1FDI

OXIDIZED FORM OF FORMATE DEHYDROGENASE H FROM E. COLI COMPLEXED WITH THE INHIBITOR NITRITE

Structural Biology Knowledgebase: 1FDI SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.192

Literature

Macromolecules
Sequence Display for 1FDI

Classification: OXIDOREDUCTASE

Total Structure Weight: 81441.02

Macromolecule Entities
Molecule Chains Length Organism Details
FORMATE DEHYDROGENASE H A 715 Escherichia coli EC#: 1.1.99.33 IUBMB 1.2.1.2 IUBMB
Details: OXIDIZED FORM (MO(VI),FE4S4(OX)) OF FDH-H COMPLEXED WITH NITRITE
Gene Name(s): fdhF b4079 JW4040
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MGD
Query on MGD

A 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9- TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN- 4-ONE GUANOSINE DINUCLEOTIDE
MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE (Synonym)
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

A IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
6MO
Query on 6MO

A MOLYBDENUM(VI) ION
Mo
HCNGUXXTNNIKCQ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NO2
Query on NO2

A NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
SEC
Query on SEC
L-PEPTIDE LINKING C3 H7 N O2 Se --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.192
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 146.80 α = 90.00
b = 146.80 β = 90.00
c = 81.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1997-01-28
  • Released Date: 1997-08-20
  • Deposition author(s): Sun, P.D., Boyington, J.C.

Revision History

  • 2014-08-06
    Type: Linkage | Details: Remove links to SEC
  • 2014-08-06
    Type: Polymer description | Details: Change SEC to one letter code
  • 2014-01-29
    Type: Polymer description | Details: Change selenocysteine CSE to SEC
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4