3DAF

The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII cocrystallized with cyanide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.187

Literature

Macromolecules
Sequence Display for 3DAF

Classification: OXIDOREDUCTASE

Total Structure Weight: 39484.26

Macromolecule Entities
Molecule Chains Length Organism Details
5,10-methenyltetrahydromethanopterin hydrogenase A 358 Methanocaldococcus jannaschii EC#: 1.12.98.2 IUBMB
Mutation: K339V
Gene Name(s): hmd MJ0784
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5- dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine
C19 H23 N6 O11 P
GTHOTKPHMGEHFD-ACDAHVMNSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE2
Query on FE2

A FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CMO
Query on CMO

A CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CYN
Query on CYN

A CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.187
  • Space Group: I 41 2 2

Unit Cell:

Length (Å) Angle (°)
a = 97.14 α = 90.00
b = 97.14 β = 90.00
c = 166.03 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-05-29
  • Released Date: 2008-12-09
  • Deposition author(s): Pilak, O., Warkentin, E., Shima, S., Thauer, R.K., Ermler, U.

Revision History

  • 2011-07-13
    Type: Advisory, Version format compliance