SMTL ID : 2d1n.2 (1 other biounit)

Collagenase-3 (MMP-13) complexed to a hydroxamic acid inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.119, H.123, H.129 Ligands: FA4.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.119, A:H.123, A:H.129 ZN.2: 5 residues within 4Å: Chain A: H.69, D.71, Y.73, H.84, H.97 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.69, A:D.71, A:H.84, A:H.97

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.76, G.77, S.79, L.81, D.99, E.102 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:G.77, A:S.79, A:L.81, A:D.99, A:E.102 CA.4: 6 residues within 4Å: Chain A: A.58, D.59, N.91, Y.92, G.93, D.95 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.59, A:N.91, A:G.93, A:D.95, H2O.1 CA.5: 4 residues within 4Å: Chain A: T.23, D.25, D.100, E.102 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.25, A:D.100, A:D.100, A:E.102

1 x FA4: SM-25453(Non-covalent)

FA4.6: 20 residues within 4Å: Chain A: Y.73, L.81, L.82, A.83, L.115, V.116, H.119, E.120, H.123, H.129, P.133, A.135, L.136, F.138, P.139, I.140, Y.141, T.142, F.149 Ligands: ZN.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.73, A:L.115, A:H.119, A:L.136, A:Y.141, A:F.149 Hydrogen bonds: A:L.82, A:A.83, A:A.83, A:P.133, A:I.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kohno, T. et al., Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453. Biochem.Biophys.Res.Commun. (2006)

Release Date

2006-06-27

Peptides

Collagenase 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Collagenase 3

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