1KYV

Lumazine Synthase from S.pombe bound to riboflavin

Structural Biology Knowledgebase: 1KYV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.180

Literature

Macromolecules
Sequence Display for 1KYV

Classification: TRANSFERASE

Total Structure Weight: 88391.37

Macromolecule Entities
Molecule Chains Length Organism Details
6,7-Dimethyl-8-ribityllumazine Synthase A, B, C, D, E 159 Schizosaccharomyces pombe EC#: 2.5.1.78 IUBMB
Gene Name(s): rib4 SPBC409.13
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D, E RIBOFLAVIN
RIBOFLAVINE; VITAMIN B2 (Synonym)
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B, C, D, E PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
RBF N/A in BindingDB
Kd: 1200 nM  BindingMOAD
Kd: 1200 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.213
  • R-Value Work: 0.180
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 111.50 α = 90.00
b = 145.52 β = 90.00
c = 128.70 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-02-06
  • Released Date: 2002-07-24
  • Deposition author(s): Gerhardt, S., Haase, I., Steinbacher, S., Kaiser, J.T., Cushman, M., Bacher, A., Huber, R., Fischer, M.

Revision History

  • 2013-01-23
    Type: Polymer description | Details: update EC number
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4