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- PDB-6nm7: PD-L1 IgV domain bound to fragment -

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Basic information

Entry
Database: PDB / ID: 6nm7
TitlePD-L1 IgV domain bound to fragment
ComponentsProgrammed cell death 1 ligand 1
Keywordsimmune system/inhibitor / Fragment-based screening / Structure-based design / PD-L1 inhibitor / Cancer drug discovery / Immunotherapy / IMMUNE SYSTEM / immune system-inhibitor 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 / 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 / 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 ...: / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
5-phenylthieno[2,3-d]pyrimidin-4(3H)-one / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.426 Å
AuthorsPerry, E. / Zhao, B.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)5T32GM065086 United States
National Science Foundation (NSF, United States)0922862 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR025677 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR026915 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2019
Title: Fragment-based screening of programmed death ligand 1 (PD-L1).
Authors: Perry, E. / Mills, J.J. / Zhao, B. / Wang, F. / Sun, Q. / Christov, P.P. / Tarr, J.C. / Rietz, T.A. / Olejniczak, E.T. / Lee, T. / Fesik, S.
History
DepositionJan 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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
Revision 1.4Nov 13, 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)29,8523
Polymers29,6242
Non-polymers2281
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-3 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.911, 94.921, 32.155
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 14811.928 Da / Num. of mol.: 2 / Mutation: V76T
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-22L / 5-phenylthieno[2,3-d]pyrimidin-4(3H)-one


Mass: 228.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8N2OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.056 M NaH2PO4, 1.344 M K2HPO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.426→50 Å / Num. obs: 10155 / % possible obs: 100 % / Redundancy: 7.7 % / Biso Wilson estimate: 33.69 Å2 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.052 / Rrim(I) all: 0.145 / Χ2: 0.942 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.43-2.477.70.8785110.7440.3390.9420.807100
2.47-2.527.60.884780.740.3410.9450.811100
2.52-2.577.60.7794860.8410.3010.8360.844100
2.57-2.627.80.6615030.8170.2540.7090.863100
2.62-2.677.70.5834970.8840.2250.6260.87100
2.67-2.747.70.4984890.9160.1910.5350.864100
2.74-2.817.80.4364980.9330.1670.4670.911100
2.81-2.887.90.3455100.9470.1310.370.879100
2.88-2.977.80.3224970.9610.1230.3450.902100
2.97-3.067.90.2544880.9720.0970.2720.946100
3.06-3.1780.2255150.9770.0850.2410.981100
3.17-3.37.80.1624900.990.0620.1730.975100
3.3-3.457.90.1365050.9930.0510.1460.984100
3.45-3.637.90.1025120.9950.0380.1091.068100
3.63-3.867.90.085000.9980.030.0861.091100
3.86-4.157.80.0715140.9980.0270.0761.017100
4.15-4.577.80.055260.9990.0190.0531.031100
4.57-5.237.70.0485220.9990.0190.0520.969100
5.23-6.597.50.0525300.9990.020.0560.929100
6.59-506.70.0435840.9990.0180.0471.0799.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NP9

6np9


Resolution: 2.426→32.155 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.08
RfactorNum. reflection% reflection
Rfree0.2686 492 4.87 %
Rwork0.2022 --
obs0.2056 10113 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.9 Å2 / Biso mean: 37.185 Å2 / Biso min: 17.92 Å2
Refinement stepCycle: final / Resolution: 2.426→32.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 16 21 2045
Biso mean--27.65 33.36 -
Num. residues----252
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4259-2.66990.35241030.27472324242798
2.6699-3.0560.29181230.231623652488100
3.056-3.84920.23971220.186924112533100
3.8492-32.15780.25821440.18125212665100

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