SMTL ID : 7omi.2 (1 other biounit)

Bs164 in complex with mannocyclophellitol epoxide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-trimer

Ligands

13 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.420, A:R.575, A:R.575 Water bridges: A:Y.258 EDO.4: 8 residues within 4Å: Chain A: V.111, G.112, E.151, W.254, E.337 Ligands: EDO.5, TLA.6, VKN.7 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.112, A:E.151, A:E.337 EDO.5: 9 residues within 4Å: Chain A: E.151, H.225, N.226, S.249, H.251, W.254, H.255 Ligands: EDO.4, VKN.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.225, A:H.255 Water bridges: A:N.226 EDO.8: 5 residues within 4Å: Chain A: P.41, K.70, Y.71 Chain B: Y.180, G.184 No protein-ligand interaction detected (PLIP) EDO.9: 8 residues within 4Å: Chain B: Y.258, F.259, C.413, L.416, S.417, E.420, R.575, F.580 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.420, B:E.420, B:R.575, B:R.575 Water bridges: B:Y.258, B:Y.258 EDO.10: 6 residues within 4Å: Chain B: E.273, R.276, S.277, N.378, N.430, K.432 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.432 Water bridges: B:R.276, B:N.430 EDO.12: 9 residues within 4Å: Chain B: E.151, H.225, N.226, S.249, H.251, W.254, H.255 Ligands: EDO.14, VKN.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.225, B:H.255 EDO.14: 9 residues within 4Å: Chain B: V.111, G.112, K.115, E.151, W.254, E.337 Ligands: EDO.12, TLA.15, VKN.17 3 PLIP interactions: 3 interactions with chain B Water bridges: B:G.112, B:G.112, B:E.151 EDO.16: 6 residues within 4Å: Chain B: R.167, W.171, F.195, D.198, Y.199, W.202 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.167 EDO.18: 8 residues within 4Å: Chain C: Y.258, F.259, C.413, L.416, S.417, E.420, R.575, F.580 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.417, C:E.420, C:R.575, C:R.575 EDO.19: 10 residues within 4Å: Chain C: P.600, M.620, I.636, V.637, G.638, G.639, K.640, G.641, N.657, W.671 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.636, C:N.657 EDO.22: 8 residues within 4Å: Chain C: V.111, G.112, E.151, W.254, E.337 Ligands: TLA.23, EDO.24, VKN.25 2 PLIP interactions: 2 interactions with chain C Water bridges: C:E.151, C:E.337 EDO.24: 9 residues within 4Å: Chain C: E.151, H.225, N.226, S.249, H.251, W.254, H.255 Ligands: EDO.22, VKN.25 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.151, C:H.225, C:H.255

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

CL.2: 6 residues within 4Å: Chain A: Q.36, R.64, R.66, T.101, N.150, W.327 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain B: Q.36, R.64, R.66, T.101, N.150, W.327 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain C: Q.36, R.64, R.66, T.101, N.150, W.327 Ligand excluded by PLIP

6 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.3: 5 residues within 4Å: Chain A: T.365, E.366, N.367, V.368, K.369 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.365, A:E.366, A:E.366, A:V.368, A:K.369 Water bridges: A:M.370 TLA.6: 7 residues within 4Å: Chain A: T.109, D.110, V.111, G.112, G.113 Chain B: R.398 Ligands: EDO.4 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.109, A:T.109, A:D.110, A:D.110, A:V.111, A:G.112, B:R.398 Salt bridges: B:R.398 TLA.13: 6 residues within 4Å: Chain B: T.365, E.366, N.367, V.368, K.369, M.370 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.366, B:E.366, B:V.368, B:K.369 Water bridges: B:M.370 TLA.15: 7 residues within 4Å: Chain B: T.109, D.110, V.111, G.112, G.113 Chain C: R.398 Ligands: EDO.14 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:T.109, B:D.110, B:D.110, B:V.111, B:G.112 Water bridges: C:R.398, C:R.398 Salt bridges: C:R.398 TLA.21: 6 residues within 4Å: Chain C: T.365, E.366, N.367, V.368, K.369, M.370 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.365, C:E.366, C:E.366, C:V.368, C:K.369 Water bridges: C:M.370 TLA.23: 7 residues within 4Å: Chain A: R.398 Chain C: T.109, D.110, V.111, G.112, G.113 Ligands: EDO.22 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:T.109, C:D.110, C:V.111, C:G.112, A:R.398 Water bridges: A:R.398

3 x VKN: (1R,2S,4S,5R)-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol(Post Translational Modification)

VKN.7: 17 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.4, EDO.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:E.288, A:W.327 Hydrogen bonds: A:R.66, A:R.66, A:N.150, A:W.254, A:R.332, A:R.332, A:E.337 Water bridges: A:E.337, A:E.337 VKN.17: 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, W.327, R.332, E.337, W.341 Ligands: EDO.12, EDO.14 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:W.254, B:R.332, B:R.332, B:E.337 Water bridges: B:E.337, B:E.337 VKN.25: 16 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, W.327, R.332, E.337, W.341 Ligands: EDO.22, EDO.24 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:E.288 Hydrogen bonds: C:R.66, C:R.66, C:N.150, C:W.254, C:R.332, C:R.332, C:E.337 Water bridges: C:E.151, C:W.327, C:E.337

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
BBB

B
EEE

C
FFF

Glyco_hydro_42M domain-containing protein

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