1VYR

Structure of pentaerythritol tetranitrate reductase complexed with picric acid

Structural Biology Knowledgebase: 1VYR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.9 Å
  • R-Value Observed: 0.100

Literature

Macromolecules
Sequence Display for 1VYR

Classification: OXIDOREDUCTASE

Total Structure Weight: 40089.86

Macromolecule Entities
Molecule Chains Length Organism Details
PENTAERYTHRITOL TETRANITRATE REDUCTASE A 364 Enterobacter cloacae Fragment: RESIDUES 2-365
Details: 2,4,6 TRINITROPHENOL IS BOUND IN THE ACTIVE SITE
Gene Name(s): onr
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE (Synonym)
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TNF
Query on TNF

A PICRIC ACID
2,4,6-TRINITROPHENOL (Synonym)
C6 H3 N3 O7
OXNIZHLAWKMVMX-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
TNF N/A in BindingDB
Kd: 5400 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.9 Å
  • R-Value Observed: 0.100
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 56.98 α = 90.00
b = 69.06 β = 90.00
c = 89.12 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-05-05
  • Released Date: 2004-06-10
  • Deposition author(s): Barna, T., Moody, P.C.E.

Revision History

  • 2014-08-13
    Type: Atom nomenclature | Details: ATOM, HETATM
  • 2014-08-13
    Type: Linkage | Details: CONECT
  • 2014-08-13
    Type: Function and keywords | Details: KEYWDS
  • 2014-08-13
    Type: Citation | Details: JRNL, REMARK 1
  • 2014-08-13
    Type: Other | Details: ANISOU, REMARK 100, TER, MASTER
  • 2013-04-17
    Type: Linkage | Details: CONECT,LINK
  • 2013-04-17
    Type: Non-polymer description | Details: FORMUL
  • 2013-04-17
    Type: Entry title | Details: TITLE
  • 2013-04-17
    Type: Sequence database correspondence | Details: DBREF
  • 2013-04-17
    Type: Polymer description | Details: COMPND
  • 2013-04-17
    Type: Geometry validation | Details: REMARK 500
  • 2013-04-17
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2013-04-17
    Type: Atom nomenclature | Details: HETATM
  • 2013-04-17
    Type: Binding sites and description | Details: SITE
  • 2013-04-17
    Type: Other | Details: REMARK 525,REMARK 280,REMARK 900
  • 2013-04-17
    Type: Version format compliance | Details: REMARK 4