[English] 日本語
Yorodumi
- PDB-6nnv: PD-L1 IgV domain complex with macro-cyclic peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nnv
TitlePD-L1 IgV domain complex with macro-cyclic peptide
Components
  • Programmed cell death 1 ligand 1
  • macrocyclic peptide
KeywordsIMMUNE SYSTEM / Fragment-based screening / Structure-based design / PD-L1 inhibitor / Cancer drug discovery / Immunotherapy
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
Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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 15, 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

-
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
C: Programmed cell death 1 ligand 1
D: Programmed cell death 1 ligand 1
I: macrocyclic peptide
J: macrocyclic peptide
K: macrocyclic peptide
L: macrocyclic peptide


Theoretical massNumber of molelcules
Total (without water)65,5838
Polymers65,5838
Non-polymers00
Water5,008278
1
A: Programmed cell death 1 ligand 1
J: macrocyclic peptide


Theoretical massNumber of molelcules
Total (without water)16,3962
Polymers16,3962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-10 kcal/mol
Surface area7020 Å2
MethodPISA
2
B: Programmed cell death 1 ligand 1
I: macrocyclic peptide


Theoretical massNumber of molelcules
Total (without water)16,3962
Polymers16,3962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-9 kcal/mol
Surface area7340 Å2
MethodPISA
3
C: Programmed cell death 1 ligand 1
K: macrocyclic peptide


Theoretical massNumber of molelcules
Total (without water)16,3962
Polymers16,3962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-10 kcal/mol
Surface area7480 Å2
MethodPISA
4
D: Programmed cell death 1 ligand 1
L: macrocyclic peptide


Theoretical massNumber of molelcules
Total (without water)16,3962
Polymers16,3962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-11 kcal/mol
Surface area7160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.840, 61.683, 80.895
Angle α, β, γ (deg.)90.00, 90.17, 90.00
Int Tables number4
Space group name H-MP1211

-
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.: 4 / 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: Protein/peptide
macrocyclic peptide


Mass: 1853.232 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 0.056 M sodium phosphate monobasic, 1.344 M potassium phosphate dibasic

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 3, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.92→30 Å / Num. obs: 41912 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.055 / Rrim(I) all: 0.105 / Rsym value: 0.061 / Χ2: 1.149 / Net I/σ(I): 10.1
Reflection shellResolution: 1.92→1.96 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.338 / Num. unique obs: 2469 / Rpim(I) all: 0.237 / Rrim(I) all: 0.415 / Rsym value: 0.367 / % possible all: 92.3

-
Processing

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

3bik


Resolution: 1.92→29.099 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 31.55
RfactorNum. reflection% reflection
Rfree0.2531 1677 4.02 %
Rwork0.2147 --
obs0.2176 41672 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.92→29.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3747 0 536 278 4561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044465
X-RAY DIFFRACTIONf_angle_d1.0466060
X-RAY DIFFRACTIONf_dihedral_angle_d9.4142410
X-RAY DIFFRACTIONf_chiral_restr0.154654
X-RAY DIFFRACTIONf_plane_restr0.006761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9203-1.97670.31961270.27973206X-RAY DIFFRACTION89
1.9767-2.04050.29871350.25263226X-RAY DIFFRACTION91
2.0405-2.11340.26411200.25193270X-RAY DIFFRACTION91
2.1134-2.19790.24891520.23483278X-RAY DIFFRACTION92
2.1979-2.29790.28511300.24683186X-RAY DIFFRACTION90
2.2979-2.41890.24921330.23593344X-RAY DIFFRACTION94
2.4189-2.57020.28681400.24763331X-RAY DIFFRACTION94
2.5702-2.76840.26591400.23583383X-RAY DIFFRACTION94
2.7684-3.04630.25821320.2273386X-RAY DIFFRACTION95
3.0463-3.48580.25371470.20563420X-RAY DIFFRACTION95
3.4858-4.38640.23961360.18253461X-RAY DIFFRACTION96
4.3864-22.5350.20581370.17263515X-RAY DIFFRACTION96
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)
10.05170.0404-0.04320.0981-0.15170.37840.0022-0.0323-0.00920.0138-0.0176-0.01070.04020.1030.01220.18990.01-0.03180.4143-0.04320.023649.125826.271433.0999
20.04130.03280.27380.5332-0.42622.6148-0.01160.0601-0.0312-0.0806-0.0754-0.0470.23510.19780.05060.18520.0148-0.00620.4460.01050.081740.973-7.149914.7078
31.1815-0.43730.67681.03660.9492.2914-0.12250.08780.1657-0.1204-0.0354-0.1016-0.61140.36740.14050.2783-0.0535-0.02530.38730.02270.071639.06146.348718.8617
40.0131-0.0690.05290.4735-0.42950.54920.00630.0630.01170.1059-0.0239-0.0365-0.04830.11520.00810.1339-0.01180.00280.4322-0.02450.028440.8184-4.981222.0634
50.5527-0.2696-0.02051.8932-0.35341.5858-0.0353-0.04190.09090.1034-0.084-0.0247-0.29490.05470.13420.1482-0.0054-0.04340.442-0.03280.095369.39423.077916.0089
61.36650.5485-0.06171.45750.26650.7556-0.09060.0383-0.165-0.15720.0075-0.10350.22470.26870.08420.21330.0060.03810.4116-0.02670.066169.5233-8.523813.532
70.24270.257-0.49720.4004-0.85961.8866-0.0456-0.05030.0127-0.0728-0.00890.0128-0.0788-0.15130.00230.17250.01360.00520.3047-0.01350.036966.96250.85958.0293
81.54452.0427-2.15092.9603-3.0153.11330.1994-0.02520.146-0.0131-0.04810.0171-0.50150.1062-0.16270.33030.05940.07780.39710.00270.144771.917937.838928.6116
90.7893-0.2517-0.6950.95110.58053.412-0.01660.05690.0174-0.0374-0.0065-0.0935-0.00530.30330.04060.2447-0.0127-0.01340.35060.03840.074780.321534.308315.7382
100.0274-0.03240.00170.07830.00310.0006-0.07490.22440.03030.01270.0181-0.0498-0.06730.11320.04620.3424-0.0563-0.03510.3889-0.00070.104178.581128.545239.5101
110.64610.0989-0.54331.5640.52762.3647-0.01250.0264-0.0071-0.022-0.01130.02670.1095-0.04250.00210.1178-0.02010.00350.25110.00050.041672.387322.470222.3408
120.60340.50350.76230.99990.23131.24610.04110.0797-0.0820.06630.0712-0.11910.19740.2162-0.19690.14520.014-0.02810.4404-0.0270.075280.614822.440523.6114
130.79110.05571.40120.6234-0.92644.17860.18270.2409-0.0889-0.1841-0.1018-0.06270.23590.4934-0.08340.2561-0.0126-0.03240.3859-0.02660.095479.112127.29978.5254
140.8395-0.1340.49172.264-2.31075.88120.0018-0.00890.03210.06560.0237-0.016-0.00310.0030.020.1531-0.0037-0.00250.05010.03840.070970.715128.698226.077
150.03820.0768-0.08450.5136-0.91261.7206-0.0729-0.04330.0082-0.03350.08860.0280.1846-0.08770.00130.19190.0056-0.0010.2689-0.00290.037874.860636.390411.4607
160.14380.0978-0.12460.74030.15341.21570.00150.039-0.0421-0.1297-0.0095-0.0180.25150.06650.0050.24360.0096-0.01180.3762-0.0240.040647.663725.632625.324
170.1737-0.2479-0.71132.09421.74633.21830.05710.18020.1249-0.3796-0.0374-0.2984-0.48720.9111-0.02890.2115-0.0455-0.00560.42580.04540.111447.369939.356125.7454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 79 through 142 )
2X-RAY DIFFRACTION2chain 'D' and (resid 18 through 53 )
3X-RAY DIFFRACTION3chain 'D' and (resid 54 through 84 )
4X-RAY DIFFRACTION4chain 'D' and (resid 85 through 140 )
5X-RAY DIFFRACTION5chain 'A' and (resid 18 through 53 )
6X-RAY DIFFRACTION6chain 'A' and (resid 54 through 94 )
7X-RAY DIFFRACTION7chain 'A' and (resid 95 through 136 )
8X-RAY DIFFRACTION8chain 'B' and (resid 18 through 26 )
9X-RAY DIFFRACTION9chain 'B' and (resid 27 through 41 )
10X-RAY DIFFRACTION10chain 'B' and (resid 42 through 53 )
11X-RAY DIFFRACTION11chain 'B' and (resid 54 through 68 )
12X-RAY DIFFRACTION12chain 'B' and (resid 69 through 101 )
13X-RAY DIFFRACTION13chain 'B' and (resid 102 through 109 )
14X-RAY DIFFRACTION14chain 'B' and (resid 110 through 119 )
15X-RAY DIFFRACTION15chain 'B' and (resid 120 through 140 )
16X-RAY DIFFRACTION16chain 'C' and (resid 18 through 61 )
17X-RAY DIFFRACTION17chain 'C' and (resid 62 through 78 )

+
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