SMTL ID : 7oms.1 (1 other biounit)

Bs164 in complex with mannocyclophellitol aziridine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-trimer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: Y.258, F.259, C.413, L.416, S.417, E.420, R.575, F.580 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.258, A:E.420, A:E.420, A:R.575, A:R.575 EDO.2: 8 residues within 4Å: Chain A: E.151, H.225, N.226, S.249, H.251, W.254, H.255 Ligands: VKH.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.225, A:H.255 EDO.5: 8 residues within 4Å: Chain B: E.151, H.225, N.226, S.249, H.251, W.254, H.255 Ligands: VKH.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.225, B:H.255 EDO.6: 9 residues within 4Å: Chain B: Y.258, G.403, N.404, S.407, I.408, G.409, A.410, C.413, R.575 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.403 EDO.7: 5 residues within 4Å: Chain B: T.109, D.110, V.111, G.112 Chain C: R.398 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.111 EDO.8: 8 residues within 4Å: Chain B: Y.258, F.259, C.413, L.416, S.417, E.420, R.575, F.580 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.258, B:E.420, B:E.420, B:R.575, B:R.575 EDO.11: 6 residues within 4Å: Chain A: R.398 Chain C: T.109, D.110, V.111, G.112, G.113 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.109, C:D.110, C:V.111, C:G.112 EDO.12: 9 residues within 4Å: Chain C: G.403, N.404, G.405, A.410, C.413, H.530, L.572, R.575, E.576 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.572, C:R.575, C:E.576

3 x VKH: (1~{R},2~{R},3~{S},4~{R},5~{R},6~{R})-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3,4-triol(Covalent)

VKH.3: 16 residues within 4Å: Chain A: R.64, R.66, V.111, G.112, N.150, E.151, S.249, H.251, W.254, E.288, S.297, W.327, R.332, E.337, W.341 Ligands: EDO.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:E.288, A:W.327 Hydrogen bonds: A:R.66, A:R.66, A:V.111, A:N.150, A:E.151, A:W.254, A:R.332, A:R.332, A:E.337 Water bridges: A:E.337 VKH.9: 16 residues within 4Å: Chain B: R.64, R.66, V.111, G.112, N.150, E.151, S.249, H.251, W.254, E.288, S.297, W.327, R.332, E.337, W.341 Ligands: EDO.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:E.288 Hydrogen bonds: B:R.66, B:R.66, B:N.150, B:E.151, B:W.254, B:R.332, B:R.332, B:E.337 Water bridges: B:E.337 VKH.13: 15 residues within 4Å: Chain C: R.64, R.66, V.111, G.112, N.150, E.151, S.249, H.251, W.254, E.288, S.297, W.327, R.332, E.337, W.341 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:E.288, C:W.327 Hydrogen bonds: C:R.66, C:R.66, C:V.111, C:N.150, C:E.151, C:E.151, C:W.254, C:R.332, C:R.332, C:E.337 Water bridges: C:W.327

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

CL.4: 6 residues within 4Å: Chain A: Q.36, R.64, R.66, T.101, N.150, W.327 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain B: Q.36, R.64, R.66, T.101, N.150, W.327 Ligand excluded by PLIP CL.14: 6 residues within 4Å: Chain C: Q.36, R.64, R.66, T.101, N.150, W.327 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McGregor, N.G.S. et al., Synthesis of broad-specificity activity-based probes for exo -beta-mannosidases. Org.Biomol.Chem. (2022)

Release Date

2022-02-02

Peptides

Glyco_hydro_42M domain-containing protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
CCC

C
BBB

Glyco_hydro_42M domain-containing protein

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