4IM7

Crystal structure of fructuronate reductase (ydfI) from E. coli CFT073 (EFI TARGET EFI-506389) complexed with NADH and D-mannonate

Structural Biology Knowledgebase: 4IM7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.173
  • R-Value Work: 0.148

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4IM7

Classification: OXIDOREDUCTASE

Total Structure Weight: 56889.65

Macromolecule Entities
Molecule Chains Length Organism Details
Hypothetical oxidoreductase ydfI A 506 Escherichia coli EC#: 1 IUBMB
Gene Name(s): c1968

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

A 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH (Synonym)
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CS2
Query on CS2

A D-MANNONIC ACID
D-MANNONATE (Synonym)
C6 H12 O7
RGHNJXZEOKUKBD-MBMOQRBOSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.173
  • R-Value Work: 0.148
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 92.49 α = 90.00
b = 92.49 β = 90.00
c = 136.00 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-01-02
  • Released Date: 2013-01-23
  • Deposition author(s): Lukk, T., Wichelecki, D., Imker, H.J., Gerlt, J.A., Nair, S.K.

Revision History

  • 2014-11-12
    Type: Function and keywords | Details: --