SMTL ID : 3czn.1

Golgi alpha-mannosidase II (D204A nucleophile mutant) in complex with GnMan5Gn

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x NDG- BMA- MAN- NAG- MAN- MAN- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose(Post Translational Modification)

NDG-BMA-MAN-NAG-MAN-MAN-MAN.1: 26 residues within 4Å: Chain A: K.63, Q.64, H.90, D.92, W.95, F.206, R.228, Y.267, Y.269, H.273, P.279, R.289, L.295, P.298, W.299, D.340, D.341, R.343, R.410, W.415, H.471, D.472, Y.727, E.875, R.876 Ligands: ZN.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.267, A:D.92, A:R.228, A:Y.269, A:Y.269, A:D.472, A:Y.727, A:H.273 Water bridges: A:Y.267, A:R.228, A:R.228, A:K.63, A:K.63, A:Q.64, A:Y.267 Hydrophobic interactions: A:P.298, A:W.299

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 1 residues within 4Å: Chain A: N.194 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.90, D.92, H.471, D.472 Ligands: NDG-BMA-MAN-NAG-MAN-MAN-MAN.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.90, A:D.92, A:H.471

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shah, N. et al., Golgi alpha-mannosidase II cleaves two sugars sequentially in the same catalytic site. Proc.Natl.Acad.Sci.Usa (2008)

Release Date

2008-06-24

Peptides

Alpha-mannosidase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-mannosidase 2

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