1E3D

[NIFE] HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS ATCC 27774

Structural Biology Knowledgebase: 1E3D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Observed: 0.167

Literature

Macromolecules
Sequence Display for 1E3D

Classification: HYDROGENASE

Total Structure Weight: 180062.77

Macromolecule Entities
Molecule Chains Length Organism Details
[NIFE] HYDROGENASE SMALL SUBUNIT A, C 266 Desulfovibrio desulfuricans Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
[NIFE] HYDROGENASE LARGE SUBUNIT B, D 542 Desulfovibrio desulfuricans Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FSX
Query on FSX

A, C BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2- -SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU- O)IRON(II)
FE4-S3-O3 CLUSTER (Synonym)
Fe4 O3 S3
BIOGFUMNBIDAOG-VNBKSMEUCR
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

A, C IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
F3S
Query on F3S

A, C FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FNE
Query on FNE

B, D (MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICARBONYLIRON- DI-(CYS,S)NICKEL(II)](FE-NI)
C3 Fe Ni O3 S
RSNJUOPWNIKDNA-LMILJAESAR
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
H2S
Query on H2S

A, B, C, D HYDROSULFURIC ACID
HYDROGEN SULFIDE (Synonym)
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Observed: 0.167
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 64.09 α = 90.00
b = 169.98 β = 92.80
c = 72.62 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-06-14
  • Released Date: 2001-06-14
  • Deposition author(s): Matias, P.M., Soares, C.M., Saraiva, L.M., Coelho, R., Morais, J., Le Gall, J., Carrondo, M.A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4