1WNI

Crystal Structure of H2-Proteinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of H2-proteinase from the venom of Trimeresurus flavoviridis.

Kumasaka, T.Yamamoto, M.Moriyama, H.Tanaka, N.Sato, M.Katsube, Y.Yamakawa, Y.Omori-Satoh, T.Iwanaga, S.Ueki, T.

(1996) J Biochem 119: 49-57

  • DOI: 10.1093/oxfordjournals.jbchem.a021215
  • Primary Citation of Related Structures:  
    1WNI

  • PubMed Abstract: 
  • The crystal structure of the zinc-protease, H2-proteinase, isolated from the venom of Trimeresurus flavoviridis has been determined. The crystallographic R factor is 0.176 for 10,635 reflections with Fobs > 2sigma(Fobs) in the 8.0 to 2.2 Angstrom resolution range ...

    The crystal structure of the zinc-protease, H2-proteinase, isolated from the venom of Trimeresurus flavoviridis has been determined. The crystallographic R factor is 0.176 for 10,635 reflections with Fobs > 2sigma(Fobs) in the 8.0 to 2.2 Angstrom resolution range. The enzyme has two domains with a cleft in which a catalytic zinc atom is located. The N-terminal domain is composed of four helices around a central five-stranded beta-sheet. The irregularly folded C-terminal domain contains one helix and two disulfide bridges. These two domains are linked by a disulfide bridge. In the zinc environment, the catalytic zinc atom forms a distorted tetrahedral coordination with three histidines and one catalytic water molecule, and the methionine-containing turn is structurally conserved. These are distinctive features of the metzincins, one of the zinc metalloprotease superfamilies. The entire structure shows good agreement with that of two Crotalus snake venom proteases, adamalysin II and atrolysin C. The H2-proteinase, however, contains no structural calcium ions, and differences of disulfide configurations and the coordination of the catalytic water molecule exist as compared with the other two proteases.


    Related Citations: 
    • Crystallization and preliminary X-ray study of H2-proteinase from the venom of Trimeresurus flavoviridis
      Kumasaka, T., Takeya, H., Yamamoto, M., Yamakawa, Y., Omori-Satoh, T., Moriyama, H., Tanaka, N., Sato, M., Katsube, Y., Iwanaga, S.
      (1995) J Biochem 117: 929

    Organizational Affiliation

    Department of Life Science, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Trimerelysin IIA201Protobothrops flavoviridisMutation(s): 0 
EC: 3.4.24.53
UniProt
Find proteins for P20165 (Protobothrops flavoviridis)
Explore P20165 
Go to UniProtKB:  P20165
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.176 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.8α = 90
b = 77.8β = 90
c = 82.3γ = 90
Software Package:
Software NamePurpose
WEISdata reduction
MLPHAREphasing
X-PLORrefinement
WEISdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-10-09
    Changes: Data collection, Database references