- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.76 Å
- Oligo State
- homo-trimer
- Ligands
- 16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 3 x CL: CHLORIDE ION(Non-functional Binders)
- 6 x TLA: L(+)-TARTARIC ACID(Non-covalent)
TLA.5: 6 residues within 4Å:- Chain A: T.365, E.366, N.367, V.368, K.369, M.370
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.7
10 PLIP interactions:6 interactions with chain A, 4 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
- Water bridges: B:R.398, B:R.398
- Salt bridges: B:R.398
TLA.14: 5 residues within 4Å:- Chain B: T.365, E.366, N.367, V.368, K.369
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.16: 7 residues within 4Å:- Chain B: T.109, D.110, V.111, G.112, G.113
- Chain C: R.398
- Ligands: EDO.15
10 PLIP interactions:6 interactions with chain B, 4 interactions with chain C- Hydrogen bonds: B:T.109, B:T.109, B:D.110, B:D.110, B:V.111, B:G.112, C:R.398
- Water bridges: C:R.398, C:R.398
- Salt bridges: C:R.398
TLA.24: 7 residues within 4Å:- Chain A: R.398
- Chain C: T.109, D.110, V.111, G.112, G.113
- Ligands: EDO.23
7 PLIP interactions:3 interactions with chain A, 4 interactions with chain C- Water bridges: A:R.398, A:R.398
- Salt bridges: A:R.398
- Hydrogen bonds: C:T.109, C:D.110, C:V.111, C:G.112
TLA.25: 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
- 3 x VKN: (1R,2S,4S,5R)-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol(Post Translational Modification)
VKN.8: 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.2, EDO.7
11 PLIP interactions:11 interactions with chain A- Hydrophobic interactions: A:E.288
- 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.151, 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.13, EDO.15
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.28: 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.23
10 PLIP interactions:10 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: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
AAAB
CCCC
DDD
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.76 Å
- Oligo State
- homo-trimer
- Ligands
- 16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 3 x CL: CHLORIDE ION(Non-functional Binders)
- 6 x TLA: L(+)-TARTARIC ACID(Non-covalent)
- 3 x VKN: (1R,2S,4S,5R)-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol(Post Translational Modification)
- 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
AAAB
CCCC
DDD