5KOH

Nitrogenase MoFeP from Gluconacetobacter diazotrophicus in dithionite reduced state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.150
  • R-Value Work: 0.129

Literature

Macromolecules
Sequence Display for 5KOH

Classification: OXIDOREDUCTASE

Total Structure Weight: 230175.45

Macromolecule Entities
Molecule Chains Length Organism Details
Nitrogenase protein alpha chain A, C 499 Gluconacetobacter diazotrophicus EC#: 1.18.6.1 IUBMB
Gene Name(s): nifD GDI0437 Gdia_1569
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Nitrogenase FeMo beta subunit protein NifK B, D 511 Gluconacetobacter diazotrophicus EC#: 1.18.6.1 IUBMB
Gene Name(s): nifK GDI0438 Gdia_1568
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, C iron-sulfur-molybdenum cluster with interstitial carbon
C Fe7 Mo S9
DDQFAOMIVKLFON-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CLF
Query on CLF

A, C FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-DHHOTQGYAO
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HCA
Query on HCA

A, C 3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

C (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MRD
Query on MRD

A (4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

B FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.150
  • R-Value Work: 0.129
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 202.60 α = 90.00
b = 202.60 β = 90.00
c = 132.57 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-06-30
  • Released Date: 2016-09-21
  • Deposition author(s): Owens, C.P., Tezcan, F.A.

Revision History

  • 2017-08-23
    Type: Data collection, Derived calculations