1Q3A

Crystal structure of the catalytic domain of human matrix metalloproteinase 10

PDB DOI: https://doi.org/10.2210/pdb1Q3A/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2003-07-29 Released: 2004-04-06
Deposition Author(s): Calderone, V., Bertini, I., Fragai, M., Luchinat, C., Mangani, S., Terni, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.298
R-Value Work: 0.276
R-Value Observed: 0.278

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of the catalytic domain of human matrix metalloproteinase 10.

Bertini, I., Calderone, V., Fragai, M., Luchinat, C., Mangani, S., Terni, B.

(2004) J Mol Biol 336: 707-716

PubMed: 15095982 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2003.12.033
Primary Citation of Related Structures:
1Q3A

PubMed Abstract:
The catalytic domain of matrix metalloproteinase-10 (MMP-10) has been expressed in Escherichia coli and its crystal structure solved at 2.1 A resolution. The availability of this structure allowed us to critically examine the small differences existing between the catalytic domains of MMP-3 and MMP-10, which show the highest sequence identity among all MMPs. Furthermore, the binding mode of N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid (NNGH), which is one of the most known commercial inhibitors of MMPs, is described for the first time.

Organizational Affiliation

CERM, University of Florence and FiorGen Foundation, Via Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy. bertini@cerm.unifi.it

Macromolecule Content

Total Structure Weight: 57.31 kDa
Atom Count: 4,175
Modelled Residue Count: 471
Deposited Residue Count: 495
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stromelysin-2	A, B, C	165	Homo sapiens	Mutation(s): 1 Gene Names: MMP10 OR STMY2 EC: 3.4.24.22
UniProt & NIH Common Fund Data Resources
Find proteins for P09238 (Homo sapiens) Explore P09238 Go to UniProtKB: P09238
PHAROS: P09238 GTEx: ENSG00000166670
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09238
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NGH Query on NGH Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain U [auth C] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain U [auth C]	I [auth A], O [auth B], U [auth C]	N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID C₁₃ H₂₀ N₂ O₅ S JIRXORZYIXSWOB-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C] Interactions & Density Focus chain I [auth A] Focus chain O [auth B] Focus chain U [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain J [auth B]	D [auth A] E [auth A] J [auth B] K [auth B] P [auth C] D [auth A], E [auth A], J [auth B], K [auth B], P [auth C], Q [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain P [auth C] Focus chain Q [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C]	F [auth A] G [auth A] H [auth A] L [auth B] M [auth B] F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], R [auth C], S [auth C], T [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C]