1GYX

THE CRYSTAL STRUCTURE OF YDCE, A 4-OXALOCROTONATE TAUTOMERASE HOMOLOGUE FROM ESCHERICHIA COLI, CONFIRMS THE STRUCTURAL BASIS FOR OLIGOMER DIVERSITY

Structural Biology Knowledgebase: 1GYX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.164
  • R-Value Work: 0.142

Literature

Macromolecules
Sequence Display for 1GYX

Classification: ISOMERASE

Total Structure Weight: 17462.03

Macromolecule Entities
Molecule Chains Length Organism Details
HYPOTHETICAL PROTEIN YDCE A, B 76 Escherichia coli Details: INACTIVATED BY HEPES AND BENZOIC ACID
Gene Name(s): pptA ydcE b1461 JW1456
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

B 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BEZ
Query on BEZ

A BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BEZ N/A in BindingDB
Ki: 3300000 nM  BindingMOAD
Ki: 3300000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.164
  • R-Value Work: 0.142
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 44.57 α = 90.00
b = 46.53 β = 90.00
c = 75.72 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-04-30
  • Released Date: 2002-10-10
  • Deposition author(s): Almrud, J., Kern, A., Wang, S., Czerwinski, R., Johnson, W., Murzin, A., Hackert, M., Whitman, C.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4