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- PDB-6r3k: Structure of human Programmed cell death 1 ligand 1 (PD-L1) with ... -

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Basic information

Entry
Database: PDB / ID: 6r3k
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 / PD-1 / immune checkpoint
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-JQT / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZak, K.M. / Grudnik, P. / Skalniak, L. / Dubin, G. / Holak, T.A.
Funding support Poland, 8items
OrganizationGrant numberCountry
Polish National Science Centre Poland
Polish National Science CentreUMO-2012/06/A/ST5/00224 Poland
Polish National Science CentreUMO-2014/12/W/NZ1/00457 Poland
Polish National Science CentreUMO-2011/01/D/NZ1/01169 Poland
Polish National Science CentreUMO-2012/07/E/NZ1/01907 Poland
Polish National Science Centre2015/19/N/ST5/00347 Poland
Polish National Science CentreUMO-2016/20/T/NZ1/00519 Poland
Polish National Science CentreUMO-2015/19/D/NZ1/02009 Poland
CitationJournal: J.Med.Chem. / Year: 2021
Title: Terphenyl-Based Small-Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1 Protein-Protein Interaction.
Authors: Muszak, D. / Surmiak, E. / Plewka, J. / Magiera-Mularz, K. / Kocik-Krol, J. / Musielak, B. / Sala, D. / Kitel, R. / Stec, M. / Weglarczyk, K. / Siedlar, M. / Domling, A. / Skalniak, L. / Holak, T.A.
History
DepositionMar 20, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionApr 3, 2019ID: 5NIX
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.2Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
D: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1218
Polymers58,7154
Non-polymers1,4064
Water4,468248
1
A: Programmed cell death 1 ligand 1
B: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0614
Polymers29,3582
Non-polymers7032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Programmed cell death 1 ligand 1
D: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0614
Polymers29,3582
Non-polymers7032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.527, 84.609, 164.116
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14678.759 Da / Num. of mol.: 4
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-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


Mass: 641.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H33ClN2O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.01 M Tris pH 8.4 containing 0.28 M sodium chloride and 27% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91842 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91842 Å / Relative weight: 1
ReflectionResolution: 2.2→45.99 Å / Num. obs: 29563 / % possible obs: 100 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.24 / Num. unique obs: 2926 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.15rc3_3435: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C3T

5c3t


Resolution: 2.2→45.939 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.47
RfactorNum. reflection% reflection
Rfree0.259 1462 4.95 %
Rwork0.2145 --
obs0.2167 29563 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→45.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3859 0 100 248 4207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0224049
X-RAY DIFFRACTIONf_angle_d1.8525506
X-RAY DIFFRACTIONf_dihedral_angle_d25.6921410
X-RAY DIFFRACTIONf_chiral_restr0.143616
X-RAY DIFFRACTIONf_plane_restr0.007693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27870.34761450.2722780X-RAY DIFFRACTION100
2.2787-2.36990.29041480.25082738X-RAY DIFFRACTION100
2.3699-2.47770.27851480.24422743X-RAY DIFFRACTION100
2.4777-2.60840.34531500.25512776X-RAY DIFFRACTION100
2.6084-2.77180.28931460.25122781X-RAY DIFFRACTION100
2.7718-2.98570.30991530.24192767X-RAY DIFFRACTION100
2.9857-3.28610.291200.23152835X-RAY DIFFRACTION100
3.2861-3.76140.26491520.20862819X-RAY DIFFRACTION100
3.7614-4.73820.20081460.17222856X-RAY DIFFRACTION100
4.7382-45.94930.21581540.19353006X-RAY DIFFRACTION100

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