SMTL ID : 7od0.2 (5 other biounits)

Mirolysin in complex with compound 9

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x V7Q: 2,1,3-benzothiadiazol-4-ylmethanamine(Non-covalent)

V7Q.1: 14 residues within 4Å: Chain A: L.127, G.128, Y.162, R.166, T.167, H.170, E.171, Y.229, D.231, Y.232, T.233, D.235, M.238 Ligands: ACT.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.127, A:T.167, A:H.170 Hydrogen bonds: A:T.233

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

EDO.2: 6 residues within 4Å: Chain A: D.155, S.160, P.161, D.163, K.164, A.236 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.155, A:D.163

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 10 residues within 4Å: Chain A: G.128, Y.129, A.130, H.170, E.171, H.174, H.180, Y.232 Ligands: V7Q.1, ZN.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.171, A:Y.232 Salt bridges: A:H.170, A:H.174, A:H.180

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: H.170, H.174, H.180, Y.232 Ligands: ACT.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.170, A:H.174, A:H.180, ACT.3

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: W.182, D.185, S.188, C.189, Q.201, G.202 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:W.182, A:D.185, A:S.188, A:G.202, H2O.3 CA.6: 3 residues within 4Å: Chain A: D.193, I.195, T.198 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.193, A:I.195, A:T.198, A:T.198, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zak, K.M. et al., Latency, thermal stability, and identification of an inhibitory compound of mirolysin, a secretory protease of the human periodontopathogen Tannerella forsythia . J Enzyme Inhib Med Chem (2021)

Release Date

2021-08-04

Peptides

Mirolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BBB

Mirolysin

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