4QGN

Human acireductone dioxygenase with iron ion and L-methionine in active center


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Human acireductone dioxygenase with iron ion and L-methionine in active center

Milaczewska, A.M.Chruszcz, M.Petkowski, J.J.Niedzialkowska, E.Minor, W.Borowski, T.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase
A
183Homo sapiensMutation(s): 0 
Gene Names: ADI1HMFT1638MTCBP1NP_060739
EC: 1.13.11.54
Find proteins for Q9BV57 (Homo sapiens)
Go to UniProtKB:  Q9BV57
NIH Common Fund Data Resources
PHAROS  Q9BV57
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MSE
Query on MSE

Download CCD File 
A
SELENOMETHIONINE
C5 H11 N O2 Se
RJFAYQIBOAGBLC-BYPYZUCNSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
FE
Query on FE

Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.195α = 90
b = 105.195β = 90
c = 40.822γ = 120
Software Package:
Software NamePurpose
HKL-3000data collection
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
Cootmodel building
HKL-3000phasing
CCP4refinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-27
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description