4AQ6

substrate bound homogentisate 1,2-dioxygenase

Structural Biology Knowledgebase: 4AQ6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.161

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4AQ6

Classification: OXIDOREDUCTASE

Total Structure Weight: 579701.75

Macromolecule Entities
Molecule Chains Length Organism Details
HOMOGENTISATE 1,2-DIOXYGENASE A, B, C..., D, E, F, G, H, I, J, K, LA, B, C, D, E, F, G, H, I, J, K, L 433 Pseudomonas putida EC#: 1.13.11.5 IUBMB
Gene Name(s): hmgA PP_4621
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
B3P
Query on B3P

K 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)- PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3- DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OMD
Query on OMD

A, B, C, D, E, F, G, H, I, J, K, L 2-(3,6-DIHYDROXYPHENYL)ACETIC ACID
HOMOGENTISIC ACID (Synonym)
C8 H8 O4
IGMNYECMUMZDDF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

A, B, C, D, E, F, G, H, I, J, K, L FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
OMD N/A in BindingDB
N/A in BindingMoad
Kd: 15800 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.161
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 93.39 α = 87.69
b = 93.71 β = 80.42
c = 162.98 γ = 68.39

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-04-12
  • Released Date: 2013-04-24
  • Deposition author(s): Jeoung, J.-H., Lin, T.-Y., Bommer, M., Dobbek, H.

Revision History

  • 2013-08-14
    Type: Citation | Details: JRNL
  • 2013-07-24
    Type: Other | Details: REMARK 900
  • 2013-07-24
    Type: Citation | Details: JRNL