1DTH

METALLOPROTEASE

• PDB DOI: https://doi.org/10.2210/pdb1DTH/pdb

• Classification: HYDROLASE
• Organism(s): Crotalus atrox
• Mutation(s): No 


• Deposited: 1996-02-12 Released: 1997-02-12 
• Deposition Author(s): Botos, I., Scapozza, L., Zhang, D., Liotta, L.A., Meyer, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.168 
• R-Value Observed: 0.168 

Literature

Batimastat, a potent matrix mealloproteinase inhibitor, exhibits an unexpected mode of binding.

Botos, I., Scapozza, L., Zhang, D., Liotta, L.A., Meyer, E.F.

(1996) Proc Natl Acad Sci U S A 93: 2749-2754

• PubMed: 8610113 
• DOI: https://doi.org/10.1073/pnas.93.7.2749
• Primary Citation of Related Structures:  
  1DTH


• PubMed Abstract: 
  

  Matrix metalloproteinase enzymes have been implicated in degenerative processes like tumor cell invasion, metastasis, and arthritis. Specific metalloproteinase inhibitors have been used to block tumor cell proliferation. We have examined the interaction of batimastat (BB-94) with a metalloproteinase [atrolysin C (Ht-d), EC 3.4.24.42] active site at 2.0-angstroms resolution (R = 16.8%). The title structure exhibits an unexpected binding geometry, with the thiophene ring deeply inserted into the primary specificity site. This unprecedented binding geometry dramatizes the significance of the cavernous primary specificity site, pointing the way for the design of a new generation of potential antitumor drugs.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, Texas A&M University, College Station, 77843, USA.

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: 47.72 kDa 
• Atom Count: 3,250 
• Modelled Residue Count: 404 
• Deposited Residue Count: 406 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATROLYSIN C	A, B	203	Crotalus atrox	Mutation(s): 0  EC: 3.4.24.42
UniProt
Find proteins for P15167 (Crotalus atrox) Explore P15167  Go to UniProtKB:  P15167

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BAT	E [auth A], H [auth B]	4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE C23 H31 N3 O4 S2 XFILPEOLDIKJHX-QYZOEREBSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.168 
• R-Value Observed: 0.168 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.21	α = 90
b = 97.21	β = 90
c = 87.91	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-02-12 
Deposition Author(s): Botos, I., Scapozza, L., Zhang, D., Liotta, L.A., Meyer, E.F.

Revision History  

• Version 1.0: 1997-02-12
  Type: Initial release
  
• Version 1.1: 2008-03-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-10-30
  Changes: Structure summary