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 

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: ADI1 (MTCBP1)
EC: 1.13.11.54
Find proteins for Q9BV57 (Homo sapiens)
Go to Gene View: ADI1
Go to UniProtKB:  Q9BV57
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FE
Query on FE

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A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
MSE
Query on MSE

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Download CCD File 
A
SELENOMETHIONINE
C5 H11 N O2 Se
RJFAYQIBOAGBLC-BYPYZUCNSA-N
 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 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 105.195α = 90.00
b = 105.195β = 90.00
c = 40.822γ = 120.00
Software Package:
Software NamePurpose
Cootmodel building
CCP4refinement
HKL-3000data scaling
HKL-3000data reduction
SCALEPACKdata scaling
DENZOdata reduction
HKL-3000data collection
REFMACrefinement
HKL-3000phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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