SMTL ID : 6zj6.1

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with cyclohexylmethyl-Glc-1,3-isofagomine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.09 Å

Oligo State

monomer

Ligands

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 7 residues within 4Å: Chain A: F.258, A.259, A.260, F.263, Y.294, V.306 Ligands: EDO.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.259, A:A.260 Water bridges: A:Y.294, A:Y.294 EDO.2: 6 residues within 4Å: Chain A: F.263, Y.294, D.296, R.300, N.303 Ligands: EDO.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.303, A:N.303 Water bridges: A:R.300 EDO.3: 8 residues within 4Å: Chain A: V.156, C.157, F.158, F.188, Y.189, P.195, L.196, F.197 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.158, A:Y.189, A:Y.189, A:L.196 EDO.4: 4 residues within 4Å: Chain A: Y.200, D.201, Y.203, F.258 No protein-ligand interaction detected (PLIP)

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

ACT.5: 7 residues within 4Å: Chain A: Y.44, D.45, F.47, Y.189, K.191, L.196, A.330 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.47, A:L.196 Hydrogen bonds: A:D.45, A:Y.189 Salt bridges: A:K.191

1 x QTE: methylcyclohexane(Non-functional Binders)

QTE.6: 1 residues within 4Å: Ligands: GLC.8 No protein-ligand interaction detected (PLIP)

1 x IFM: 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE(Non-covalent)

IFM.7: 9 residues within 4Å: Chain A: Y.51, W.131, H.159, E.161, Y.200, Y.257, E.338, E.341 Ligands: GLC.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.200 Water bridges: A:R.300, A:E.341, A:E.341, A:E.341, A:E.341, A:E.341

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.8: 10 residues within 4Å: Chain A: H.65, H.68, W.131, I.299, R.300, E.338, H.340, E.341 Ligands: QTE.6, IFM.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.300 Water bridges: A:R.300

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sobala, L.F. et al., Structure of human endo-alpha-1,2-mannosidase (MANEA), an antiviral host-glycosylation target. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-11-18

Peptides

Glycosyl hydrolase family 71: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Glycosyl hydrolase family 71

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