SMTL ID : 7sci.1

AM0627 metallopeptidase from Akkermansia muciniphila

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.306, H.310, E.324, N.327 Ligands: FMT.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.306, A:H.310, A:E.324, A:E.324

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 6 residues within 4Å: Chain A: D.53, Y.54, A.57, Y.181, R.186, R.195 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.181, A:R.186, A:R.195 Water bridges: A:D.53, A:Y.54, A:Y.54

8 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 5 residues within 4Å: Chain A: H.306, E.307, H.310, E.324 Ligands: ZN.1 No protein-ligand interaction detected (PLIP) FMT.4: 4 residues within 4Å: Chain A: Q.347, K.352, D.369, F.371 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.352, A:K.352 FMT.5: 3 residues within 4Å: Chain A: D.291, E.293, N.294 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.293, A:N.294 FMT.6: 4 residues within 4Å: Chain A: Y.252, D.395, E.398, Y.399 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.252, A:Y.399 Water bridges: A:N.402, A:N.402 FMT.7: 5 residues within 4Å: Chain A: R.272, H.310, T.323, E.324, Y.451 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.272, A:H.310 FMT.8: 5 residues within 4Å: Chain A: N.112, H.133, K.134, K.135, T.150 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.150 FMT.9: 1 residues within 4Å: Chain A: D.351 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.351, A:E.487, A:E.487 FMT.10: 3 residues within 4Å: Chain A: K.51, Y.54, A.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.51, A:K.51 Water bridges: A:Q.199

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 3 residues within 4Å: Chain A: W.302, H.306, N.328 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shon, D.J. et al., Structure-guided mutagenesis of a mucin-selective metalloprotease from Akkermansia muciniphila alters substrate preferences. J.Biol.Chem. (2022)

Release Date

2022-04-27

Peptides

Peptidase M60 domain-containing protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peptidase M60 domain-containing protein