SMTL ID : 5m3w.1

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-1,2-dideoxymannose and alpha-1,2-mannobiose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.04 Å

Oligo State

monomer

Ligands

1 x 7D1- MAN: alpha-D-mannopyranose-(1-3)-1,5-anhydro-2-deoxy-D-arabino-hexitol(Non-covalent)

7D1-MAN.1: 15 residues within 4Å: Chain A: Y.51, W.53, H.65, H.68, W.131, H.159, E.161, Y.200, Y.257, I.299, R.300, E.338, H.340, E.341 Ligands: MAN-MAN.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.161, A:R.300, A:E.341 Water bridges: A:H.65

1 x MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.2: 13 residues within 4Å: Chain A: Y.200, D.201, Y.203, Y.257, F.258, F.263, T.264, Y.294, R.300, N.303, E.341 Ligands: 7D1-MAN.1, 7D1-MAN.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.300, A:R.300, A:N.303, A:N.303

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

ACT.3: 2 residues within 4Å: Chain A: K.212, S.219 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.219, A:S.219 Salt bridges: A:K.212 ACT.4: 7 residues within 4Å: Chain A: D.45, F.47, Y.189, K.191, L.196, S.329, A.330 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.330 Hydrogen bonds: A:D.45, A:D.45, A:Y.189 Salt bridges: A:K.191

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

EDO.5: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petricevic, M. et al., Contribution of Shape and Charge to the Inhibition of a Family GH99 endo-alpha-1,2-Mannanase. J. Am. Chem. Soc. (2017)

Release Date

2017-01-11

Peptides

Glycosyl hydrolase family 71: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycosyl hydrolase family 71

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