SMTL ID : 5kk7.2 (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 Compare

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: 19 residues within 4Å: Chain A: F.85, E.86, 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, ACT.5 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.5, H2O.6, H2O.6

1 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

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

BU1.4: 6 residues within 4Å: Chain A: V.343, K.344, P.345, R.348, Q.401 Ligands: ACT.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.343, A:Q.401 Hydrogen bonds: A:K.344, A:R.348 Water bridges: A:E.342 BU1.7: 3 residues within 4Å: Chain A: Y.4, W.377, Q.381 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.381

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

ACT.5: 3 residues within 4Å: Chain A: R.353 Ligands: Z5L-MAN.1, Z5L-MAN.1 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.90, A:R.90, A:R.90 Salt bridges: A:R.353 ACT.6: 4 residues within 4Å: Chain A: R.338, E.342, V.343 Ligands: BU1.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.342, A:V.343 Water bridges: A:Q.401 ACT.8: 2 residues within 4Å: Chain A: P.120, R.123 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.123 Salt bridges: A:R.123

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
B

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

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