1P4M

CRYSTAL STRUCTURE OF RIBOFLAVIN KINASE

Structural Biology Knowledgebase: 1P4M SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.186

Literature

Macromolecules
Sequence Display for 1P4M

Classification: TRANSFERASE

Total Structure Weight: 17680.09

Macromolecule Entities
Molecule Chains Length Organism Details
RIBOFLAVIN KINASE A 147 Homo sapiens EC#: 2.7.1.26 IUBMB
Mutation: H142Y
Gene Name(s): RFK Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ADP
Query on ADP

A ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.186
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 57.10 α = 90.00
b = 57.10 β = 90.00
c = 82.48 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-04-23
  • Released Date: 2003-05-13
  • Deposition author(s): Karthikeyan, S., Zhou, Q., Mseeh, F., Grishin, N.V., Osterman, A.L., Zhang, H.
  • Previous versions: 1NBG

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor