SMTL ID : 6zbw.1 (1 other biounit)

Structure of the D125N mutant of the catalytic domain of the Bacillus circulans alpha-1,6 Mannanase in complex with an alpha-1,6-alpha-manno-cyclophellitol trisaccharide inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.1: 11 residues within 4Å: Chain A: W.159, N.168, C.170, D.215, R.216, D.226, T.228, Y.230, N.279, L.282 Ligands: PBW.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.216, A:R.216, A:D.226

1 x PBW: (1~{S},4~{S},5~{R})-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol(Covalent)

PBW.2: 8 residues within 4Å: Chain A: W.60, F.109, D.111, N.112, W.159, C.170, D.281 Ligands: MAN-MAN.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.109, A:D.111 Hydrogen bonds: A:D.111, A:N.112, A:N.112 Water bridges: A:W.60, A:W.115, A:D.281

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

EDO.3: 2 residues within 4Å: Chain A: Q.305, Y.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.306 EDO.4: 4 residues within 4Å: Chain A: F.59, Y.100, W.104, N.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.104, A:N.107 Water bridges: A:Y.100 EDO.5: 6 residues within 4Å: Chain A: Q.177, L.180, Y.181, G.237, S.238, G.241 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.177 Water bridges: A:G.241 EDO.6: 6 residues within 4Å: Chain A: T.38, S.51, N.329, D.331, I.333, Y.347 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.329, A:N.329

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schroder, S.P. et al., Development of Non-Hydrolysable Oligosaccharide Activity-Based Inactivators for Endoglycanases: A Case Study on alpha-1,6 Mannanases. Chemistry (2021)

Release Date

2021-04-28

Peptides

Alpha-1,6-mannanase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-1,6-mannanase

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