recorded VVH 5-[[5-[[2-[bis(fluoranyl)methyl]-3-(2,3-dihydro-1,4-benzodioxin-6-yl)phenyl]methoxy]-2-[(2-hydroxyethylamino)methyl]phenoxy]methyl]pyridine-3-carbonitrile × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.0 M Ammonium sulfate and 0.1 M Sodium cacodylate pH 6.5
Resolution 2.70 Å R-free 0.276
9HRT Structure of human PD-L1 in complex with clinically evaluated inhibitor Deposited 2024-12-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Not recorded A1IXH (2~{R})-2-[[3-[(~{E})-2-[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methyl-phenyl]ethenyl]-4-(trifluoromethyl)phenyl]methylamino]-2-methyl-3-oxidanyl-propanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Ammonium sulfate; 0.1 soudium cacodylate; 6.53% w/v PEG 8000
Resolution 2.30 Å R-free 0.263
9I0U Structure of human PD-L1 in complex with clinically evaluated inhibitor Deposited 2025-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Not recorded GOL GLYCEROL × 2 A1IZJ (5~{S})-5-[[[5-[2-chloranyl-3-[2-chloranyl-3-[6-methoxy-5-[[[(2~{S})-5-oxidanylidenepyrrolidin-2-yl]methylamino]methyl]pyrazin-2-yl]phenyl]phenyl]-3-methoxy-pyrazin-2-yl]methylamino]methyl]pyrrolidin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.0M ammonium sulfate; 0.1M sodium acetate pH 4.6
Resolution 1.46 Å R-free 0.202
9I0W Structure of human PD-L1 in complex with clinically evaluated inhibitor Deposited 2025-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Not recorded A1IZP (3~{R})-1-[[7-(iminomethyl)-2-[2-methyl-3-[2-methyl-3-[[3-[[(3~{R})-3-oxidanylpyrrolidin-1-yl]methyl]-1,7-naphthyridin-8-yl]amino]phenyl]phenyl]-1,3-benzoxazol-5-yl]methyl]pyrrolidine-3-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350
Resolution 2.10 Å R-free 0.299
9IJT Crystal Structure of human Programmed cell death 1 ligand 1 (PD-L1) bound to Small molecule inhibitor Compound-10 Deposited 2024-06-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Chain C 18–134（117 aa）
Chain D 18–134（117 aa）
Not recorded A1L2P (2~{S})-1-[[4-methoxy-2-[(2-methyl-3-phenyl-phenyl)methoxy]pyrimidin-5-yl]methyl]piperidine-2-carboxylic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；299 K；0.1M Tris pH 8.5, 0.1M Magnesium chloride, 25% PEG 4000
Resolution 2.05 Å R-free 0.260
9INU Novel PD-L1/VISTA dual inhibitor as potential immunotherapy agents Deposited 2024-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain B 18–134（117 aa）
Not recorded A1D9R (2~{S})-2-[[6-methoxy-2-[(2-methyl-3-phenyl-phenyl)amino]pyrimidin-4-yl]methylamino]-3-oxidanyl-propanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；Tris, potassium sodium tartrate tetrahydrate
Resolution 2.70 Å R-free 0.287
9KSB Crystal structure of X163 Deposited 2024-11-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 18–134（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.279
9KSB Crystal structure of X163 Deposited 2024-11-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 18–134（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.279
9KSB Crystal structure of X163 Deposited 2024-11-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 18–134（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.279
9KSB Crystal structure of X163 Deposited 2024-11-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 18–134（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.279
9KSB Crystal structure of X163 Deposited 2024-11-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 18–134（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.279
9KSB Crystal structure of X163 Deposited 2024-11-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 18–134（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.00 Å R-free 0.279
9LJ3 Crystal structure of P25 Deposited 2025-01-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 18–134（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M Sodium phosphate dibasic dihydrate,pH 9.1 20% w/v Polyethylene glycol 3,350
Resolution 3.15 Å R-free 0.285
9LJ3 Crystal structure of P25 Deposited 2025-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 18–134（117 aa）
Not recorded A1EJ6 3-[[4-chloranyl-2-[(2-hydroxyethylamino)methyl]-5-[[2-methyl-3-[3-[2-[2-[(3~{R})-3-oxidanylpyrrolidin-1-yl]ethoxy]ethoxy]phenyl]phenyl]methoxy]phenoxy]methyl]benzenecarbonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M Sodium phosphate dibasic dihydrate,pH 9.1 20% w/v Polyethylene glycol 3,350
Resolution 3.15 Å R-free 0.285
9LJ3 Crystal structure of P25 Deposited 2025-01-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 18–134（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M Sodium phosphate dibasic dihydrate,pH 9.1 20% w/v Polyethylene glycol 3,350
Resolution 3.15 Å R-free 0.285
9LJ3 Crystal structure of P25 Deposited 2025-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 18–134（117 aa）
Not recorded A1EJ6 3-[[4-chloranyl-2-[(2-hydroxyethylamino)methyl]-5-[[2-methyl-3-[3-[2-[2-[(3~{R})-3-oxidanylpyrrolidin-1-yl]ethoxy]ethoxy]phenyl]phenyl]methoxy]phenoxy]methyl]benzenecarbonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M Sodium phosphate dibasic dihydrate,pH 9.1 20% w/v Polyethylene glycol 3,350
Resolution 3.15 Å R-free 0.285
9LJ3 Crystal structure of P25 Deposited 2025-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 18–134（117 aa）
Not recorded A1EJ6 3-[[4-chloranyl-2-[(2-hydroxyethylamino)methyl]-5-[[2-methyl-3-[3-[2-[2-[(3~{R})-3-oxidanylpyrrolidin-1-yl]ethoxy]ethoxy]phenyl]phenyl]methoxy]phenoxy]methyl]benzenecarbonitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M Sodium phosphate dibasic dihydrate,pH 9.1 20% w/v Polyethylene glycol 3,350
Resolution 3.15 Å R-free 0.285
9LJ3 Crystal structure of P25 Deposited 2025-01-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 18–134（117 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M Sodium phosphate dibasic dihydrate,pH 9.1 20% w/v Polyethylene glycol 3,350
Resolution 3.15 Å R-free 0.285
9MAP Crystal structure of GAGWLP and PD-L1 Deposited 2025-03-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 18–133（116 aa）
Not recorded PO4 PHOSPHATE ION × 6 CA CALCIUM ION × 6 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；pH 6.0,2.04M NaH2PO4 and K2HPO4
Resolution 3.00 Å R-free 0.284
9MAP Crystal structure of GAGWLP and PD-L1 Deposited 2025-03-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 18–133（116 aa）
Not recorded PO4 PHOSPHATE ION × 4 CA CALCIUM ION × 4 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；pH 6.0,2.04M NaH2PO4 and K2HPO4
Resolution 3.00 Å R-free 0.284
9MAP Crystal structure of GAGWLP and PD-L1 Deposited 2025-03-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 18–133（116 aa）
Not recorded PO4 PHOSPHATE ION × 1 CA CALCIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；pH 6.0,2.04M NaH2PO4 and K2HPO4
Resolution 3.00 Å R-free 0.284
9QSM small molecule inhibitor in complex with PD-L1 Deposited 2025-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–134（117 aa）
Chain D 18–134（117 aa）
Not recorded A1JAE ~{N}-[2-chloranyl-3-[2-chloranyl-3-[4-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]-3-methoxy-phenyl]phenyl]phenyl]-5-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1MBis-Tris 6.520% w/v PEG 5000 MME
Resolution 1.75 Å R-free 0.270
9QSM small molecule inhibitor in complex with PD-L1 Deposited 2025-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 18–134（117 aa）
Chain C 18–134（117 aa）
Not recorded A1JAE ~{N}-[2-chloranyl-3-[2-chloranyl-3-[4-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]-3-methoxy-phenyl]phenyl]phenyl]-5-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1MBis-Tris 6.520% w/v PEG 5000 MME
Resolution 1.75 Å R-free 0.270
9QSM small molecule inhibitor in complex with PD-L1 Deposited 2025-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 18–134（117 aa）
Chain F 18–134（117 aa）
Not recorded A1JAE ~{N}-[2-chloranyl-3-[2-chloranyl-3-[4-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]-3-methoxy-phenyl]phenyl]phenyl]-5-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)propan-2-yl]amino]methyl]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1MBis-Tris 6.520% w/v PEG 5000 MME
Resolution 1.75 Å R-free 0.270

74 other PDB entries and 123 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PD1L1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 2–223； UniProt 18–239 Author chain D； PDBConstruct 2–223； UniProt 18–239

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 5ius

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5ius
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5ius
Deposition date deposition_date2016-03-18
Structure title titleCrystal structure of human PD-L1 in complex with high affinity PD-1 mutant
Keywords keywordsimmune checkpoint, tumor surveillance, cancer, receptor, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.21 Å
Radius of gyration Rg (electron density) rg_electron29.31 Å
Forward intensity I(0) i087870800.00
Molecular weight molecular_weight72108.0 kDa
Excluded volume excluded_volume89662 ų
Envelope volume envelope_volume120020 ų
Hydration-shell volume shell_volume34466 ų
Envelope diameter envelope_diameter98.3 Å
Shell Rg shell_rg36.00 Å
Envelope Rg envelope_rg29.08 Å
Shape Rg shape_rg29.33 Å
Total Rg total_rg29.94 Å
Total atoms total_atoms5081
Residues n_residues657
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax90.8 Å
Rg (real space) rg_real30.07 Å
Rg uncertainty (real space) rg_real_error0.54 Å
I(0) (real space) i0_real8.7870e+07
I(0) uncertainty (real space) i0_real_error1.1290e+06
Rg (reciprocal space) rg_reciprocal30.13 Å
I(0) (reciprocal space) i0_reciprocal87880000.0000
Solution quality estimate total_estimate0.9015
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.9 Å
Skewness Skewness skewness0.128
Kurtosis Kurtosis kurtosis-0.440
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11390000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.863
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5iusa1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd5iusa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5iusb1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd5iusb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id5iusA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5iusB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5iusC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5iusD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)