SMTL ID : 5kk7.1 (1 other biounit)

Crystal structure of the class I human endoplasmic reticulum 1,2-alpha-mannosidase T688A mutant and Thio-disaccharide substrate analog complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

1 x Z5L- MAN: alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside(Non-covalent)

Z5L-MAN.1: 18 residues within 4Å: Chain A: F.85, I.89, R.90, A.152, E.153, A.216, R.217, D.219, L.281, R.353, P.354, E.355, F.415, E.419, A.444, E.445 Ligands: CA.2, BU1.6 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.353, A:E.355, A:A.444, A:E.445, A:E.153, A:E.153, A:R.217, A:D.219 Water bridges: A:R.90, A:N.83, A:E.86, A:E.86, A:D.219, A:D.219, A:E.355

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: A.444 Ligands: Z5L-MAN.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:A.444, H2O.3, H2O.4, H2O.6, H2O.6

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

SO4.3: 3 residues within 4Å: Chain A: T.207, H.208, L.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.208, A:L.209 SO4.4: 3 residues within 4Å: Chain A: Y.99, H.100, G.103 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.99, A:G.103 Salt bridges: A:H.100

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

1PS.5: 5 residues within 4Å: Chain A: R.21, W.25, E.65, W.69, K.73 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.21, A:W.25 Hydrogen bonds: A:W.25, A:W.25 Water bridges: A:W.69, A:W.69 1PS.10: 2 residues within 4Å: Chain A: D.11, R.388 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.11

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

BU1.6: 5 residues within 4Å: Chain A: L.351, R.353, E.413 Ligands: Z5L-MAN.1, Z5L-MAN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.353, A:R.353 BU1.7: 1 residues within 4Å: Chain A: V.139 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.139

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

ACT.8: 4 residues within 4Å: Chain A: E.29, W.40, K.411, E.413 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.40 Water bridges: A:R.90, A:K.411 Salt bridges: A:K.411 ACT.9: 2 residues within 4Å: Chain A: R.388, P.390 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.388, A:R.388, A:R.388 Salt bridges: A:R.388

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

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