1ATL

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

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This is version 1.3 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 U S A 91: 8447-8451

  • DOI: 10.1073/pnas.91.18.8447
  • Primary Citation of Related Structures:  
    1ATL, 1HTD

  • 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 study illuminates the nature of inhibitor binding with natural (< Glu-Asn-Trp, where < Glu is pyroglutamic acid) and synthetic (SCH 47890) ligands ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Snake venom metalloproteinase atrolysin-DA, B202Crotalus atroxMutation(s): 0 
EC: 3.4.24.42
UniProt
Find proteins for P15167 (Crotalus atrox)
Explore P15167 
Go to UniProtKB:  P15167
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15167
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0QI
Query on 0QI
Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]		O-methyl-N-[(2S)-4-methyl-2-(sulfanylmethyl)pentanoyl]-L-tyrosine
C17 H25 N O4 S
PRPWYZNFKBFGFI-HIFRSBDPSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
0QI Binding MOAD:  1ATL Ki: 520 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.32α = 90
b = 97.32β = 90
c = 87.76γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2020-06-24
    Changes: Advisory, Database references, Derived calculations, Other, Source and taxonomy, Structure summary