1DY7

CYTOCHROME CD1 NITRITE REDUCTASE, CO COMPLEX

Structural Biology Knowledgebase: 1DY7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 1DY7

Classification: OXIDOREDUCTASE

Total Structure Weight: 127758.48

Macromolecule Entities
Molecule Chains Length Organism Details
NITRITE REDUCTASE A, B 567 Paracoccus pantotrophus EC#: 1.7.2.1 IUBMB
Gene Name(s): nirS
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B HEME D
C34 H32 Fe N4 O10
XLQCGNUTSJTZNF-SOFPVUHFDM
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEC
Query on HEC

B HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CMO
Query on CMO

A, B CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.178
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 106.94 α = 90.00
b = 61.04 β = 111.77
c = 100.39 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-01-28
  • Released Date: 2000-09-24
  • Deposition author(s): Sjogren, T., Svensson-Ek, M., Hajdu, J., Brzezinski, P.

Revision History

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