1NDO

NAPHTHALENE 1,2-DIOXYGENASE

Structural Biology Knowledgebase: 1NDO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.190

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1NDO

Classification: NON-HEME IRON DIOXYGENASE

Total Structure Weight: 218597.36

Macromolecule Entities
Molecule Chains Length Organism Details
NAPHTHALENE 1,2-DIOXYGENASE A, C, E 449 Pseudomonas putida EC#: 1.14.12.12 IUBMB
Details: CHAIN A,C,E AND B,D,F ARE THE LARGE AND THE SMALL SUBUNITS RESPECTIVELY
Gene Name(s): ndoB nahA3 nahAC ndoC2
NAPHTHALENE 1,2-DIOXYGENASE B, D, F 194 Pseudomonas putida EC#: 1.14.12.12 IUBMB
Details: CHAIN A,C,E AND B,D,F ARE THE LARGE AND THE SMALL SUBUNITS RESPECTIVELY
Gene Name(s): ndoC nahAD

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

A, C, E FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

A, C, E FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.240
  • R-Value Work: 0.190
  • Space Group: I 2 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 105.00 α = 90.00
b = 174.00 β = 90.00
c = 282.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-01-11
  • Released Date: 1999-03-23
  • Deposition author(s): Ramaswamy, S., Kauppi, B., Carredano, E.

Revision History

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