SMTL ID : 6zbm.1

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 carbasugar-stabilised trisaccharide inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: E.302, T.303, G.304 No protein-ligand interaction detected (PLIP) EDO.2: 2 residues within 4Å: Chain A: Q.305, Y.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.305, A:Y.306 Water bridges: A:Y.306

1 x QE8: (1~{R},2~{R},3~{R},4~{S},5~{R})-4-[[(1~{S},2~{S},3~{S},4~{R},5~{R})-5-(hydroxymethyl)-2,3,4-tris(oxidanyl)cyclohexyl]oxymethyl]cyclohexane-1,2,3,5-tetrol(Covalent)

QE8.3: 12 residues within 4Å: Chain A: W.60, F.109, D.111, N.112, W.159, N.168, C.170, D.215, Y.230, N.279, D.281 Ligands: MAN.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.109, A:D.111 Hydrogen bonds: A:D.111, A:N.112, A:N.168, A:D.215, A:R.216, A:D.281 Water bridges: A:W.60, A:W.115, A:R.216, A:Y.230, A:Y.230, A:N.231

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

MAN.4: 6 residues within 4Å: Chain A: D.215, R.216, D.226, T.228, L.282 Ligands: QE8.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.216, A:R.216, A:D.226 Water bridges: A:N.279

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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