4HM4

Naphthalene 1,2-Dioxygenase bound to indan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Naphthalene 1,2-Dioxygenase bound to indan

Ferraro, D.J.Ramaswamy, S.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Naphthalene 1,2-dioxygenase subunit alpha
A
449Pseudomonas sp. (strain C18)Mutation(s): 0 
Gene Names: doxB
EC: 1.14.12.12
Find proteins for P0A111 (Pseudomonas sp. (strain C18))
Go to UniProtKB:  P0A111
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Naphthalene 1,2-dioxygenase subunit beta
B
194Pseudomonas sp. (strain C18)Mutation(s): 0 
Gene Names: doxD
Find proteins for P0A113 (Pseudomonas sp. (strain C18))
Go to UniProtKB:  P0A113
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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Download CCD File 
A
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
16N
Query on 16N

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Download CCD File 
A
2,3-dihydro-1H-indene
indan
C9 H10
PQNFLJBBNBOBRQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.159 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 140.097α = 90.00
b = 140.097β = 90.00
c = 208.222γ = 120.00
Software Package:
Software NamePurpose
d*TREKdata reduction
d*TREKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-30
    Type: Initial release