SMTL ID : 6t6g.2 (1 other biounit)

Bacteroides salyersiae GH164 beta-mannosidase in complex with noeuromycin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-trimer

Ligands

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

EDO.1: 9 residues within 4Å: Chain A: E.151, H.225, N.226, S.249, H.251, W.254, H.255, E.288 Ligands: MNM.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.225, A:H.255 EDO.4: 8 residues within 4Å: Chain B: E.151, H.225, N.226, S.249, H.251, W.254, H.255 Ligands: MNM.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.151, B:H.225, B:H.255 EDO.7: 8 residues within 4Å: Chain C: E.151, H.225, N.226, S.249, H.251, W.254, H.255 Ligands: MNM.8 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.151, C:H.225, C:H.255

3 x MNM: (2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-HYDROXYMETHYL-PIPERIDINE(Non-covalent)

MNM.2: 15 residues within 4Å: Chain A: R.64, R.66, V.111, G.112, N.150, E.151, H.251, W.254, E.288, S.297, W.327, R.332, E.337, W.341 Ligands: EDO.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.327 Hydrogen bonds: A:R.66, A:R.66, A:V.111, A:N.150, A:E.151, A:H.251, A:W.254, A:R.332, A:R.332, A:E.337 Water bridges: A:E.337, A:E.337 MNM.5: 14 residues within 4Å: Chain B: R.64, R.66, V.111, G.112, N.150, E.151, H.251, W.254, E.288, W.327, R.332, E.337, W.341 Ligands: EDO.4 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:W.327 Hydrogen bonds: B:R.66, B:R.66, B:V.111, B:N.150, B:E.151, B:H.251, B:W.254, B:R.332, B:R.332, B:E.337 Water bridges: B:E.337, B:E.337 MNM.8: 14 residues within 4Å: Chain C: R.64, R.66, V.111, G.112, N.150, E.151, H.251, W.254, E.288, W.327, R.332, E.337, W.341 Ligands: EDO.7 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.327 Hydrogen bonds: C:R.66, C:R.66, C:V.111, C:N.150, C:E.151, C:H.251, C:W.254, C:R.332, C:R.332, C:E.337 Water bridges: C:W.327, C:E.337

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: Q.36, R.64, R.66, T.101, W.327 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain B: Q.36, R.64, R.66, T.101, W.327 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain C: Q.36, R.64, R.66, T.101, W.327 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Armstrong, Z. et al., Structure and function ofBs164 beta-mannosidase fromBacteroides salyersiaethe founding member of glycoside hydrolase family GH164. J.Biol.Chem. (2020)

Release Date

2020-01-01

Peptides

Glyco_hydro_42M domain-containing protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
DDD

B
FFF

C
EEE

Glyco_hydro_42M domain-containing protein

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