1KQF

FORMATE DEHYDROGENASE N FROM E. COLI

Structural Biology Knowledgebase: 1KQF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.195
  • R-Value Work: 0.177

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1KQF

Classification: OXIDOREDUCTASE

Total Structure Weight: 176806.94

Macromolecule Entities
Molecule Chains Length Organism Details
FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, MAJOR SUBUNIT A 1015 Escherichia coli EC#: 1.1.5.6 IUBMB
Details: Native (oxidized) structure
Gene Name(s): fdnG b1474 JW1470
FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, IRON-SULFUR SUBUNIT B 294 Escherichia coli EC#: 1.2.1.2 IUBMB
Details: Native (oxidized) structure
Gene Name(s): fdnH b1475 JW1471
FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, CYTOCHROME B556(FDN) SUBUNIT C 217 Escherichia coli EC#: 1.2.1.2 IUBMB
Details: Native (oxidized) structure
Gene Name(s): fdnI b1476 JW1472

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Electron Transport Chain Complexes: Complex II

Protein Name: Formate dehydrogenase-N


Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CDL
Query on CDL

C CARDIOLIPIN
3'-SN-GLYCEROL, (Synonym)
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

C PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

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

A MOLYBDENUM(VI) ION
Mo
HCNGUXXTNNIKCQ-UHFFFAOYSA-N
Ligand Explorer
 
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: 1.6 Å
  • R-Value Free: 0.195
  • R-Value Work: 0.177
  • Space Group: P 21 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 203.00 α = 90.00
b = 203.00 β = 90.00
c = 203.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-01-05
  • Released Date: 2002-03-15
  • Deposition author(s): Jormakka, M., Tornroth, S., Byrne, B., Iwata, S.

Revision History

  • 2014-08-06
    Type: Polymer description | Details: Use one letter codes for SEC
  • 2014-08-06
    Type: Linkage | Details: Remove backbone links to SEC
  • 2014-02-19
    Type: Polymer description | Details: Change CSE to SEC
  • 2014-02-19
    Type: Atom nomenclature | Details: Change CSE to SEC
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4