1ATL

Structural interaction of natural and synthetic inhibitors with the VENOM METALLOPROTEINASE, ATROLYSIN C (FORM-D)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structural interaction of natural and synthetic inhibitors with the venom metalloproteinase, atrolysin C (form d).

Zhang, D., Botos, I., Gomis-Ruth, F.X., Doll, R., Blood, C., Njoroge, F.G., Fox, J.W., Bode, W., Meyer, E.F.

(1994) Proc.Natl.Acad.Sci.USA 91: 8447-8451

  • DOI: 10.1073/pnas.91.18.8447
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The structure of the metalloproteinase and hemorrhagic toxin atrolysin C form d (EC 3.4.24.42), from the venom of the western diamondback rattlesnake Crotalus atrox, has been determined to atomic resolution by x-ray crystallographic methods. This stu ...

    The structure of the metalloproteinase and hemorrhagic toxin atrolysin C form d (EC 3.4.24.42), from the venom of the western diamondback rattlesnake Crotalus atrox, has been determined to atomic resolution by x-ray crystallographic methods. This study illuminates the nature of inhibitor binding with natural (< Glu-Asn-Trp, where < Glu is pyroglutamic acid) and synthetic (SCH 47890) ligands. The primary specificity pocket is exceptionally deep; the nature of inhibitor and productive substrate binding is discussed. Insights gained from the study of these complexes facilitate the design of potential drugs to treat diseases where matrix metalloproteinases have been implicated, e.g., arthritis and tumor metastasis.

    Related Citations: 
    • Structure of a Retro-Binding Peptide Inhibitor Complexed with Human Alpha-Thrombin
      Tabernero, L.,Chang, C.Y.,Ohringer, S.L.,Lau, W.F.,Iwanowicz, E.J.,Han, W.C.,Wang, T.C.,Seiler, S.M.,Roberts, D.G.,Sack, J.S.
      (1995) J.Mol.Biol. 246: 14

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATROLYSIN C
A, B
202Crotalus atroxMutation(s): 0 
EC: 3.4.24.42
Find proteins for P15167 (Crotalus atrox)
Go to UniProtKB:  P15167
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
0QI
Query on 0QI
Download SDF File 
Download CCD File 
A, B
O-methyl-N-[(2S)-4-methyl-2-(sulfanylmethyl)pentanoyl]-L-tyrosine
C17 H25 N O4 S
PRPWYZNFKBFGFI-HIFRSBDPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0QIKi: 520 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.160 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 97.320α = 90.00
b = 97.320β = 90.00
c = 87.760γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance