1EP2

CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B COMPLEXED WITH OROTATE

Structural Biology Knowledgebase: 1EP2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.190

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1EP2

Classification: OXIDOREDUCTASE

Total Structure Weight: 63110.59

Macromolecule Entities
Molecule Chains Length Organism Details
DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT) A 311 Lactococcus lactis EC#: 1.3.1.14 IUBMB
Mutation: R123A, V255D, R266A
Gene Name(s): pyrDB llmg_1106
DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT) B 261 Lactococcus lactis EC#: 1.3.98.1 IUBMB
Gene Name(s): pyrK llmg_1105

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FAD
Query on FAD

B FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
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)
FES
Query on FES

B FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ORO
Query on ORO

A OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.190
  • Space Group: H 3 2

Unit Cell:

Length (Å) Angle (°)
a = 202.42 α = 90.00
b = 202.42 β = 90.00
c = 80.88 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-03-27
  • Released Date: 2001-01-17
  • Deposition author(s): Rowland, P., Norager, S., Jensen, K.F., Larsen, S.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4