SMTL ID : 5kij.1

Crystal structure of the class I human endoplasmic reticulum 1,2-alpha-mannosidase and Man9GlcNAc2-PA complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

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

NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1: 32 residues within 4Å: Chain A: N.83, F.85, E.86, I.89, R.90, S.131, D.132, P.143, R.144, W.145, A.152, E.153, A.216, R.217, D.219, K.277, D.279, L.281, E.326, I.327, A.346, D.347, H.349, R.353, P.354, E.355, F.415, E.419, T.444, E.445 Ligands: LA.2, BU1.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.145, A:R.217, A:R.217, A:R.144, A:R.144, A:R.217 Water bridges: A:R.217, A:R.217

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

LA.2: 2 residues within 4Å: Chain A: T.444 Ligands: NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.444, H2O.3, H2O.4, H2O.5, H2O.10

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

SO4.3: 2 residues within 4Å: Chain A: H.208, L.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.208, A:L.209 SO4.4: 4 residues within 4Å: Chain A: N.331, L.332, Y.333, Q.335 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.332, A:Y.333, A:Q.335

4 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)

BU1.5: 2 residues within 4Å: Chain A: S.34, D.410 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.34 Water bridges: A:S.34, A:D.410 BU1.6: 5 residues within 4Å: Chain A: N.116, R.117, P.120, R.123, I.135 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.120 Hydrogen bonds: A:N.116, A:R.123, A:R.123, A:I.135 Water bridges: A:G.138 BU1.8: 6 residues within 4Å: Chain A: L.351, R.353 Ligands: NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.351 Hydrogen bonds: A:R.353, A:R.353 Water bridges: A:R.90 BU1.9: 2 residues within 4Å: Chain A: R.388, P.390 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.390 Hydrogen bonds: A:R.388, A:R.388 Water bridges: A:P.390

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

1PS.7: 5 residues within 4Å: Chain A: R.21, W.25, E.65, W.69, K.73 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.25 Water bridges: A:W.69 Salt bridges: A:K.73 pi-Stacking: A:W.25

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

2017-05-10

Peptides

Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase