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- PDB-6nm8: IgV-V76T BMS compound 105 -

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Basic information

Entry
Database: PDB / ID: 6nm8
TitleIgV-V76T BMS compound 105
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 / T cell costimulation / response to cytokine / positive regulation of T cell proliferation / recycling endosome membrane / actin cytoskeleton / cellular response to lipopolysaccharide / early endosome membrane / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / 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
Chem-KSD / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.792 Å
AuthorsPerry, E. / Zhao, B. / Fesik, S.
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)30,0593
Polymers29,6242
Non-polymers4361
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-4 kcal/mol
Surface area13230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.455, 54.604, 141.272
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 18 through 30 or resid 32 through 35 or resid 37 through 142))
21(chain B and (resid 18 through 30 or resid 32 through 35 or resid 37 through 141 or resid 143))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAVALVAL(chain A and (resid 18 through 30 or resid 32 through 35 or resid 37 through 142))AA18 - 302 - 14
12TYRTYRASNASN(chain A and (resid 18 through 30 or resid 32 through 35 or resid 37 through 142))AA32 - 3516 - 19
13THRTHRHISHIS(chain A and (resid 18 through 30 or resid 32 through 35 or resid 37 through 142))AA37 - 14221 - 126
21ALAALAVALVAL(chain B and (resid 18 through 30 or resid 32 through 35 or resid 37 through 141 or resid 143))BB18 - 302 - 14
22TYRTYRASNASN(chain B and (resid 18 through 30 or resid 32 through 35 or resid 37 through 141 or resid 143))BB32 - 3516 - 19
23THRTHRHISHIS(chain B and (resid 18 through 30 or resid 32 through 35 or resid 37 through 141 or resid 143))BB37 - 14121 - 125
24HISHISHISHIS(chain B and (resid 18 through 30 or resid 32 through 35 or resid 37 through 141 or resid 143))BB143127

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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-KSD / N-({2,6-dimethoxy-4-[(2-methyl[1,1'-biphenyl]-3-yl)methoxy]phenyl}methyl)-D-alanine


Mass: 435.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H29NO5
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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 29% PEG 4000, 0.28 M NaCl, 0.01 M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0003 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0003 Å / Relative weight: 1
ReflectionResolution: 2.792→50 Å / Num. obs: 6839 / % possible obs: 99.3 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.036 / Rrim(I) all: 0.126 / Χ2: 0.962 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.8512.60.5923220.9450.1720.6170.919100
2.85-2.912.20.6573240.9330.1940.6860.87999.4
2.9-2.9612.10.6853180.9520.2050.7151.459100
2.96-3.0211.70.4873510.9510.1470.5090.92100
3.02-3.0810.90.4393430.9510.1370.4611.02498.8
3.08-3.1511.30.3393100.9860.1040.3550.919100
3.15-3.2311.90.3283480.9840.0970.3420.97199.7
3.23-3.32130.2633400.9880.0750.2740.962100
3.32-3.4212.80.2253350.9870.0650.2341.047100
3.42-3.5312.60.1733340.990.050.180.985100
3.53-3.6512.40.1553480.9930.0450.1621.009100
3.65-3.8120.1223420.9940.0370.1280.967100
3.8-3.9711.40.1133330.9920.0350.1181.071100
3.97-4.1810.10.0843530.9970.0270.0880.898100
4.18-4.4411.90.0793350.9960.0240.0820.976100
4.44-4.7912.50.0653640.9970.0190.0670.9199.7
4.79-5.2711.70.0743380.9950.0230.0780.90199.7
5.27-6.0311.40.0683600.9980.0210.0710.731100
6.03-7.599.60.0783690.9970.0250.0820.799100
7.59-509.90.0713720.9980.0210.0740.87390.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NP9

6np9


Resolution: 2.792→20.263 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.25
RfactorNum. reflection% reflection
Rfree0.3041 345 5.08 %
Rwork0.1947 --
obs0.1999 6786 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.9 Å2 / Biso mean: 38.911 Å2 / Biso min: 7.94 Å2
Refinement stepCycle: final / Resolution: 2.792→20.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 32 0 2020
Biso mean--29.97 --
Num. residues----251
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A724X-RAY DIFFRACTION8.769TORSIONAL
12B724X-RAY DIFFRACTION8.769TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7919-3.51450.37621570.23653098325598
3.5145-20.26380.27341880.176333433531100

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