7T2A

Crystal structure of HLA-DP4 in complex with Ply


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DP alpha 1 chain
A, D
181Homo sapiensMutation(s): 0 
Gene Names: HLA-DPA1HLA-DP1AHLASB
UniProt & NIH Common Fund Data Resources
Find proteins for P20036 (Homo sapiens)
Explore P20036 
Go to UniProtKB:  P20036
PHAROS:  P20036
GTEx:  ENSG00000231389 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20036
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DP beta 1 chain
B, E
188Homo sapiensMutation(s): 0 
Gene Names: HLA-DPB1HLA-DP1B
UniProt & NIH Common Fund Data Resources
Find proteins for P04440 (Homo sapiens)
Explore P04440 
Go to UniProtKB:  P04440
PHAROS:  P04440
GTEx:  ENSG00000223865 
Entity Groups  
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UniProt GroupP04440
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Pneumolysin-derived peptide
C, F
15Streptococcus pneumoniaeMutation(s): 0 
Gene Names: plySPD_1726
UniProt
Find proteins for Q04IN8 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466))
Explore Q04IN8 
Go to UniProtKB:  Q04IN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04IN8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.669α = 90
b = 101.669β = 90
c = 215.187γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2023-07-12
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description