5GUW

Complex of Cytochrome cd1 Nitrite Reductase and Nitric Oxide Reductase in Denitrification of Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.210

Literature

Macromolecules
Sequence Display for 5GUW

Classification: MEMBRANE PROTEIN

Total Structure Weight: 270808.75

Macromolecule Entities
Molecule Chains Length Organism Details
Nitric oxide reductase subunit C A, C 146 Pseudomonas aeruginosa Fragment: Nitric oxide reductase subunit c
Mutation: N100K
Gene Name(s): norC PA0523
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Nitric oxide reductase subunit B B, D 465 Pseudomonas aeruginosa EC#: 1.7.2.5 IUBMB
Fragment: Nitric oxide reductase subunit b
Mutation: ΔR301
Gene Name(s): norB PA0524
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Nitrite reductase M, N 568 Pseudomonas aeruginosa EC#: 1.7.2.1 IUBMB
Fragment: cd1 nitrite reductase
Gene Name(s): nirS PA0519
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Nitric Oxide Reductases

Protein Name: Nitric Oxide Reductase


Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DHE
Query on DHE

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

A, C, M, N HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

B, D PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
10M
Query on 10M

A, C, D decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta- D-glucopyranoside
4,,3R (Synonym)
C22 H42 O10 S
YZNNXXWNKQOETJ-HYLFJBCQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

B, D FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, C CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

M, N CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
O
Query on O

B, D OXYGEN ATOM
O
XLYOFNOQVPJJNP-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: 0.254
  • R-Value Work: 0.210
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 111.87 α = 90.00
b = 128.61 β = 106.83
c = 127.81 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-08-31
  • Released Date: 2017-08-16
  • Deposition author(s): Terasaka, E., Sugimoto, H., Shiro, Y., Tosha, T.

Revision History

  • Version 1_0: 2017-08-16

    Type: Initial release

  • Version 1_1: 2017-09-27

    Type: Database references