3DRB | pdb_00003drb

Crystal structure of Human Brain-type Creatine Kinase

• PDB DOI: https://doi.org/10.2210/pdb3DRB/pdb

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


• Deposited: 2008-07-11 Released: 2009-03-17 
• Deposition Author(s): Moon, J.H., Bong, S.M., Hwang, K.Y., Chi, Y.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.227 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

Structural studies of human brain-type creatine kinase complexed with the ADP-Mg2+-NO3- -creatine transition-state analogue complex

Bong, S.M., Moon, J.H., Nam, K.H., Lee, K.S., Chi, Y.M., Hwang, K.Y.

(2008) FEBS Lett 582: 3959-3965

• PubMed: 18977227 
• DOI: https://doi.org/10.1016/j.febslet.2008.10.039
• Primary Citation Related Structures: 
  3B6R, 3DRB, 3DRE


• PubMed Abstract: 
  

  Creatine kinase is a member of the phosphagen kinase family, which catalyzes the reversible phosphoryl transfer reaction that occurs between ATP and creatine to produce ADP and phosphocreatine. Here, three structural aspects of human-brain-type-creatine-kinase (hBB-CK) were identified by X-ray crystallography: the ligand-free-form at 2.2A; the ADP-Mg2+, nitrate, and creatine complex (transition-state-analogue complex; TSAC); and the ADP-Mg2+-complex at 2.0A. The structures of ligand-bound hBB-CK revealed two different monomeric states in a single homodimer. One monomer is a closed form, either bound to TSAC or the ADP-Mg2+-complex, and the second monomer is an unliganded open form. These structural studies provide a detailed mechanism indicating that the binding of ADP-Mg2+ alone may trigger conformational changes in hBB-CK that were not observed with muscle-type-CK.

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Organizational Affiliation: 
• Division of Biotechnology, College of Life Sciences, Korea University, Seoul 136-713, Republic of Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 85.85 kDa 
• Atom Count: 6,478 
• Modeled Residue Count: 752 
• Deposited Residue Count: 762 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Creatine kinase B-type	A, B	381	Homo sapiens	Mutation(s): 0  EC: 2.7.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P12277 (Homo sapiens) Explore P12277  Go to UniProtKB:  P12277
PHAROS:  P12277 GTEx:  ENSG00000166165

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.227 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.72	α = 90
b = 97.72	β = 90
c = 166.91	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-17 
Deposition Author(s): Moon, J.H., Bong, S.M., Hwang, K.Y., Chi, Y.M.

Revision History  

• Version 1.0: 2009-03-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations