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- PDB-5j8o: Structure of human Programmed cell death 1 ligand 1 (PD-L1) with ... -

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Basic information

Entry
Database: PDB / ID: 5j8o
TitleStructure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor
ComponentsProgrammed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / PD-L1 / Programmed cell death 1 ligand 1 / cell cycle
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 / adaptive immune response / transcription coactivator activity / 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 ...: / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-6GZ / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsZak, K.M. / Grudnik, P. / Guzik, K. / Zieba, B.J. / Musielak, B. / Doemling, P. / Dubin, G. / Holak, T.A.
Funding support Poland, 7items
OrganizationGrant numberCountry
European Community Framework ProgrammeMarie Curie FP7-Reintegration-Grant Poland
National Science CentreUMO-2012/06/A/ST5/00224 Poland
National Science CentreUMO-2014/12/W/NZ1/00457 Poland
National Science CentreUMO-2011/01/D/NZ1/01169 Poland
National Science CentreUMO-2012/07/E/NZ1/01907 Poland
European Union structural fundsPOIG.02.01.00-12-064/08 Poland
European Union structural fundsPOIG.02.01.00-12-167/08 Poland
CitationJournal: Oncotarget / Year: 2016
Title: Structural basis for small molecule targeting of the programmed death ligand 1 (PD-L1).
Authors: Zak, K.M. / Grudnik, P. / Guzik, K. / Zieba, B.J. / Musielak, B. / Domling, A. / Dubin, G. / Holak, T.A.
History
DepositionApr 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Jan 10, 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)28,7473
Polymers28,2522
Non-polymers4941
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-2 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.313, 55.182, 141.773
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 14126.172 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 (E. coli) / References: UniProt: Q9NZQ7
#2: Chemical ChemComp-6GZ / (2R)-1-({3-bromo-4-[(2-methyl[1,1'-biphenyl]-3-yl)methoxy]phenyl}methyl)piperidine-2-carboxylic acid


Mass: 494.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28BrNO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M ammonium formate and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.3→47.26 Å / Num. obs: 12626 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.4
Reflection shellRmerge(I) obs: 0.465

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.18 Å43.54 Å
Translation2.18 Å43.54 Å

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASER2.5.6phasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5c3t

5c3t


Resolution: 2.3→47.26 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.877 / SU B: 10.253 / SU ML: 0.25 / SU R Cruickshank DPI: 0.3909 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.391 / ESU R Free: 0.289
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3052 610 4.8 %RANDOM
Rwork0.2412 ---
obs0.2445 11974 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 88.7 Å2 / Biso mean: 44.112 Å2 / Biso min: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20 Å20 Å2
2--2.3 Å2-0 Å2
3----4.53 Å2
Refinement stepCycle: final / Resolution: 2.3→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 32 30 1968
Biso mean--42.77 46.53 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191979
X-RAY DIFFRACTIONr_bond_other_d0.0020.021870
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.9752689
X-RAY DIFFRACTIONr_angle_other_deg1.08934280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.035244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25424.88486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2415322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.198157
X-RAY DIFFRACTIONr_chiral_restr0.2140.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022240
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02447
X-RAY DIFFRACTIONr_mcbond_it3.3024.369982
X-RAY DIFFRACTIONr_mcbond_other3.3014.368983
X-RAY DIFFRACTIONr_mcangle_it4.7596.5411224
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 32 -
Rwork0.267 846 -
all-878 -
obs--99.89 %

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