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7vux

Complex structure of PD1 and 609A-Fab

Method: X-RAY DIFFRACTION Dmax: 119.6 Å Quality: GOOD
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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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 32–160 Not recorded Heavy chain of Fab fragment × 1 Light chain of Fab fragment × 1 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

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 7VUX 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 oligomeric state Different ligand/ion 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 ligand/ion 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 oligomeric state 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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
5IUS Crystal structure of human PD-L1 in complex with high affinity PD-1 mutant Deposited 2016-03-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 26–146（121 aa）
Mutation：V64H, N66V, Y68H, M70E, N74G, K78T, C93A, L122V, A125V, A132I 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
5IUS Crystal structure of human PD-L1 in complex with high affinity PD-1 mutant Deposited 2016-03-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 26–146（121 aa）
Mutation：V64H, N66V, Y68H, M70E, N74G, K78T, C93A, L122V, A125V, A132I No recorded non-water small molecule 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
5JXE Human PD-1 ectodomain complexed with Pembrolizumab Fab Deposited 2016-05-13 Different construct Different ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 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 oligomeric state Different ligand/ion 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 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 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 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 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 oligomeric state 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 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 ligand/ion 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 ligand/ion 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 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 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 ligand/ion 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
7WSL PD-1 in complex with Dostarlimab Deposited 2022-01-30 Different construct Different ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 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 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 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 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 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 oligomeric state Different ligand/ion 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 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 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 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 ligand/ion 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 ligand/ion 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 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 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）
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 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 ligand/ion 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 ligand/ion 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 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 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 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 56 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 2–130； UniProt 32–160

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 7vux

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7vux
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7vux
Deposition date deposition_date2021-11-04
Structure title titleComplex structure of PD1 and 609A-Fab
Keywords keywordsPD1 Fab complex, 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_guinier30.57 Å
Radius of gyration Rg (electron density) rg_electron30.28 Å
Forward intensity I(0) i063485000.00
Molecular weight molecular_weight61399.0 kDa
Excluded volume excluded_volume76268 ų
Envelope volume envelope_volume99234 ų
Hydration-shell volume shell_volume29534 ų
Envelope diameter envelope_diameter128.2 Å
Shell Rg shell_rg34.83 Å
Envelope Rg envelope_rg30.54 Å
Shape Rg shape_rg30.23 Å
Total Rg total_rg30.84 Å
Total atoms total_atoms4315
Residues n_residues551
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 dmax119.6 Å
Rg (real space) rg_real30.91 Å
Rg uncertainty (real space) rg_real_error1.38 Å
I(0) (real space) i0_real6.3480e+07
I(0) uncertainty (real space) i0_real_error1.0940e+06
Rg (reciprocal space) rg_reciprocal30.76 Å
I(0) (reciprocal space) i0_reciprocal63480000.0000
Solution quality estimate total_estimate0.7621
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.9 Å
Skewness Skewness skewness0.638
Kurtosis Kurtosis kurtosis0.064
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10120000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.505; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.435; Smooth: 0.954
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id7vuxH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7vuxH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7vuxL01
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)