3RND

W116I-OYE1 complexed with 2-(Hydroxymethyl)-cyclopent-2-enone

Structural Biology Knowledgebase: 3RND SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.168
  • R-Value Work: 0.150

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3RND

Classification: OXIDOREDUCTASE

Total Structure Weight: 45484.98

Macromolecule Entities
Molecule Chains Length Organism Details
NADPH dehydrogenase 1 A 399 Saccharomyces pastorianus EC#: 1.6.99.1 IUBMB
Mutation: W116I
Gene Name(s): OYE1

Small Molecules
Ligands 3 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
3RN
Query on 3RN

A 2-(hydroxymethyl)cyclopent-2-en-1-one
C6 H8 O2
DQTFESRTIZHRRO-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.168
  • R-Value Work: 0.150
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 141.18 α = 90.00
b = 141.18 β = 90.00
c = 42.79 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-04-22
  • Released Date: 2011-08-03
  • Deposition author(s): Pompeu, Y.A., Stewart, J.D.

Revision History

  • 2011-11-16
    Type: Atom occupancy | Details: Atom occupancy
  • 2011-08-17
    Type: Biological assembly | Details: --