1PBY

Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase from Paracoccus denitrificans at 1.7 A Resolution

Structural Biology Knowledgebase: 1PBY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.224
  • R-Value Work: 0.191

Literature

Macromolecules
Sequence Display for 1PBY

Classification: OXIDOREDUCTASE

Total Structure Weight: 100107.73

Macromolecule Entities
Molecule Chains Length Organism Details
quinohemoprotein amine dehydrogenase 60 kDa subunit A 489 Paracoccus denitrificans EC#: 1.4.9.1 IUBMB
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
quinohemoprotein amine dehydrogenase 40 kDa subunit B 337 Paracoccus denitrificans Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
quinohemoprotein amine dehydrogenase 9 kDa subunit C 79 Paracoccus denitrificans Mutation: W43X

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

A PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TBU
Query on TBU

A, B TERTIARY-BUTYL ALCOHOL
2-METHYL-2-PROPANOL (Synonym)
C4 H10 O
DKGAVHZHDRPRBM-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TRW
Query on TRW
C L-PEPTIDE LINKING C17 H18 N4 O2 TRP

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.224
  • R-Value Work: 0.191
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 99.24 α = 90.00
b = 99.24 β = 90.00
c = 213.06 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-05-15
  • Released Date: 2003-09-02
  • Deposition author(s): Datta, S., Ikeda, T., Kano, K., Mathews, F.S.

Revision History

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