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

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Basic information

Entry
Database: PDB / ID: 6nos
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
Chem-KWA / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 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 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
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
B: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3593
Polymers29,1032
Non-polymers2561
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-4 kcal/mol
Surface area12690 Å2
Unit cell
Length a, b, c (Å)84.014, 97.401, 33.182
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 14551.618 Da / Num. of mol.: 2 / Fragment: UNP residues 18-134
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) / References: UniProt: Q9NZQ7
#2: Chemical ChemComp-KWA / 1-[5-(3,5-dichlorophenyl)furan-2-yl]-N-methylmethanamine


Mass: 256.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11Cl2NO

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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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 0.056 M sodium phosphate monobasic, 1.344 M potassium phosphate dibasic

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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: RAYONIX MX-300 / Detector: CCD / Date: Nov 28, 2016
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 7548 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / CC1/2: 0.079 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.066 / Rrim(I) all: 0.146 / Rsym value: 0.095 / Net I/σ(I): 7.2
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.469 / Num. unique obs: 354 / Rpim(I) all: 0.309 / Rrim(I) all: 0.566 / Rsym value: 0.649 / % possible all: 89.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I8L

1i8l


Resolution: 2.701→29.421 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 23.96
RfactorNum. reflection% reflection
Rfree0.2754 601 9.99 %
Rwork0.1853 --
obs0.1944 6015 75.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.701→29.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 16 0 1941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012052
X-RAY DIFFRACTIONf_angle_d1.4152782
X-RAY DIFFRACTIONf_dihedral_angle_d10.5281220
X-RAY DIFFRACTIONf_chiral_restr0.068311
X-RAY DIFFRACTIONf_plane_restr0.008353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7008-2.97230.2827570.2371511X-RAY DIFFRACTION30
2.9723-3.40190.33451510.2231357X-RAY DIFFRACTION77
3.4019-4.28390.32071900.19191719X-RAY DIFFRACTION95
4.2839-29.42230.22552030.15941827X-RAY DIFFRACTION98
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)
11.3613-0.6722-0.9361.36981.26341.2648-0.2661-0.4512-0.03110.38750.2036-0.0923-0.05010.1407-0.24870.46540.1359-0.22640.36910.0246-0.134124.2965104.31718.5511
20.1850.3832-0.28471.2273-0.00311.16630.19790.36910.36390.1171-0.1238-0.54040.11560.44270.0165-0.01080.0083-0.01670.5606-0.13830.466923.4939110.508210.3854
32.1362-0.66531.12672.1048-0.34362.6515-0.27180.2656-0.74530.0613-0.28080.26550.14710.0048-0.0534-0.02350.0620.07750.39160.06330.422523.102899.634.0273
43.89350.37243.36511.1889-0.06463.03610.13480.5717-0.2898-0.39780.0842-0.0427-0.10970.4730.00750.4970.2927-0.16770.7235-0.02010.459825.1885100.0684-3.7167
58.77882.5942-0.11917.9171-3.97242.17040.61460.9232-0.5128-0.8337-0.17070.2857-0.02380.04620.0380.5266-0.039-0.13150.3115-0.02550.396216.0011107.4117-4.8261
68.78920.15854.76694.69140.5632.9553-0.74181.11011.2867-0.0239-0.0317-1.0517-1.12260.93040.53950.2772-0.12740.05260.36650.04680.744530.5496110.29624.6714
73.2623-0.0067-0.10342.7003-0.42570.99150.01730.31890.4335-0.2738-0.0437-0.4674-0.04980.22950.47560.1588-0.11790.14140.23970.13050.189619.3226106.23196.8162
82.9288-2.28370.89642.6624-0.89011.3367-0.1986-0.4749-0.10680.39570.11610.33570.1394-0.37070.120.1284-0.10560.0250.0873-0.02830.373315.3383104.683813.7048
94.83151.07790.49451.7106-0.4680.8536-0.28320.7128-0.5871-0.46170.45550.02620.2826-0.3196-0.18470.3625-0.3937-0.25930.65260.19830.438-1.9018114.83910.1012
104.00480.98251.20390.69270.73551.0363-0.20970.47340.2944-0.11980.0561-0.0307-0.18070.0785-0.12830.4548-0.0396-0.29970.43930.06830.033420.75182.18922.3904
112.0614-0.1082-0.24791.9417-1.00791.50790.12110.1829-0.02990.2365-0.0889-0.13440.14310.1981-0.05230.36060.0164-0.15370.24170.01110.49397.080975.425512.9235
127.22620.3807-1.06872.39540.93143.6561-0.0580.54250.0937-0.1318-0.3272-0.051-0.26380.61320.1580.14450.0588-0.00740.12560.13460.153524.26184.038413.689
133.95060.8139-2.43642.35560.08783.81070.48290.1469-0.24430.7324-0.2969-0.3680.69121.20130.09420.69450.1708-0.1030.69260.14270.296823.502886.469724.361
140.6287-1.0730.94743.03-1.55631.83990.2116-0.91620.10930.3203-0.11050.2561-0.3684-0.14530.14610.31050.15360.21850.69660.12440.566111.819582.575925.7475
158.4283-0.6982-3.16423.30350.79623.2342-0.5081-0.643-1.33560.22390.4541-0.17640.3553-0.0569-0.17890.26670.0451-0.09180.3420.0640.367719.336975.643816.4987
163.261-0.6232-0.74452.6757-0.97242.1354-0.29020.06270.2141-0.109-0.213-0.18670.03430.3073-0.76990.39220.1729-0.0286-0.0352-0.030.088316.413386.107612.0136
174.17550.9087-0.33933.0031-0.84342.2134-0.11240.28980.47080.092-0.22370.0883-0.2231-0.257-0.22140.11580.18740.01610.126-0.03010.420412.021585.0217.2355
188.22731.27350.0613.49043.62464.47550.3093-0.9451.01820.6466-0.229-0.5851-0.59460.35250.04990.3541-0.05810.05390.46250.01080.383-7.242981.751821.1317
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 120 )
8X-RAY DIFFRACTION8chain 'A' and (resid 121 through 131 )
9X-RAY DIFFRACTION9chain 'A' and (resid 132 through 142 )
10X-RAY DIFFRACTION10chain 'B' and (resid 18 through 26 )
11X-RAY DIFFRACTION11chain 'B' and (resid 27 through 38 )
12X-RAY DIFFRACTION12chain 'B' and (resid 39 through 68 )
13X-RAY DIFFRACTION13chain 'B' and (resid 69 through 78 )
14X-RAY DIFFRACTION14chain 'B' and (resid 79 through 84 )
15X-RAY DIFFRACTION15chain 'B' and (resid 85 through 105 )
16X-RAY DIFFRACTION16chain 'B' and (resid 106 through 120 )
17X-RAY DIFFRACTION17chain 'B' and (resid 121 through 131 )
18X-RAY DIFFRACTION18chain 'B' and (resid 132 through 143 )

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