SMTL ID : 6z2o.1

Crystal structure of wild type OgpA from Akkermansia muciniphila in P 21 21 21

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: H.182, H.192, S.210, G.211, Y.213 Ligands: ZN.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.211 EDO.2: 5 residues within 4Å: Chain A: Y.48, Q.51, F.52, K.55 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.11 Water bridges: A:K.55 EDO.3: 7 residues within 4Å: Chain A: Y.93, G.139, G.140, V.141, F.143, L.153, W.176 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.140, A:V.141 Water bridges: A:N.133, A:N.133, A:N.133 EDO.4: 6 residues within 4Å: Chain A: Y.48, F.215, G.216, S.218, T.220 Ligands: EDO.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.48, A:Y.48, A:G.216, A:T.220 Water bridges: A:T.220 EDO.5: 4 residues within 4Å: Chain A: T.239, Q.242, K.278, A.337 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.242, A:K.278, A:K.278 EDO.6: 3 residues within 4Å: Chain A: F.346, T.347, Y.356 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.347, A:T.347 Water bridges: A:H.345, A:T.347, A:T.347 EDO.7: 4 residues within 4Å: Chain A: V.5, R.12, L.47, G.75 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.76

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain A: H.182, H.186, H.192 Ligands: EDO.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.182, A:H.186, A:H.192, H2O.1, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trastoy, B. et al., Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila. Nat Commun (2020)

Release Date

2020-09-30

Peptides

O-glycan protease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

O-glycan protease

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