2VHS

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.220 (Depositor), 0.230 (DCC)
R-Value Work:
0.188 (Depositor), 0.200 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1039/b718264c
Primary Citation of 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.

Organizational Affiliation

SIPBS, University of Strathclyde, 27 Taylor Street, Glasgow, Scotland, UK.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07711
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D]	E [auth A] F [auth A] G [auth B] H [auth B] I [auth C] 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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.220 (Depositor), 0.230 (DCC)
R-Value Work: 0.188 (Depositor), 0.200 (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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-03-11

Deposition Author(s):

Revision History (Full details and data files)

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