Programmed cell death 1 ligand 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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 1–238 | Not recorded | DBL2_02 binder × 1 | 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 |
| 2 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain D； UniProt 1–238 | Not recorded | DBL2_02 binder × 1 | 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 |
| 3 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain F； UniProt 1–238 | Not recorded | DBL2_02 binder × 1 | 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 |
| 4 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain H； UniProt 1–238 | Not recorded | DBL2_02 binder × 1 | 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 |
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 7XAD | 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 ligand/ion 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 |
| 5IUS Crystal structure of human PD-L1 in complex with high affinity PD-1 mutant Deposited 2016-03-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
18–239（222 aa）
|
Not recorded | 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 experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
18–239（222 aa）
|
Not recorded | 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 |
| 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 |
| 7XAE Crystal strucutre of PD-L1 and 3ONJA protein Deposited 2022-03-17 | 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 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 121 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | PD1L1_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–238； UniProt 1–238 Author chain D； PDBConstruct 1–238； UniProt 1–238 Author chain F； PDBConstruct 1–238； UniProt 1–238 Author chain H； PDBConstruct 1–238； UniProt 1–238 |
