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- PDB-9lj3: Crystal structure of P25 -

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Basic information

Entry
Database: PDB / ID: 9lj3
TitleCrystal structure of P25
ComponentsProgrammed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / PD-L1 / P25 / complex
Function / homology
Function and homology information


negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of T cell mediated immune response to tumor cell / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / negative regulation of type II interferon production ...negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of T cell mediated immune response to tumor cell / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / negative regulation of type II interferon production / positive regulation of interleukin-10 production / Co-inhibition by PD-1 / negative regulation of T cell proliferation / T cell costimulation / positive regulation of T cell proliferation / response to cytokine / recycling endosome membrane / actin cytoskeleton / cellular response to lipopolysaccharide / early endosome membrane / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / immune response / receptor ligand activity / external side of plasma membrane / signal transduction / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsYang, P. / Chen, M.R. / Xiao, Y.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery and Crystallography Study of Novel Resorcinol Dibenzyl Ether-Based PD-1/PD-L1 Inhibitors with Improved Drug-like and Pharmacokinetic Properties for Cancer Treatment.
Authors: Yang, Z. / Yang, P. / Xu, J. / Yang, X. / Zhou, J. / He, H. / Li, L. / Ren, Y. / Chen, M. / Xiao, Y. / Chen, J.
History
DepositionJan 14, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Programmed cell death 1 ligand 1
A: Programmed cell death 1 ligand 1
C: Programmed cell death 1 ligand 1
D: Programmed cell death 1 ligand 1
E: Programmed cell death 1 ligand 1
F: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3989
Polymers85,3406
Non-polymers2,0593
Water724
1
B: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)14,2231
Polymers14,2231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9092
Polymers14,2231
Non-polymers6861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)14,2231
Polymers14,2231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9092
Polymers14,2231
Non-polymers6861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9092
Polymers14,2231
Non-polymers6861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)14,2231
Polymers14,2231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.422, 77.159, 78.099
Angle α, β, γ (deg.)90.00, 97.98, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Programmed cell death 1 ligand 1 / PD-L1 / PDCD1 ligand 1 / Programmed death ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1


Mass: 14223.255 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ7
#2: Chemical ChemComp-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


Mass: 686.236 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C39H44ClN3O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium phosphate dibasic dihydrate,pH 9.1 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.15→34.87 Å / Num. obs: 27821 / % possible obs: 99.23 % / Redundancy: 6.7 % / Biso Wilson estimate: 73.02 Å2 / CC1/2: 0.993 / Net I/σ(I): 8.37
Reflection shellResolution: 3.15→3.263 Å / Num. unique obs: 1454 / CC1/2: 0.859

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C3T

5c3t


Resolution: 3.15→34.87 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2852 2760 9.92 %
Rwork0.2434 --
obs0.2478 27821 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→34.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5568 0 147 4 5719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035823
X-RAY DIFFRACTIONf_angle_d0.6467866
X-RAY DIFFRACTIONf_dihedral_angle_d16.8682169
X-RAY DIFFRACTIONf_chiral_restr0.051873
X-RAY DIFFRACTIONf_plane_restr0.003984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.20.43471390.38821264X-RAY DIFFRACTION99
3.2-3.260.40821410.39621285X-RAY DIFFRACTION99
3.26-3.330.42181330.36791227X-RAY DIFFRACTION99
3.33-3.390.40891380.3571261X-RAY DIFFRACTION99
3.39-3.470.3551320.32681227X-RAY DIFFRACTION98
3.47-3.550.30291390.30741267X-RAY DIFFRACTION99
3.55-3.640.29921400.28431233X-RAY DIFFRACTION99
3.64-3.730.29761420.28771287X-RAY DIFFRACTION99
3.73-3.840.30521340.27211213X-RAY DIFFRACTION99
3.84-3.970.28451390.26461255X-RAY DIFFRACTION99
3.97-4.110.34641430.25461266X-RAY DIFFRACTION99
4.11-4.270.30341360.22871240X-RAY DIFFRACTION99
4.27-4.470.27661410.22681279X-RAY DIFFRACTION99
4.47-4.70.29021390.20021253X-RAY DIFFRACTION100
4.7-4.990.22371420.19411269X-RAY DIFFRACTION99
5-5.380.25561380.1821244X-RAY DIFFRACTION99
5.38-5.920.26731390.1961269X-RAY DIFFRACTION99
5.92-6.770.23321380.20841255X-RAY DIFFRACTION100
6.77-8.510.25521400.21841266X-RAY DIFFRACTION99
8.51-34.870.19991270.18691201X-RAY DIFFRACTION95

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