SMTL ID : 7odj.1

Exo-mannosidase from Cellvibrio mixtus bound to N-alkyl mannocyclophellitol aziridine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: A.65, Y.115, E.119, K.122, R.123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.119 Salt bridges: A:K.122, A:R.123 SO4.2: 4 residues within 4Å: Chain A: N.28, G.29, G.30, H.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.30 Salt bridges: A:H.31 SO4.3: 1 residues within 4Å: Chain A: R.26 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.26, A:R.26 Salt bridges: A:R.26 SO4.5: 3 residues within 4Å: Chain A: H.23, R.26, Q.35 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.35 Water bridges: A:G.36 Salt bridges: A:R.26

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

ACT.4: 6 residues within 4Å: Chain A: W.135, Q.136, W.137, W.162, Q.403 Ligands: VEE.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.135, A:W.162 Hydrogen bonds: A:W.137, A:Q.403

1 x VEE: (1R,2S,3R,4S,5R,6R)-5-(8-azidooctylamino)-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol(Covalent)

VEE.6: 20 residues within 4Å: Chain A: R.80, W.135, W.137, W.162, M.166, N.214, E.215, R.217, E.256, H.283, W.285, N.288, W.289, E.330, W.376, P.401, Q.403, E.404, Y.409 Ligands: ACT.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.162, A:W.285, A:N.288, A:E.330 Hydrogen bonds: A:W.137, A:N.214, A:N.288, A:W.376, A:Q.403 Water bridges: A:R.287, A:E.404, A:E.404, A:E.404

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McGregor, N.G.S. et al., Synthesis of broad-specificity activity-based probes for exo -beta-mannosidases. Org.Biomol.Chem. (2022)

Release Date

2022-02-16

Peptides

Man5A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Man5A

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