1HAK

CRYSTAL STRUCTURE OF RECOMBINANT HUMAN PLACENTAL ANNEXIN V COMPLEXED WITH K-201 AS A CALCIUM CHANNEL ACTIVITY INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb1HAK/pdb

• Classification: CALCIUM/PHOSPHOLIPID-BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-12-10 Released: 1999-02-16 
• Deposition Author(s): Ago, H., Inagaki, E., Miyano, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.331 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 

Starting Model: experimental

Literature

Crystal structure of annexin V with its ligand K-201 as a calcium channel activity inhibitor.

Kaneko, N., Ago, H., Matsuda, R., Inagaki, E., Miyano, M.

(1997) J Mol Biol 274: 16-20

• PubMed: 9398511 
• DOI: https://doi.org/10.1006/jmbi.1997.1375
• Primary Citation of Related Structures:  
  1HAK


• PubMed Abstract: 
  

  The crystal structure of recombinant human annexin V complexed with K-201, an inhibitor of the calcium ion channel activity of annexin V, was solved at 3.0 A by molecular replacement including the apo and high-calcium forms. K-201 was bound at the hinge region cavity formed by the N-terminal strand and domains II, III and IV, at the side opposite the calcium and membrane-binding surface, in an L-shaped conformation. Based on the complex and other annexin structures, K-201 is proposed to restrain the hinge movement of annexin V in an allosteric manner, resulting in the inhibition of calcium movement across the annexin V molecule.

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Organizational Affiliation: 

Department of Cardiology, Tokyo Women's Medical College, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 72.81 kDa 
• Atom Count: 5,195 
• Modelled Residue Count: 636 
• Deposited Residue Count: 640 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ANNEXIN V	A [auth B], B [auth A]	320	Homo sapiens	Mutation(s): 0  Gene Names: CDNA
UniProt & NIH Common Fund Data Resources
Find proteins for P08758 (Homo sapiens) Explore P08758  Go to UniProtKB:  P08758
PHAROS:  P08758 GTEx:  ENSG00000164111

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K21	C [auth B], D [auth A]	4-[3-{1-(4-BENZYL)PIPERODINYL}PROPIONYL]-7-METHOXY-2,3,4,5-TERTRAHYDRO-1,4-BENZOTHIAZEPINE C25 H32 N2 O2 S KCWGETCFOVJEPI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.331 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.3	α = 90
b = 99.3	β = 90
c = 130.5	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-02-16 
Deposition Author(s): Ago, H., Inagaki, E., Miyano, M.

Revision History  

• Version 1.0: 1999-02-16
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Database references, Derived calculations, Refinement description
• Version 1.4: 2024-05-22
  Changes: Data collection