1CXV | pdb_00001cxv

STRUCTURE OF RECOMBINANT MOUSE COLLAGENASE-3 (MMP-13)

PDB DOI: https://doi.org/10.2210/pdb1CXV/pdb

Classification: HYDROLASE
Organism(s): Mus musculus
Mutation(s): No

Deposited: 1999-08-30 Released: 2000-08-30
Deposition Author(s): Botos, I., Meyer, E., Swanson, S.M., Lemaitre, V., Eeckhout, Y., Meyer, E.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.234 (Depositor)
R-Value Work:
0.196 (Depositor)
R-Value Observed:
0.196 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of recombinant mouse collagenase-3 (MMP-13).

Botos, I., Meyer, E., Swanson, S.M., Lemaitre, V., Eeckhout, Y., Meyer, E.F.

(1999) J Mol Biology 292: 837-844

PubMed: 10525409 Search on PubMed
DOI: https://doi.org/10.1006/jmbi.1999.3068
Primary Citation Related Structures:
1CXV

PubMed Abstract:
The matrix metalloproteinases are crucial in the physiological and pathological degradation of the mammalian extracellular matrix, including breast tumours, and osteoarthritic cartilage. These enzymes are classified according to their matrix substrate specificity. Collagenase-3 (MMP-13) is a member of this family and preferentially cleaves type II collagen, cartilage, fibronectin and aggrecan. Collagenase-3 is normally expressed in hypertrophic chondrocytes, periosteal cells, and osteoblasts during bone development. The structure of the catalytic domain of recombinant mouse collagenase-3, complexed to the hydroxamate inhibitor (RS-113456), is reported at 2.0 A resolution. Molecular replacement and weak phasing information from a single derivative determined the structure. Neither molecular replacement nor derivative methods had a sufficient radius of convergence to yield a refinable structure. The structure illuminates the atomic zinc ion interactions with functional groups in the active site, emphasizing zinc ligation and the very voluminous hydrophobic P1' group for the inhibitor potency. The structure provides insight into the specificity of this enzyme, facilitating design of specific inhibitors to target various diseases.

Organizational Affiliation

Department of Biochemistry and Biophysics, Texas A&M University, TX, 77843-2128, USA.

Macromolecule Content

Total Structure Weight: 38.31 kDa
Atom Count: 2,953
Modeled Residue Count: 320
Deposited Residue Count: 328
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (COLLAGENASE-3)	A, B	164	Mus musculus	Mutation(s): 0 EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for P33435 (Mus musculus) Explore P33435 Go to UniProtKB: P33435
IMPC: MGI:1340026
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33435
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CBP Query on CBP Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B]	2-{4-[4-(4-CHLORO-PHENOXY)-BENZENESULFONYL]-TETRAHYDRO-PYRAN-4-YL}-N-HYDROXY-ACETAMIDE C₁₉ H₂₀ Cl N O₆ S QOPFTBAEAJQKSY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.234 (Depositor)
R-Value Work: 0.196 (Depositor)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.36	α = 90
b = 48.46	β = 108.15
c = 74.94	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2000-08-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-08-30
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: 2024-02-07
Changes: Data collection, Database references, Derived calculations