1KI0

The X-ray Structure of Human Angiostatin

• PDB DOI: https://doi.org/10.2210/pdb1KI0/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2001-12-02 Released: 2002-05-29 
• Deposition Author(s): Abad, M.C., Arni, R.K., Grella, D.K., Castellino, F.J., Tulinsky, A., Geiger, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.263 
• R-Value Work: 0.196 

Literature

The X-ray crystallographic structure of the angiogenesis inhibitor angiostatin.

Abad, M.C., Arni, R.K., Grella, D.K., Castellino, F.J., Tulinsky, A., Geiger, J.H.

(2002) J Mol Biol 318: 1009-1017

• PubMed: 12054798 
• DOI: https://doi.org/10.1016/S0022-2836(02)00211-5
• Primary Citation of Related Structures:  
  1KI0


• PubMed Abstract: 
  

  Angiogenesis inhibitors have gained much public attention recently as anti-cancer agents and several are currently in clinical trials, including angiostatin (Phase I, Thomas Jefferson University Hospital, Philadelphia, PA). We report here the bowl-shaped structure of angiostatin kringles 1-3, the first multi-kringle structure to be determined. All three kringle lysine-binding sites contain a bound bicine molecule of crystallization while the former of kringle 2 and kringle 3 are cofacial. Moreover, the separation of the kringle 2 and kringle 3 lysiner binding sites is sufficient to accommodate the alpha-helix of the 30 residue peptide VEK-30 found in the kringle 2/VEK-30 complex. Together the three kringles produce a central cavity suggestive of a unique domain where they may function in concert.

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Organizational Affiliation: 

Department of Chemistry, Michigan State University, East Lansing 48824, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.57 kDa 
• Atom Count: 2,447 
• Modelled Residue Count: 253 
• Deposited Residue Count: 253 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ANGIOSTATIN	A	253	Homo sapiens	Mutation(s): 1  EC: 3.4.21.7
UniProt & NIH Common Fund Data Resources
Find proteins for P00747 (Homo sapiens) Explore P00747  Go to UniProtKB:  P00747
PHAROS:  P00747 GTEx:  ENSG00000122194

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BCN	B [auth A], C [auth A], D [auth A]	BICINE C6 H13 N O4 FSVCELGFZIQNCK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.263 
• R-Value Work: 0.196 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.943	α = 90
b = 56.943	β = 90
c = 192.966	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-29 
Deposition Author(s): Abad, M.C., Arni, R.K., Grella, D.K., Castellino, F.J., Tulinsky, A., Geiger, J.H.

Revision History  

• Version 1.0: 2002-05-29
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-06
  Changes: Data collection, Structure summary