5n2f

Structure of PD-L1/small-molecule inhibitor complex

Method: X-RAY DIFFRACTION D_max: 66.2 Å Quality: GOOD

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

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 18–134 Chain B； UniProt 18–134	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

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 5N2F	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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 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 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 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 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 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 mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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 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 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 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 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 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 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 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 ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain 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 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 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 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 ligand/ion 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 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 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
5NIU Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor Deposited 2017-03-27	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 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain 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 mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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 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 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 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 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 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 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 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 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 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 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 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 mutation/modification 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 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain 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 ligand/ion 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 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 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 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 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 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 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 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 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 mutation/modification 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 18–134（117 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 6 WHL N,N'-(1,4-phenylene)diacetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；1.1 M Sodium Malonate pH 7.0, 0.1 M HEPES pH 7.0, 0.5% v/v Jeffamine ED-2001 Reagent pH 7.0.	Resolution 2.89 Å R-free 0.228
7VUN Design, modification, evaluation and cocrystal studies of novel phthalimides regulating PD-1/PD-L1 interaction Deposited 2021-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 18–134（117 aa） Chain B 18–134（117 aa） Chain C 18–134（117 aa） Chain D 18–134（117 aa） Chain E 18–134（117 aa） Chain F 18–134（117 aa） Chain G 18–134（117 aa） Chain H 18–134（117 aa）	Not recorded	8H7 (2~{S},3~{S})-2-[[6-[(3-cyanophenyl)methoxy]-2-(2-methyl-3-phenyl-phenyl)-1,3-bis(oxidanylidene)isoindol-5-yl]methylamino]-3-oxidanyl-butanoic acid × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；PEG 3350, 1,4 - Dioxane, Tris	Resolution 2.70 Å R-free 0.289
7XAD Crystal strucutre of PD-L1 and DBL2_02 designed protein binder Deposited 2022-03-17	Different construct Different 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 1–238（238 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M potassium/sodium tartrate, 0.1 M Bis Tris propane, pH 6.5 ,20 % w/v PEG 3350	Resolution 3.00 Å R-free 0.294
7XAD Crystal strucutre of PD-L1 and DBL2_02 designed protein binder Deposited 2022-03-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–238（238 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M potassium/sodium tartrate, 0.1 M Bis Tris propane, pH 6.5 ,20 % w/v PEG 3350	Resolution 3.00 Å R-free 0.294
7XAD Crystal strucutre of PD-L1 and DBL2_02 designed protein binder Deposited 2022-03-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–238（238 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M potassium/sodium tartrate, 0.1 M Bis Tris propane, pH 6.5 ,20 % w/v PEG 3350	Resolution 3.00 Å R-free 0.294
7XAD Crystal strucutre of PD-L1 and DBL2_02 designed protein binder Deposited 2022-03-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–238（238 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M potassium/sodium tartrate, 0.1 M Bis Tris propane, pH 6.5 ,20 % w/v PEG 3350	Resolution 3.00 Å R-free 0.294
7XAE Crystal strucutre of PD-L1 and 3ONJA protein Deposited 2022-03-17	Different construct Different 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 1–238（238 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium citrate tribasic dihydrate pH 5.5, 16% w/v Polyethylene glycol 8,000	Resolution 3.44 Å R-free 0.262
7XAE Crystal strucutre of PD-L1 and 3ONJA protein Deposited 2022-03-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 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 ligand/ion 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 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 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 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 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 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 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 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 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 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 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 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 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 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 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 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 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 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 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 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification 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	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 mutation/modification 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	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 mutation/modification Different oligomeric state Different ligand/ion 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 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 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 mutation/modification 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state 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 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 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 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 124 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PD1L1_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–117； UniProt 18–134 Author chain B； PDBConstruct 1–117； UniProt 18–134

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	5n2f
Deposition date deposition_date	2017-02-07
Structure title title	Structure of PD-L1/small-molecule inhibitor complex
Keywords keywords	PD-L1, PD-1, small-molecule inhibitor, immune system; 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	20.52 Å
Radius of gyration Rg (electron density) rg_electron	19.62 Å
Forward intensity I(0) i0	13525200.00
Molecular weight molecular_weight	28124.0 kDa
Excluded volume excluded_volume	35421 Å³
Envelope volume envelope_volume	42715 Å³
Hydration-shell volume shell_volume	18466 Å³
Envelope diameter envelope_diameter	69.0 Å
Shell Rg shell_rg	25.66 Å
Envelope Rg envelope_rg	20.12 Å
Shape Rg shape_rg	19.64 Å
Total Rg total_rg	20.43 Å
Total atoms total_atoms	1983
Residues n_residues	250
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	66.2 Å
Rg (real space) rg_real	20.49 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	1.3530e+07
I(0) uncertainty (real space) i0_real_error	1.7270e+05
Rg (reciprocal space) rg_reciprocal	20.50 Å
I(0) (reciprocal space) i0_reciprocal	13530000.0000
Solution quality estimate total_estimate	0.7903
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	25.9 Å
Skewness Skewness skewness	0.273
Kurtosis Kurtosis kurtosis	-0.501
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4886000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.806; Stabil: 0.951; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Programmed cell death 1 ligand 1
Molecular weight formula_weight	14402.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2307

AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAALEHHHH

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	Programmed cell death 1 ligand 1
Molecular weight formula_weight	14126.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAALEHH

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 3 Entity 3 non-polymer

Description description	;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 ;
Molecular weight formula_weight	497.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	271

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5n2fa1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d5n2fa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5n2fb1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d5n2fb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	5n2fA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5n2fB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	51.815 Å
Unit-cell length b length_b	52.379 Å
Unit-cell length c length_c	111.526 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	4

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	36.837 Å
R factor r_factor	0.1925
R_work r_work	0.1907
R_free r_free	0.2297

fit	/app/data/saxs_computation/n2/5n2f/5n2f.fit
pddf	/app/data/pr_computation/n2/5n2f/5n2f.pr.out
profile	/app/data/saxs_computation/n2/5n2f/5n2f.dat

Structure of PD-L1/small-molecule inhibitor complex

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

Programmed cell death 1 ligand 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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)