3K5T

Crystal structure of human diamine oxidase in space group C2221

Structural Biology Knowledgebase: 3K5T SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.290
  • R-Value Work: 0.236

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3K5T

Classification: OXIDOREDUCTASE

Total Structure Weight: 84770.52

Macromolecule Entities
Molecule Chains Length Organism Details
Diamine oxidase A 731 Homo sapiens EC#: 1.4.3.22 IUBMB
Mutation: P21R, T592S, H645D
Gene Name(s): AOC1 Gene View ABP1 DAO1

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CU
Query on CU

A COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TPQ
Query on TPQ
A L-PEPTIDE LINKING C9 H9 N O5 TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.290
  • R-Value Work: 0.236
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 94.77 α = 90.00
b = 96.95 β = 90.00
c = 178.06 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-10-08
  • Released Date: 2010-02-09
  • Deposition author(s): McGrath, A.P., Guss, J.M.

Revision History

  • 2012-03-28
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4