SMTL ID : 7jrl.1

The structure of CBM51-2 in complex with GlcNAc and INT domains from Clostridium perfringens ZmpB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: S.185, V.228, D.230, G.232, D.236 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.185, A:S.185, A:V.228, A:D.236, H2O.10

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.2: 5 residues within 4Å: Chain A: S.120, H.153, N.234, W.235, H.237 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.120, A:S.120, A:W.235, A:H.237

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

EDO.3: 7 residues within 4Å: Chain A: D.169, T.170, W.171, R.211, D.242, K.244 Ligands: PO4.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.211, A:R.211, A:D.242, A:D.242 EDO.4: 2 residues within 4Å: Chain A: N.231, N.234 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.231, A:N.234 EDO.5: 3 residues within 4Å: Chain A: N.35, R.97, T.98 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.35, A:T.98 Water bridges: A:S.96, A:R.97 EDO.6: 2 residues within 4Å: Chain A: K.114, S.115 No protein-ligand interaction detected (PLIP)

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 8 residues within 4Å: Chain A: A.37, Y.38, S.39, E.42, R.211, K.244, R.246 Ligands: EDO.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.39 Water bridges: A:S.39, A:S.39, A:R.211, A:K.244, A:K.244 Salt bridges: A:R.211, A:K.244, A:R.246

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.8: 5 residues within 4Å: Chain A: S.109, D.110, K.125, D.126, K.148 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.109, A:K.125, A:D.126, A:D.126 Water bridges: A:K.148, A:K.148, A:K.148

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