SMTL ID : 4ayq.1

Structure of The GH47 processing alpha-1,2-mannosidase from Caulobacter strain K31 in complex with mannoimidazole

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: T.428 Ligands: MVL.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.428, A:T.428, H2O.21, H2O.28, H2O.28 CA.2: 2 residues within 4Å: Chain A: E.230, Q.297 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.230, H2O.22, H2O.22, H2O.22, H2O.22, H2O.25

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

NA.3: 6 residues within 4Å: Chain A: E.61, D.64, S.109, 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 MVL: (5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL(Non-covalent)

MVL.4: 12 residues within 4Å: Chain A: I.101, R.102, D.226, L.287, R.340, P.341, E.342, Y.400, E.404, T.428, E.429 Ligands: CA.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.340, A:E.342, A:E.404, A:E.429 Water bridges: A:R.102, A:D.226, A:D.226, A:D.226, A:D.226

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 6 residues within 4Å: Chain A: K.199, I.200, D.253, A.254, A.257 Ligands: PEG.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.257 Water bridges: A:A.254 PEG.6: 3 residues within 4Å: Chain A: D.253 Ligands: PEG.5, PEG.9 No protein-ligand interaction detected (PLIP) PEG.7: 5 residues within 4Å: Chain A: S.174, Q.175, R.180, F.183 Ligands: PEG.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.175 PEG.8: 4 residues within 4Å: Chain A: S.174, G.178, R.180 Ligands: PEG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.180 Water bridges: A:R.180 PEG.9: 5 residues within 4Å: Chain A: R.197, S.198, G.201, E.250 Ligands: PEG.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thompson, A.J. et al., The Reaction Coordinate of a Bacterial Gh47 Alpha-Mannosidase: A Combined Quantum Mechanical and Structural Approach. Angew.Chem.Int.Ed.Engl. (2012)

Release Date

2013-01-30

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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