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- PDB-6vqn: Co-crystal structure of human PD-L1 complexed with Compound A -

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Basic information

Entry
Database: PDB / ID: 6vqn
TitleCo-crystal structure of human PD-L1 complexed with Compound A
ComponentsProgrammed cell death 1 ligand 1
KeywordsCELL CYCLE / 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 / positive regulation of interleukin-10 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 / positive regulation of interleukin-10 production / negative regulation of type II interferon production / PD-1 signaling / positive regulation of T cell proliferation / T cell costimulation / response to cytokine / recycling endosome membrane / actin cytoskeleton / early endosome membrane / cellular response to lipopolysaccharide / transcription coactivator activity / adaptive immune response / cell surface receptor signaling pathway / receptor ligand activity / positive regulation of cell migration / immune response / 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
Chem-R81 / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsWhite, A. / Lakshminarasimhan, D. / Leo, C. / Suto, R.K.
CitationJournal: Nat Commun / Year: 2021
Title: Checkpoint inhibition through small molecule-induced internalization of programmed death-ligand 1.
Authors: Park, J.J. / Thi, E.P. / Carpio, V.H. / Bi, Y. / Cole, A.G. / Dorsey, B.D. / Fan, K. / Harasym, T. / Iott, C.L. / Kadhim, S. / Kim, J.H. / Lee, A.C.H. / Nguyen, D. / Paratala, B.S. / Qiu, R. ...Authors: Park, J.J. / Thi, E.P. / Carpio, V.H. / Bi, Y. / Cole, A.G. / Dorsey, B.D. / Fan, K. / Harasym, T. / Iott, C.L. / Kadhim, S. / Kim, J.H. / Lee, A.C.H. / Nguyen, D. / Paratala, B.S. / Qiu, R. / White, A. / Lakshminarasimhan, D. / Leo, C. / Suto, R.K. / Rijnbrand, R. / Tang, S. / Sofia, M.J. / Moore, C.B.
History
DepositionFeb 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,5675
Polymers44,4303
Non-polymers1,1372
Water2,504139
1
A: Programmed cell death 1 ligand 1
B: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1893
Polymers29,6202
Non-polymers5691
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Programmed cell death 1 ligand 1
hetero molecules

C: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7574
Polymers29,6202
Non-polymers1,1372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)99.003, 172.173, 80.585
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 14809.955 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NZQ7
#2: Chemical ChemComp-R81 / N,N'-(2,2'-dimethyl[1,1'-biphenyl]-3,3'-diyl)bis(5-{[(2-hydroxyethyl)amino]methyl}pyridine-2-carboxamide)


Mass: 568.666 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H36N6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.86 Å3/Da / Density % sol: 68.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM NaCitrate, pH 6.5 and 22% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97928 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.49→80.58 Å / Num. obs: 24239 / % possible obs: 99.1 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.038 / Rrim(I) all: 0.104 / Net I/σ(I): 14.6 / Num. measured all: 177368 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.49-2.627.71.1632692234830.7110.4431.246299.1
7.87-80.586.30.04252518290.9990.0180.04634.697.1

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZQK

4zqk


Resolution: 2.49→58.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.357 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.213
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1117 4.6 %RANDOM
Rwork0.1767 ---
obs0.1791 23114 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 158.48 Å2 / Biso mean: 53.871 Å2 / Biso min: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.24 Å2-0 Å20 Å2
2---1.87 Å2-0 Å2
3---5.12 Å2
Refinement stepCycle: final / Resolution: 2.49→58.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2912 0 63 139 3114
Biso mean--46.41 56.56 -
Num. residues----365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133037
X-RAY DIFFRACTIONr_bond_other_d0.0040.0172838
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.6674107
X-RAY DIFFRACTIONr_angle_other_deg1.3781.6036566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5855362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91623.182154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.81315529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.131515
X-RAY DIFFRACTIONr_chiral_restr0.0670.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023353
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02623
LS refinement shellResolution: 2.49→2.555 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 67 -
Rwork0.328 1703 -
all-1770 -
obs--98.83 %

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