Macromolecules
Sequence Display for 1OGY

Classification: OXIDOREDUCTASE

Total Structure Weight: 862971.75

Macromolecule Entities
Molecule Chains Length Organism Details
PERIPLASMIC NITRATE REDUCTASE A, C, E..., G, I, K, M, OA, C, E, G, I, K, M, O 802 Rhodobacter sphaeroides EC#: 1.7.99.4 IUBMB
Fragment: CATALYTIC SUBUNIT, RESIDUES 30-831
Gene Name(s): napA RHOS4_40230 RSP_4116
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE B, D, F..., H, J, L, N, PB, D, F, H, J, L, N, P 130 Rhodobacter sphaeroides Fragment: CYTOCHROME SUBUNIT, RESIDUES 25-154
Gene Name(s): napB RHOS4_40240 RSP_4117
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MGD
Query on MGD

A, C, E, G, I, K, M, O 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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEC
Query on HEC

B, D, F, H, J, L, N, P HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

A, C, E, G, I, K, M, O IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MO
Query on MO

A, C, E, G, I, K, M, O MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.250
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 123.00 α = 90.00
b = 225.20 β = 92.10
c = 154.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-05-19
  • Released Date: 2003-10-09
  • Deposition author(s): Arnoux, P., Sabaty, M., Alric, J., Frangioni, B., Guigliarelli, B., Adriano, J.-M., Pignol, D.

Revision History

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