[English] 日本語
Yorodumi
- PDB-7nld: Structure of human Programmed cell death 1 ligand 1 (PD-L1) with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nld
TitleStructure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor
ComponentsProgrammed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / PD-L1 / cancer / 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 / 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 / positive regulation of T cell proliferation / negative regulation of T cell proliferation / T cell costimulation / response to cytokine / 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 / positive regulation of cell migration / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-UGZ / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSala, D. / Magiera-Mularz, K. / Muszak, D. / Surmiak, E. / Grudnik, P. / Holak, T.A.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Terphenyl-Based Small-Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1 Protein-Protein Interaction.
Authors: Muszak, D. / Surmiak, E. / Plewka, J. / Magiera-Mularz, K. / Kocik-Krol, J. / Musielak, B. / Sala, D. / Kitel, R. / Stec, M. / Weglarczyk, K. / Siedlar, M. / Domling, A. / Skalniak, L. / Holak, T.A.
History
DepositionFeb 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Programmed cell death 1 ligand 1
A: Programmed cell death 1 ligand 1
B: Programmed cell death 1 ligand 1
D: Programmed cell death 1 ligand 1
E: Programmed cell death 1 ligand 1
F: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5829
Polymers88,0736
Non-polymers1,5093
Water75742
1
C: Programmed cell death 1 ligand 1
D: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8613
Polymers29,3582
Non-polymers5031
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Programmed cell death 1 ligand 1
B: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8613
Polymers29,3582
Non-polymers5031
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Programmed cell death 1 ligand 1
hetero molecules

F: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)29,8613
Polymers29,3582
Non-polymers5031
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y+1/2,-z-11
Unit cell
Length a, b, c (Å)67.087, 75.255, 74.354
Angle α, β, γ (deg.)90.000, 96.290, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Programmed cell death 1 ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1


Mass: 14678.759 Da / Num. of mol.: 6
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-UGZ / N-(2-((2'-chloro-3'-(2,3-dihydrobenzo[b][1,4]dioxin-6-yl)-3-methoxy-[1,1'-biphenyl]-4-yl)(methyl)amino)ethyl)methanesulfonamide / ~{N}-[2-[[4-[2-chloranyl-3-(2,3-dihydro-1,4-benzodioxin-6-yl)phenyl]-2-methoxy-phenyl]methylamino]ethyl]methanesulfonamide


Mass: 503.010 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H27ClN2O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M sodium cocdylate pH 6.5; 25% PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.3→47.01 Å / Num. obs: 32474 / % possible obs: 99 % / Redundancy: 13.4 % / CC1/2: 1 / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.42 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 1720 / CC1/2: 0.77 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O45

5o45


Resolution: 2.3→43.03 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 39.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2939 1606 4.99 %
Rwork0.2426 30584 -
obs0.2443 32190 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.6 Å2 / Biso mean: 56.2346 Å2 / Biso min: 28.02 Å2
Refinement stepCycle: final / Resolution: 2.3→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5210 0 102 42 5354
Biso mean--73.14 57.56 -
Num. residues----696
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.37420.46531410.4129271697
2.3742-2.45910.44561380.3819263493
2.4591-2.55750.47261440.3579275298
2.5575-2.67390.41271460.3425277599
2.6739-2.81490.41361490.3069280799
2.8149-2.99120.34061480.3052280299
2.9912-3.22210.35251450.2832277598
3.2221-3.54620.34141490.2544281999
3.5462-4.0590.28011470.2232281699
4.059-5.11260.22071480.1824280999
5.1126-43.030.21361510.1968287999

+
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