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- PDB-7bea: Structure of human Programmed cell death 1 ligand 1 (PD-L1) with ... -

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Basic information

Entry
Database: PDB / ID: 7bea
TitleStructure of human Programmed cell death 1 ligand 1 (PD-L1) with inhibitor
ComponentsProgrammed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / PD-L1 / immune checkpoint
Function / homology
Function and homology information


positive regulation of tolerance induction to tumor cell / 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 / 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 ...positive regulation of tolerance induction to tumor cell / 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 / 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 / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / 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-TK2 / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMagiera-Mularz, K. / Butera, R. / Wazynska, M. / Holak, T. / Domling, A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Design, Synthesis, and Biological Evaluation of Imidazopyridines as PD-1/PD-L1 Antagonists.
Authors: Butera, R. / Wazynska, M. / Magiera-Mularz, K. / Plewka, J. / Musielak, B. / Surmiak, E. / Sala, D. / Kitel, R. / de Bruyn, M. / Nijman, H.W. / Elsinga, P.H. / Holak, T.A. / Domling, A.
History
DepositionDec 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8203
Polymers29,3582
Non-polymers4631
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-3 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.617, 54.616, 140.962
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-307-

HOH

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Components

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


Mass: 14678.759 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NZQ7
#2: Chemical ChemComp-TK2 / 2-(aminomethyl)-6-[(2-methyl-3-phenyl-phenyl)methoxy]-~{N}-(2-phenylethyl)imidazo[1,2-a]pyridin-3-amine


Mass: 462.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H30N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.2 M Sodium citrate tribasic dihydrate 0.01 M Sodium borate, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.45→46.99 Å / Num. obs: 9843 / % possible obs: 99.8 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.138 / Net I/σ(I): 10.9
Reflection shellResolution: 2.45→2.55 Å / Num. unique obs: 956 / CC1/2: 0.474 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMACv1.0refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O45

5o45


Resolution: 2.45→46.99 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rwork0.2741 --
Rfree-981 -
obs-9843 99.8 %
Displacement parametersBiso max: 86.48 Å2 / Biso mean: 36.7667 Å2 / Biso min: 20.21 Å2
Refinement stepCycle: LAST / Resolution: 2.45→46.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 35 39 1980
LS refinement shellResolution: 2.45→2.55 Å /
RfactorNum. reflection
Rfree0.3895 -
Rwork0.3569 -
obs-956

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