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- PDB-6np9: PD-L1 IgV domain V76T with fragment -

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Basic information

Entry
Database: PDB / ID: 6np9
TitlePD-L1 IgV domain V76T with fragment
ComponentsProgrammed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / Fragment-based screening / Structure-based design / PD-L1 inhibitor / Cancer drug discovery / Immunotherapy
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 / Immunoglobulins ...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
Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsZhao, B. / Perry, E.
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 17, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7353
Polymers14,5431
Non-polymers1922
Water2,018112
1
A: Programmed cell death 1 ligand 1
hetero molecules

A: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4696
Polymers29,0852
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2650 Å2
ΔGint-70 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.331, 54.111, 85.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

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Components

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


Mass: 14542.585 Da / Num. of mol.: 1 / 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 K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q9NZQ7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 291 K / Method: evaporation / Details: Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.27→40 Å / Num. obs: 32928 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.018 / Rsym value: 0.046 / Net I/σ(I): 61
Reflection shellResolution: 1.27→1.29 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 7.1 / Num. unique obs: 1604 / CC1/2: 0.937 / Rpim(I) all: 0.112 / Rsym value: 0.336 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BIK

3bik


Resolution: 1.27→28.427 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 11.95 / Phase error: 21.49
RfactorNum. reflection% reflection
Rfree0.2183 2016 6.13 %
Rwork0.2016 --
obs0.204 32914 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.27→28.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 0 10 112 1080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061013
X-RAY DIFFRACTIONf_angle_d0.8951380
X-RAY DIFFRACTIONf_dihedral_angle_d8.213581
X-RAY DIFFRACTIONf_chiral_restr0.086157
X-RAY DIFFRACTIONf_plane_restr0.005174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2707-1.30250.25411450.2642185X-RAY DIFFRACTION93
1.3025-1.33770.27931460.25862147X-RAY DIFFRACTION94
1.3377-1.3770.27131400.252186X-RAY DIFFRACTION94
1.377-1.42150.27151410.23192204X-RAY DIFFRACTION94
1.4215-1.47230.27481460.24382187X-RAY DIFFRACTION94
1.4723-1.53120.29171400.22722213X-RAY DIFFRACTION94
1.5312-1.60080.24371440.22072161X-RAY DIFFRACTION94
1.6008-1.68520.21951430.22092201X-RAY DIFFRACTION94
1.6852-1.79070.22191420.21392224X-RAY DIFFRACTION94
1.7907-1.92880.22231470.20862199X-RAY DIFFRACTION94
1.9288-2.12270.21741450.20142233X-RAY DIFFRACTION94
2.1227-2.42920.19071400.19532227X-RAY DIFFRACTION94
2.4292-3.05840.2311470.19142248X-RAY DIFFRACTION94
3.0584-18.54410.18781500.17272269X-RAY DIFFRACTION90
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.70361.19250.55661.70761.33282.84870.26-0.1964-0.16870.1532-0.1597-0.13290.4338-0.1825-0.17360.1562-0.0437-0.02550.09230.01710.109616.2605-4.344922.1422
21.21470.4990.85250.86980.9641.67540.0798-0.1105-0.0454-0.02-0.08920.1147-0.0066-0.28710.09080.1083-0.0043-0.00070.1291-0.00180.06359.20153.818917.7726
31.58640.57441.1071.19731.02632.8594-0.01690.08980.0128-0.09290.03340.0222-0.020.0631-0.01990.09550.0041-0.00820.06680.00160.055220.5899.072716.5329
41.209-0.4873-0.34731.1155-0.91351.31840.05290.01120.2139-0.06160.12920.028-0.254-0.2012-0.08470.14410.0097-0.01090.10110.00620.091321.323417.438917.1363
56.30181.5894-2.4483.8679-2.66724.3748-0.09260.32380.8720.0989-0.061-0.0606-0.73-0.10380.11950.25360.0061-0.07310.14440.04510.17612.814815.74538.3371
62.52420.5434-0.48144.0923-3.19796.09110.0193-0.31450.13480.2359-0.06070.327-0.4526-0.6042-0.06110.14980.0153-0.00610.1655-0.04280.094710.870110.41725.2412
74.0559-0.78173.38872.3756-1.55963.2015-0.0549-0.29960.08410.0710.09480.0732-0.2515-0.58390.1160.11670.01710.00320.1112-0.01520.059310.42957.405219.5186
83.1029-1.60950.27232.85932.6395.7969-0.09210.03990.2552-0.2672-0.02520.0097-0.6406-0.1420.17830.18840.0145-0.03430.1116-0.00120.08358.31199.625.0167
92.35960.21022.87980.18830.35634.12680.062-0.0304-0.10980.00750.02380.02160.0754-0.0884-0.18270.1088-0.0111-0.01650.06570.00190.060217.76540.692915.2154
103.0659-0.6043-1.1972.94710.02210.92090.18850.07360.01170.2034-0.24370.0028-0.7624-0.22310.00610.27260.0461-0.02680.15140.00210.06464.83429.3134-6.1423
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 49 )
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 78 )
5X-RAY DIFFRACTION5chain 'A' and (resid 79 through 84 )
6X-RAY DIFFRACTION6chain 'A' and (resid 85 through 94 )
7X-RAY DIFFRACTION7chain 'A' and (resid 95 through 101 )
8X-RAY DIFFRACTION8chain 'A' and (resid 102 through 109 )
9X-RAY DIFFRACTION9chain 'A' and (resid 110 through 131 )
10X-RAY DIFFRACTION10chain 'A' and (resid 132 through 141 )

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