SMTL ID : 4jqg.1 (2 other biounits)

Crystal structure of an inactive mutant of MMP-9 catalytic domain in complex with a fluorogenic synthetic peptidic substrate with a fluorine atom.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x 8MC- PRO- LEU- GLY- PFF- DNW- ALA- ARG- NH2: fluorogenic peptidic substrate (8MC)PLG(PFF)(DNW)AR(NH2)(Non-covalent)

8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.1: 26 residues within 4Å: Chain A: Q.3, T.4, F.5, Y.74, D.77, G.81, L.82, L.83, A.84, H.85, A.86, F.87, I.93, Y.113, V.118, H.121, H.125, H.131, Y.140, P.141, M.142, Y.143 Ligands: AZI.2, ZN.3, EDO.10, EDO.11 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:Q.3, A:F.5, A:Y.74, A:Y.74, A:Y.74, A:L.82, A:L.83, A:H.85, A:F.87, A:F.87, A:Y.113, A:V.118, A:H.121, A:Y.143 Hydrogen bonds: A:Q.3, A:G.81, A:L.83, A:A.84, A:A.84, A:A.86, A:A.86, A:P.141, A:Y.143, A:Y.143 Water bridges: A:Q.3, A:F.5, A:G.81, A:Y.143 pi-Stacking: A:F.5, A:H.121

1 x AZI: AZIDE ION(Non-covalent)

AZI.2: 11 residues within 4Å: Chain A: A.84, H.85, A.86, H.121, A.122, H.125, H.131 Ligands: 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.1, 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.1, 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.1, ZN.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.84

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.121, H.125, H.131 Ligands: 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.1, AZI.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.121, A:H.125, A:H.131 ZN.4: 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

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: D.77, G.78, D.80, L.82, D.100, E.103 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.77, A:G.78, A:D.80, A:L.82, A:D.100, A:E.103 CA.7: 4 residues within 4Å: Chain A: D.26, D.101, E.103 Ligands: PGO.14 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.26, A:D.101, A:E.103, H2O.8

1 x SR: STRONTIUM ION(Non-functional Binders)

SR.6: 5 residues within 4Å: Chain A: A.59, D.60, G.92, Q.94, D.96 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.60, A:G.92, A:Q.94, A:D.96, H2O.7

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 4 residues within 4Å: Chain A: K.10, R.160, L.162, G.164 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.10 EDO.10: 6 residues within 4Å: Chain A: Y.74, L.82, H.85 Ligands: 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.1, 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.1, 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.85 EDO.11: 7 residues within 4Å: Chain A: A.137, L.138, M.142, Y.143, R.144, T.146 Ligands: 8MC-PRO-LEU-GLY-PFF-DNW-ALA-ARG-NH2.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.142, A:R.144 Water bridges: A:E.136, A:R.144 EDO.12: 5 residues within 4Å: Chain A: K.10, W.11, H.12, H.13 Ligands: EDO.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.12, A:H.12, A:H.13 EDO.13: 4 residues within 4Å: Chain A: H.13, G.90, P.91 Ligands: EDO.12 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain A: L.9, P.88, G.128, L.129, D.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.129, A:D.130 Water bridges: A:G.128

1 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.14: 5 residues within 4Å: Chain A: D.26, D.102, E.103, L.104 Ligands: CA.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.26, A:L.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tranchant, I. et al., Halogen Bonding Controls Selectivity of FRET Substrate Probes for MMP-9. Chem.Biol. (2014)

Release Date

2014-03-12

Peptides

Matrix metalloproteinase-9: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Matrix metalloproteinase-9

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