8u32

Crystal structure of PD-1 in complex with a Fab

Method: X-RAY DIFFRACTION D_max: 115.8 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Programmed cell death protein 1

Homo sapiens

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 25–146	Mutation：C93S	Fab light chain × 1 Fab heavy chain × 1	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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 25–146	Mutation：C93S	Fab light chain × 1 Fab heavy chain × 1 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

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 8U32	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 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 construct Different mutation/modification 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 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 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 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 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 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 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 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 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 mutation/modification 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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）	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
9EHT Crystal Structure of PD-1/retifanlimab complex Deposited 2024-11-25	Different construct Different mutation/modification 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 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 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 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 16–137； UniProt 25–146 Author chain D； PDBConstruct 16–137； UniProt 25–146

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8u32
Deposition date deposition_date	2023-09-07
Structure title title	Crystal structure of PD-1 in complex with a Fab
Keywords keywords	PD-1, Fab, STRUCTURAL PROTEIN, STRUCTURAL PROTEIN-IMMUNE SYSTEM complex; STRUCTURAL PROTEIN/IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	36.43 Å
Radius of gyration Rg (electron density) rg_electron	35.83 Å
Forward intensity I(0) i0	228072000.00
Molecular weight molecular_weight	119140.0 kDa
Excluded volume excluded_volume	148130 Å³
Envelope volume envelope_volume	203280 Å³
Hydration-shell volume shell_volume	48109 Å³
Envelope diameter envelope_diameter	120.4 Å
Shell Rg shell_rg	41.68 Å
Envelope Rg envelope_rg	34.88 Å
Shape Rg shape_rg	35.80 Å
Total Rg total_rg	36.35 Å
Total atoms total_atoms	8394
Residues n_residues	1105
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	115.8 Å
Rg (real space) rg_real	36.31 Å
Rg uncertainty (real space) rg_real_error	0.79 Å
I(0) (real space) i0_real	2.2810e+08
I(0) uncertainty (real space) i0_real_error	3.7030e+06
Rg (reciprocal space) rg_reciprocal	36.39 Å
I(0) (reciprocal space) i0_reciprocal	228100000.0000
Solution quality estimate total_estimate	0.8842
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	48.5 Å
Skewness Skewness skewness	0.219
Kurtosis Kurtosis kurtosis	-0.321
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	18120000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.835

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Programmed cell death protein 1
Molecular weight formula_weight	15765.3 kDa
Mutation mutation	C93S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	8539

HHHHHHGENLYFQGSLDSPDRPWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTEGNS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Fab light chain
Molecular weight formula_weight	23509.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

AAQLTQSPSSLSASVGDRVTITCQSSQSVYNNNDLAWYQQKPGKPPKLLIYTPSSLTSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLGGYDDDSDNAFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	Fab heavy chain
Molecular weight formula_weight	24010.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

EQQLVESGGGVVQPGRSLRLSCAASGFSFSSTYWLSWVRQAPGKGLEWIAAIYVGSSGNTYYANWAKGRFTISKDSSSTTVFLQMNSLRAEDTAVYFCARAGGAGGGVYTLTRLDLWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	145

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8. Citations (1)

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Unit-cell length a length_a	76.482 Å
Unit-cell length b length_b	88.881 Å
Unit-cell length c length_c	235.859 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.510 Å
Low-resolution limit resolution_low	34.960 Å
R factor r_factor	0.1972
R_work r_work	0.1954
R_free r_free	0.2304

fit	/app/data/saxs_computation/u3/8u32/8u32.fit
pddf	/app/data/pr_computation/u3/8u32/8u32.pr.out
profile	/app/data/saxs_computation/u3/8u32/8u32.dat

Crystal structure of PD-1 in complex with a Fab

1. Protein Identity and Related Structures Protein Identity & Related Structures

Programmed cell death protein 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)