SMTL ID : 6hv2.1

MMP-13 in complex with the peptide IMISF

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

monomer

Ligands

1 x ILE- MET- ILE- SER- PHE: Collagenase 3(Non-covalent)

ILE-MET-ILE-SER-PHE.1: 18 residues within 4Å: Chain A: S.80, G.81, L.82, L.83, A.84, H.85, Y.112, V.117, H.120, E.121, H.124, H.130, F.139, P.140, I.141, Y.142 Ligands: ZN.2, GOL.7 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.85 Hydrogen bonds: A:G.81, A:G.81, A:L.83, A:A.84, A:A.84, A:Y.112, A:H.130, A:P.140, A:Y.142

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.120, H.124, H.130 Ligands: ILE-MET-ILE-SER-PHE.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.120, A:H.124, A:H.130 ZN.3: 4 residues within 4Å: Chain A: H.70, D.72, H.85, H.98 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.70, A:D.72, A:H.85, A:H.98

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: D.77, G.78, S.80, L.82, D.100, E.103 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.77, A:G.78, A:S.80, A:L.82, A:D.100, A:E.103 CA.5: 5 residues within 4Å: Chain A: D.60, N.92, Y.93, G.94, D.96 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.60, A:N.92, A:G.94, A:D.96, H2O.1, H2O.2 CA.6: 4 residues within 4Å: Chain A: T.24, D.26, D.101, E.103 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.26, A:D.26, A:D.101, A:E.103

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: A.86, H.124, H.130 Ligands: ILE-MET-ILE-SER-PHE.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.86, A:A.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gall, F.M. et al., Drug Design Inspired by Nature: Crystallographic Detection of an Auto-Tailored Protease Inhibitor Template. Angew.Chem.Int.Ed.Engl. (2019)

Release Date

2019-01-30

Peptides

Collagenase 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Collagenase 3