1D5Z

X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH PEPTIDOMIMETIC AND SEB

Structural Biology Knowledgebase: 1D5Z SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.234

Literature

Macromolecules
Sequence Display for 1D5Z

Classification: IMMUNE SYSTEM / PEPTIDE INHIBITOR

Total Structure Weight: 72863.52

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (HLA CLASS II HISTOCOMPATIBILITY ANTIGEN) A 181 Homo sapiens Fragment: DR ALPHA CHAIN, EXTRACELLULAR DOMAIN
Gene Name(s): HLA-DRA Gene View HLA-DRA1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEIN (HLA CLASS II HISTOCOMPATIBILITY ANTIGEN) B 192 Homo sapiens Fragment: DR-4 BETA CHAIN, EXTRACELLULAR DOMAIN
Gene Name(s): HLA-DRB1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEIN (ENTEROTOXIN TYPE B) C 239 Staphylococcus aureus Gene Name(s): entB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEIN (PEPTIDOMIMETIC INHIBITOR) D 8 synthetic

Small Molecules
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000456
Query on PRD_000456
D ACE-ALC-ARG-ALA-ODA-SER-LEU-NH2 Peptide-like /
Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.234
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 78.34 α = 90.00
b = 100.17 β = 90.00
c = 100.18 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-10-12
  • Released Date: 2000-06-28
  • Deposition author(s): Swain, A., Crowther, R., Kammlott, U.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry