SMTL ID : 7jnf.1

The structure of CBM32-1 and CBM32-2 domains from Clostridium perfringens ZmpB in complex with GalNAc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.1: 7 residues within 4Å: Chain A: Y.82, E.100, R.131, S.134, A.135, K.138, W.196 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.82, A:E.100, A:R.131, A:R.131, A:K.138 Water bridges: A:W.196 Salt bridges: A:K.138

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: K.89, D.92, N.94, T.97, A.200, E.201 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:K.89, A:D.92, A:N.94, A:A.200, A:E.201 CA.3: 6 residues within 4Å: Chain A: K.314, D.317, D.319, T.322, N.422, E.423 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:K.314, A:D.319, A:T.322, A:T.322, A:E.423

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: Y.280, Y.286, R.350 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.280, A:Y.286, A:R.350 GOL.5: 4 residues within 4Å: Chain A: T.232, L.233, L.263, T.264 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.233 Water bridges: A:T.232, A:E.234, A:T.264 GOL.6: 4 residues within 4Å: Chain A: D.155, F.157, K.186, K.188 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.155, A:K.186 Water bridges: A:F.157 GOL.7: 4 residues within 4Å: Chain A: R.291, P.293, Y.294, K.295 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.291, A:R.291, A:Y.294, A:K.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pluvinage, B. et al., Architecturally complex O -glycopeptidases are customized for mucin recognition and hydrolysis. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-02-03

Peptides

F5/8 type C domain protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F5/8 type C domain protein

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