6R3K

Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor

Zak, K.M.Grudnik, P.Skalniak, L.Dubin, G.Holak, T.A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Programmed cell death 1 ligand 1
A, B, C, D
128Homo sapiensMutation(s): 0 
Gene Names: CD274B7H1PDCD1L1PDCD1LG1PDL1
Find proteins for Q9NZQ7 (Homo sapiens)
Go to UniProtKB:  Q9NZQ7
NIH Common Fund Data Resources
PHAROS  Q9NZQ7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JQT
Query on JQT

Download CCD File 
B, D
(2~{S},4~{R})-1-[[5-chloranyl-2-[(3-cyanophenyl)methoxy]-4-[[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methyl-phenyl]methoxy]phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxylic acid
C36 H33 Cl N2 O7
QBXVXKRWOVBUDB-MVSFAKPFSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, C
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.527α = 90
b = 84.609β = 90
c = 164.116γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland--
Polish National Science CentrePolandUMO-2012/06/A/ST5/00224
Polish National Science CentrePolandUMO-2014/12/W/NZ1/00457
Polish National Science CentrePolandUMO-2011/01/D/NZ1/01169
Polish National Science CentrePolandUMO-2012/07/E/NZ1/01907
Polish National Science CentrePoland2015/19/N/ST5/00347
Polish National Science CentrePolandUMO-2016/20/T/NZ1/00519
Polish National Science CentrePolandUMO-2015/19/D/NZ1/02009

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Advisory, Data collection, Derived calculations