Experimental Data Snapshot

  • Resolution: 1.00 Å
  • R-Value Free: 0.178 
  • R-Value Observed: 0.148 

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Structure of the zinc-binding site in the crystal structure of a zinc endoprotease from Streptomyces caespitosus at 1 A resolution.

Kurisu, G.Kai, Y.Harada, S.

(2000) J Inorg Biochem 82: 225-228

  • DOI: https://doi.org/10.1016/s0162-0134(00)00136-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A zinc endoprotease produced by Streptomyces caespitosus (ScNP) contains a H83E84TGH87VLG90LPD93-Met103 sequence. Except for D93, this amino acid sequence is the same as a characteristic consensus HEXXHXXGXXH-M motif found in one class of zinc endoprotease called 'metzincins'. We analyzed the structural and functional role of the consensus sequence located around a catalytically essential zinc ion based on the crystal structure of ScNP. The structure was determined at the highest level on resolution (1 A resolution) and accuracy among crystal structures of zinc endoproteases ever determined. The zinc ion of ScNP is tetrahedrally coordinated by three amino acid side-chains (H83, H87 and D93) and a water molecule. The distances between the zinc ion and the coordinating atoms are 2.01, 2.01 and 1.95 A for H83N epsilon, H87N epsilon and D93O delta, respectively. These distances agree very well with those normally found in crystal structures of zinc-containing small molecules in the Cambridge Structural Database. On the other hand, the distance between the zinc ion and the coordinating water molecule (1.93 A) is slightly shorter than the typical value (2.01 A) found in the database. In addition, E84O epsilon makes a short hydrogen bond to this water molecule with the distance of 2.54 A. Two hydrogen bonds (H83N delta-L102O, H87N delta-L91O) and van der Waals interactions between the side-chain of M103 and the two imidazole rings of H83 and H87 are also observed. These interactions are probably important for the imidazole rings to construct the tetrahedral coordination arrangement toward the zinc ion.

  • Organizational Affiliation

    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ZINC ENDOPROTEASE132Streptomyces caespitosusMutation(s): 0 
EC: 3.4.24
Find proteins for P56406 (Streptomyces caespitosus)
Explore P56406 
Go to UniProtKB:  P56406
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56406
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.00 Å
  • R-Value Free: 0.178 
  • R-Value Observed: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.103α = 90
b = 55.199β = 90
c = 37.243γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-25
    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: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations