[English] 日本語
Yorodumi
- PDB-5n2f: Structure of PD-L1/small-molecule inhibitor complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5n2f
TitleStructure of PD-L1/small-molecule inhibitor complex
Components(Programmed cell death 1 ligand 1) x 2
KeywordsIMMUNE SYSTEM / PD-L1 / PD-1 / small-molecule inhibitor
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 / Regulation of PD-L1(CD274) translation / negative regulation of T cell mediated immune response to tumor cell / negative regulation of CD4-positive, alpha-beta T cell proliferation / TRIF-dependent toll-like receptor signaling pathway / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / PD-L1(CD274) glycosylation and translocation to plasma membrane ...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 / Regulation of PD-L1(CD274) translation / negative regulation of T cell mediated immune response to tumor cell / negative regulation of CD4-positive, alpha-beta T cell proliferation / TRIF-dependent toll-like receptor signaling pathway / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / PD-L1(CD274) glycosylation and translocation to plasma membrane / negative regulation of T cell activation / 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 receptor signaling pathway / negative regulation of T cell proliferation / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / T cell costimulation / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / SPOP-mediated proteasomal degradation of PD-L1(CD274) / positive regulation of T cell proliferation / response to cytokine / recycling endosome membrane / cellular response to lipopolysaccharide / early endosome membrane / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / nuclear speck / immune response / receptor ligand activity / external side of plasma membrane / Golgi membrane / endoplasmic reticulum membrane / signal transduction / extracellular exosome / nucleoplasm / plasma membrane / cytosol
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-8HW / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGuzik, K. / Zak, K.M. / Grudnik, P. / Dubin, G. / Holak, T.A.
Funding support Poland, 7items
OrganizationGrant numberCountry
National Science CenterUMO-2012/06/A/ST5/00224 Poland
National Science CenterUMO-2014/12/W/NZ1/00457 Poland
National Science CenterUMO-2011/01/D/NZ1/01169 Poland
National Science CenterUMO-2012/07/E/NZ1/01907 Poland
National Science CenterUMO-2015/19/N/ST5/00347 Poland
National Science CenterUMO-2016/20/T/NZ1/00519 Poland
National Science CenterUMO-2015/19/D/NZ1/02009 Poland
CitationJournal: J. Med. Chem. / Year: 2017
Title: Small-Molecule Inhibitors of the Programmed Cell Death-1/Programmed Death-Ligand 1 (PD-1/PD-L1) Interaction via Transiently Induced Protein States and Dimerization of PD-L1.
Authors: Guzik, K. / Zak, K.M. / Grudnik, P. / Magiera, K. / Musielak, B. / Torner, R. / Skalniak, L. / Domling, A. / Dubin, G. / Holak, T.A.
History
DepositionFeb 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)29,0263
Polymers28,5292
Non-polymers4971
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-4 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.815, 52.379, 111.526
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

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


Mass: 14402.465 Da / Num. of mol.: 1
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: Protein Programmed cell death 1 ligand 1 / Programmed death ligand 1 / B7 homolog 1 / B7-H1


Mass: 14126.172 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-8HW / 4-[[4-[[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methyl-phenyl]methoxy]-2,5-bis(fluoranyl)phenyl]methylamino]-3-oxidanylidene-butanoic acid


Mass: 497.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H25F2NO6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.01 M Tris pH 8.4 , 0.28 M sodium chloride, 27% (w/v) PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→36.84 Å / Num. all: 222441 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.026 / Net I/σ(I): 33.3
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 12071 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5c3t

5c3t


Resolution: 1.7→36.837 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.5
RfactorNum. reflection% reflection
Rfree0.2297 1664 4.87 %
Rwork0.1907 --
obs0.1925 34155 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→36.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 36 271 2254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092090
X-RAY DIFFRACTIONf_angle_d1.0252852
X-RAY DIFFRACTIONf_dihedral_angle_d20.4071264
X-RAY DIFFRACTIONf_chiral_restr0.059317
X-RAY DIFFRACTIONf_plane_restr0.006364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.34511030.28222719X-RAY DIFFRACTION100
1.75-1.80650.32671440.2492652X-RAY DIFFRACTION100
1.8065-1.87110.25681420.2262649X-RAY DIFFRACTION100
1.8711-1.9460.26561510.21342674X-RAY DIFFRACTION100
1.946-2.03460.23931330.20282659X-RAY DIFFRACTION100
2.0346-2.14180.25971300.21922681X-RAY DIFFRACTION100
2.1418-2.2760.25591520.21532702X-RAY DIFFRACTION100
2.276-2.45170.24881380.21242685X-RAY DIFFRACTION100
2.4517-2.69840.27691460.2162694X-RAY DIFFRACTION100
2.6984-3.08860.23441680.20262712X-RAY DIFFRACTION100
3.0886-3.89070.19331330.17052754X-RAY DIFFRACTION100
3.8907-36.84520.18821240.15722910X-RAY DIFFRACTION99
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)
11.75451.20830.81291.43311.30842.5330.1438-0.1335-0.12950.1598-0.0333-0.08940.0842-0.2512-0.14740.21870.0206-0.02040.1789-0.01050.220416.56497.178125.6869
22.4578-0.22810.46012.03431.01263.15710.1951-0.16510.10030.2078-0.05210.14510.214-0.0133-0.11110.28430.0350.0480.20310.01110.256817.966315.915135.5387
35.21681.91511.04884.69780.20333.1090.08170.56490.0069-0.10450.3948-0.6349-0.37780.6518-0.48340.25820.01670.00910.2296-0.04950.29825.585518.9991125.7383
47.59260.3154-0.49263.153.93475.0106-0.37770.73521.6766-0.20810.7689-0.4947-1.64970.2945-0.45051.0363-0.1045-0.07580.35160.06240.457624.574726.0349122.8329
56.90383.1498-2.78567.90790.22491.4705-0.07481.07590.7133-1.1907-0.01060.3309-1.00441.1334-0.03450.5523-0.0591-0.06730.71350.09080.256919.152719.9995114.0609
63.2556-0.3326-2.1451.02371.352.69910.22750.1046-0.01860.0516-0.04580.5034-1.3526-1.2466-0.00570.37250.0952-0.02260.3581-0.00410.349213.888220.6021130.7039
72.29691.3092.85390.99582.07484.4093-0.20190.11770.0393-0.10630.03010.0013-0.45120.20420.07220.23590.0197-0.0110.23780.00740.24815.68413.5789118.7482
82.01711.8222.90143.07515.0868.8998-0.05880.04820.05790.22910.1287-0.07250.05260.1899-0.27510.26620.0395-0.04060.2244-0.10710.289425.791313.3338129.1942
95.62893.46042.15373.58492.46841.6754-0.0190.3127-0.36050.18440.3495-0.31290.02320.4972-0.47640.23410.055-0.02740.1739-0.05190.232123.14726.5785125.326
103.91583.9089-0.63144.13320.00036.8108-0.26330.2980.2207-0.5817-0.0162-0.7314-0.67810.39450.28640.3458-0.02550.04490.32510.00510.35316.01785.6153101.2903
111.9417-0.3421-1.51881.5541.61752.37350.1176-0.06290.3504-0.08890.0556-0.2044-0.18450.0511-0.15090.2196-0.0103-0.00310.2253-0.02050.240448.438911.665122.5388
120.67050.03430.08373.37621.21793.6576-0.0417-0.38720.24340.8658-0.19-0.384-0.895-0.005-0.15380.6125-0.0095-0.1160.3264-0.14340.517345.56222.4687134.1875
135.5387-1.4107-1.47134.66121.80793.60580.06-0.4217-0.19940.44780.06170.13320.0566-0.53460.00830.2347-0.0072-0.01540.2836-0.00680.197438.94379.2192132.829
143.63080.63250.1695.4831-4.06813.1264-0.1497-0.4778-0.19120.6685-0.287-0.1089-0.2581-0.34030.38760.3199-0.0465-0.01330.27010.00640.365440.14363.0447137.3715
155.2527-3.940.26193.0235-0.63032.7903-0.1297-0.79-0.54860.89540.2962-0.65570.45750.31920.0730.33740.02750.00140.3587-0.01280.357348.59642.7592134.628
164.17634.3977-0.86964.7098-0.5142.2522-0.3787-1.0520.63541.0048-0.2397-2.0579-0.36990.26610.45440.4277-0.0227-0.20070.3869-0.15970.733549.902618.0865135.901
174.336-1.6995-0.17354.85731.54263.0398-0.015-0.2332-0.03110.2084-0.06790.0351-0.068-0.13970.08990.1508-0.01740.00290.2167-0.00760.139743.40818.0656127.0223
188.3733-5.8961-5.9254.4664.83656.16510.23970.33540.1833-0.0633-0.3653-0.0083-0.2307-0.46420.33740.2211-0.0005-0.00140.2267-0.0480.195941.452112.0207121.2676
191.73660.92522.11173.11233.67188.2831-0.0977-0.5735-0.23680.69750.54730.00060.8868-1.0313-0.33540.2788-0.02360.00430.27330.08540.282649.4161-10.8137114.2982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 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 109 )
8X-RAY DIFFRACTION8chain 'A' and (resid 110 through 119 )
9X-RAY DIFFRACTION9chain 'A' and (resid 120 through 131 )
10X-RAY DIFFRACTION10chain 'A' and (resid 132 through 143 )
11X-RAY DIFFRACTION11chain 'B' and (resid 18 through 38 )
12X-RAY DIFFRACTION12chain 'B' and (resid 39 through 49 )
13X-RAY DIFFRACTION13chain 'B' and (resid 50 through 68 )
14X-RAY DIFFRACTION14chain 'B' and (resid 69 through 81 )
15X-RAY DIFFRACTION15chain 'B' and (resid 82 through 88 )
16X-RAY DIFFRACTION16chain 'B' and (resid 89 through 98 )
17X-RAY DIFFRACTION17chain 'B' and (resid 99 through 119 )
18X-RAY DIFFRACTION18chain 'B' and (resid 120 through 131 )
19X-RAY DIFFRACTION19chain 'B' and (resid 132 through 141 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more