SMTL ID : 5meh.1

Crystal structure of alpha-1,2-mannosidase from Caulobacter K31 strain in complex with 1-deoxymannojirimycin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.95 Å

Oligo State

monomer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: F.97, A.161, V.223, Y.224, A.225, D.226 Ligands: DMJ.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.224, A:A.225, A:D.226 Water bridges: A:D.226, A:D.226 GOL.2: 3 residues within 4Å: Chain A: D.253, L.256, A.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.253 Water bridges: A:D.253

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: T.428 Ligands: DMJ.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.428, A:T.428, H2O.1, H2O.3, H2O.7 CA.4: 1 residues within 4Å: Chain A: E.230 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.230, H2O.2, H2O.3, H2O.4, H2O.6, H2O.8

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 5 residues within 4Å: Chain A: E.61, D.64, S.403, K.407, N.431 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.61, A:S.109, A:K.407 Water bridges: A:E.61

1 x DMJ: 1-DEOXYMANNOJIRIMYCIN(Non-covalent)

DMJ.6: 12 residues within 4Å: Chain A: I.101, R.102, L.287, R.340, P.341, E.342, Y.400, E.404, T.428, E.429 Ligands: GOL.1, CA.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.340, A:E.342, A:E.404, A:E.429 Water bridges: A:R.102

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

ACT.7: 3 residues within 4Å: Chain A: A.205, Y.224, M.271 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.224 Water bridges: A:N.206, A:S.216, A:S.220, A:S.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van Rijssel, E.R. et al., Conformational Behaviour of Azasugars Based on Mannuronic Acid. Chembiochem (2017)

Release Date

2016-12-21

Peptides

Mannosyl-oligosaccharide 1,2-alpha-mannosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mannosyl-oligosaccharide 1,2-alpha-mannosidase

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