2VHS | pdb_00002vhs

Cathsilicatein, a chimera

• PDB DOI: https://doi.org/10.2210/pdb2VHS/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2007-11-24 Released: 2008-03-11 
• Deposition Author(s): Fairhead, M., Kowatz, T., McMahon, S.A., Carter, L.G., Oke, M., Johnson, K.A., Liu, H., Naismith, J.H., Wal, C.F.V.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.220 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure and Silica Condensing Activities of Silicatein Alpha-Cathepsin L Chimeras.

Fairhead, M., Johnson, K.A., Kowatz, T., Mcmahon, S.A., Carter, L.G., Oke, M., Liu, H., Naismith, J.H., Van Der Walle, C.F.

(2008) Chem Commun (Camb) : 1765

• PubMed: 18379686 
• DOI: https://doi.org/10.1039/b718264c
• Primary Citation Related Structures: 
  2VHS


• PubMed Abstract: 
  

  Cathepsin L mutants with the ability to condense silica from solution have been generated and a 1.5 A crystal structure of one of these chimeras allows us to rationalise the catalytic mechanism of silicic acid condensation.

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Organizational Affiliation: 
• SIPBS, University of Strathclyde, 27 Taylor Street, Glasgow, Scotland, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 95.65 kDa 
• Atom Count: 7,848 
• Modeled Residue Count: 860 
• Deposited Residue Count: 868 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATHSILICATEIN	A, B, C, D	217	Homo sapiens	Mutation(s): 11  EC: 3.4.22.15
UniProt & NIH Common Fund Data Resources
Find proteins for P07711 (Homo sapiens) Explore P07711  Go to UniProtKB:  P07711
PHAROS:  P07711 GTEx:  ENSG00000135047

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.220 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.826	α = 105.67
b = 58.102	β = 104.97
c = 70.209	γ = 105.05

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-11 
Deposition Author(s): Fairhead, M., Kowatz, T., McMahon, S.A., Carter, L.G., Oke, M., Johnson, K.A., Liu, H., Naismith, J.H., Wal, C.F.V.D.

Revision History  

• Version 1.0: 2008-03-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary