2IV2

Reinterpretation of reduced form of formate dehydrogenase H from E. coli

Structural Biology Knowledgebase: 2IV2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.175

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2IV2

Classification: OXIDOREDUCTASE

Total Structure Weight: 81397.03

Macromolecule Entities
Molecule Chains Length Organism Details
FORMATE DEHYDROGENASE H X 715 Escherichia coli EC#: 1.1.99.33 IUBMB 1.2.1.2 IUBMB
Details: REDUCED FORM (MO(IV), FE4S4(RED)) OF FDH-H
Gene Name(s): fdhF b4079 JW4040
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

X GUANYLATE-O'-PHOSPHORIC ACID MONO-(2-AMINO- 5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A- OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN- 7-YLMETHYL) ESTER
MOLYBDENUM COFACTOR,BIS (MOLYBDOPTERIN GUANINE DINUCLEOTIDE) (Synonym)
C20 H28 N10 O13 P2 S2
YDYCAANTTOPADF-JKOCJXFLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MGD
Query on MGD

X 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)
SF4
Query on SF4

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

X MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNX
Query on UNX

X UNKNOWN ATOM OR ION
X
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: 2.27 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.175
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 146.40 α = 90.00
b = 146.40 β = 90.00
c = 81.27 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-06-08
  • Released Date: 2006-06-12
  • Deposition author(s): Raaijmakers, H.C.A., Romao, M.J.

Revision History

  • 2014-02-19
    Type: Version format compliance | Details: REMARK 4
  • 2014-02-19
    Type: Polymer description | Details: SEQRES
  • 2014-02-19
    Type: Other | Details: REMARK 375,MODRES,REMARK 525
  • 2014-02-19
    Type: Atom nomenclature | Details: ATOM,HETATM
  • 2014-02-19
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2014-02-19
    Type: Linkage | Details: CONECT,LINK
  • 2014-02-19
    Type: Function and keywords | Details: KEYWDS
  • 2014-02-19
    Type: Binding sites and description | Details: REMARK 800
  • 2014-02-19
    Type: Non-polymer description | Details: HETSYN,FORMUL,HETNAM,HET
  • 2014-02-19
    Type: Geometry validation | Details: REMARK 500