Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.22 kDa 
• Atom Count: 1350 
• Residue Count: 147 
• Unique protein chains: 1

1NB0

Crystal Structure of Human Riboflavin Kinase

• DOI: 10.2210/pdb1NB0/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-12-01 Released: 2003-03-11 
• Deposition Author(s): Karthikeyan, S., Zhou, Q., Mseeh, F., Grishin, N.V., Osterman, A.L., Zhang, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.221 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

Crystal Structure of Human Riboflavin Kinase Reveals a Beta Barrel Fold and a Novel Active Site Arch

Karthikeyan, S., Zhou, Q., Mseeh, F., Grishin, N.V., Osterman, A.L., Zhang, H.

(2003) Structure 11: 265-273

• PubMed: 12623014 
• DOI: 10.1016/s0969-2126(03)00024-8
• Primary Citation of Related Structures:  
  1NB9, 1NB0, 1P4M


• PubMed Abstract: 
  

Riboflavin kinase (RFK) is an essential enzyme catalyzing the phosphorylation of riboflavin (vitamin B(2)) to form FMN, an obligatory step in vitamin B(2) utilization and flavin cofactor synthesis. The structure of human RFK revealed a six-stranded antiparallel beta barrel core structurally similar to the riboflavin synthase/ferredoxin reductase FAD binding domain fold. The binding site of an intrinsically bound MgADP defines a novel nucleotide binding motif that encompasses a loop, a 3(10) helix, and a reverse turn followed by a short beta strand. This active site loop forms an arch with ATP and riboflavin binding at the opposite side and the phosphoryl transfer appears to occur through the hole underneath the arch. The invariant residues Asn36 and Glu86 are implicated in the catalysis.

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Organizational Affiliation: 

Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein FLJ11149	A	147	Homo sapiens	Mutation(s): 0  Gene Names: FLJ11149, RFK EC: 2.7.1.26
Find proteins for Q969G6 (Homo sapiens) Explore Q969G6  Go to UniProtKB:  Q969G6
NIH Common Fund Data Resources
PHAROS  Q969G6 GTEx  ENSG00000135002

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	A	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.221 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.096	α = 90
b = 57.096	β = 90
c = 82.505	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-12-01 
• Released Date: 2003-03-11 
Deposition Author(s): Karthikeyan, S., Zhou, Q., Mseeh, F., Grishin, N.V., Osterman, A.L., Zhang, H.

Revision History 

• Version 1.0: 2003-03-11
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance