SMTL ID : 5kkb.1 (1 other biounit)

Structure of mouse Golgi alpha-1,2-mannosidase IA and Man9GlcNAc2-PA complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

monomer

Ligands

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

NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1: 27 residues within 4Å: Chain A: H.55, S.57, S.58, L.59, F.106, I.110, R.111, W.164, W.166, A.167, I.173, A.175, E.176, G.237, L.238, D.240, L.301, N.365, Y.368, R.372, P.373, E.374, F.432, E.436, T.460, E.461 Ligands: LA.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.58, A:S.58 Water bridges: A:H.55, A:S.168

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

NAG.2: 3 residues within 4Å: Chain A: E.337, N.340, K.345 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.345 Water bridges: A:H.336, A:N.340, A:N.340

1 x LA: LANTHANUM (III) ION(Non-covalent)

LA.3: 2 residues within 4Å: Chain A: T.460 Ligands: NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.460, A:T.460, H2O.1, H2O.2, H2O.8

1 x 1PS: 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE(Non-covalent)

1PS.4: 5 residues within 4Å: Chain A: L.140, P.141, H.144, V.195, K.199 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:H.144 Salt bridges: A:K.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiang, Y. et al., Substrate recognition and catalysis by GH47 alpha-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway. Proc. Natl. Acad. Sci. U.S.A. (2016)

Release Date

2016-12-07

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mannosyl-oligosaccharide 1,2-alpha-mannosidase IA

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