- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- hetero-3-3-mer
- Ligands
- 3 x MN: MANGANESE (II) ION(Non-covalent)
- 3 x GOL: GLYCEROL(Non-functional Binders)
GOL.2: 6 residues within 4Å:- Chain A: Y.11, V.42, N.78, R.114, Q.116
- Chain B: Y.39
8 PLIP interactions:7 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:N.78, A:N.78, A:R.114, A:R.114, B:Y.39
- Water bridges: A:E.299, A:E.299, A:E.301
GOL.12: 6 residues within 4Å:- Chain D: Y.11, V.42, N.78, R.114, Q.116
- Chain E: Y.39
12 PLIP interactions:11 interactions with chain D, 1 interactions with chain E- Hydrogen bonds: D:N.78, D:N.78, D:R.114, D:R.114, D:Q.116
- Water bridges: D:Y.11, D:Y.11, D:E.40, D:E.299, D:E.299, D:E.301, E:Y.39
GOL.18: 6 residues within 4Å:- Chain F: Y.11, V.42, N.78, R.114, Q.116, E.299
4 PLIP interactions:4 interactions with chain F- Hydrogen bonds: F:N.78, F:N.78, F:R.114, F:Q.116
- 12 x SO4: SULFATE ION(Non-functional Binders)
SO4.3: 4 residues within 4Å:- Chain A: G.85, D.86, R.87
- Chain B: T.125
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:T.125
- Water bridges: A:R.87
SO4.6: 4 residues within 4Å:- Chain B: F.21, W.22, K.95
- Chain D: Y.134
5 PLIP interactions:3 interactions with chain B, 2 interactions with chain D- Hydrogen bonds: B:W.22, D:Y.134, D:Y.134
- Water bridges: B:W.22
- Salt bridges: B:K.95
SO4.7: 8 residues within 4Å:- Chain B: E.62, N.63, I.64, S.65, G.74
- Chain D: V.99, K.103, F.130
6 PLIP interactions:5 interactions with chain B, 1 interactions with chain D- Hydrogen bonds: B:E.62, B:S.65
- Water bridges: B:I.64, B:I.64, B:G.74
- Salt bridges: D:K.103
SO4.9: 4 residues within 4Å:- Chain C: I.47, D.48, E.49, V.75
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:I.47
- Water bridges: C:I.47, C:I.50, C:L.78
SO4.10: 5 residues within 4Å:- Chain A: Y.67
- Chain C: F.21, W.22, K.95
- Chain F: Y.134
5 PLIP interactions:3 interactions with chain C, 2 interactions with chain F- Hydrogen bonds: C:W.22, F:Y.134, F:Y.134
- Water bridges: C:W.22
- Salt bridges: C:K.95
SO4.13: 8 residues within 4Å:- Chain D: A.178, K.180, N.182, L.239, T.240, H.267, A.277, I.278
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:N.182
- Salt bridges: D:H.267
SO4.15: 4 residues within 4Å:- Chain E: I.47, D.48, E.49, L.78
5 PLIP interactions:5 interactions with chain E- Hydrogen bonds: E:D.48
- Water bridges: E:I.47, E:I.50, E:H.79, E:H.79
SO4.16: 6 residues within 4Å:- Chain E: K.19, N.20, Q.31, N.142
- Chain F: E.25, Y.68
5 PLIP interactions:3 interactions with chain E, 2 interactions with chain F- Hydrogen bonds: E:N.20, E:N.142, F:Y.68
- Salt bridges: E:K.19
- Water bridges: F:R.29
SO4.19: 8 residues within 4Å:- Chain C: E.62, N.63, I.64, S.65, G.74
- Chain F: V.99, K.103, F.130
3 PLIP interactions:1 interactions with chain F, 2 interactions with chain C- Salt bridges: F:K.103
- Hydrogen bonds: C:E.62
- Water bridges: C:F.97
SO4.20: 4 residues within 4Å:- Chain F: V.53, S.54, D.55, K.107
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:V.53, F:D.55
- Salt bridges: F:K.107
SO4.21: 7 residues within 4Å:- Chain F: A.178, K.180, P.181, N.182, L.239, H.267, A.277
2 PLIP interactions:2 interactions with chain F- Hydrogen bonds: F:N.182
- Salt bridges: F:H.267
SO4.22: 1 residues within 4Å:- Chain F: K.196
1 PLIP interactions:1 interactions with chain F- Salt bridges: F:K.196
- 4 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)
EPE.4: 8 residues within 4Å:- Chain B: I.47, D.48, E.49, I.50, A.61, V.75, L.78, H.79
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:I.50
- Water bridges: B:H.79, B:H.79
EPE.5: 7 residues within 4Å:- Chain B: R.6, D.11, V.12, V.13, G.134, S.135, K.136
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:R.6, B:V.12, B:V.13, B:S.135, B:S.135
- Salt bridges: B:D.11
EPE.8: 7 residues within 4Å:- Chain C: R.6, D.11, V.12, V.13, G.134, S.135, K.136
6 PLIP interactions:6 interactions with chain C- Hydrogen bonds: C:R.6, C:V.12, C:V.13, C:S.135
- Salt bridges: C:D.11, C:D.11
EPE.14: 7 residues within 4Å:- Chain E: R.6, D.11, V.12, V.13, G.134, S.135, K.136
6 PLIP interactions:6 interactions with chain E- Hydrogen bonds: E:R.6, E:V.12, E:V.13, E:S.135
- Salt bridges: E:D.11, E:K.136
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mori, T. et al., C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes. Nat Commun (2021)
- Release Date
- 2021-11-03
- Peptides
- AP_endonuc_2 domain-containing protein: ADF
DgpB: BCE - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
EF
GB
BC
DE
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- hetero-3-3-mer
- Ligands
- 3 x MN: MANGANESE (II) ION(Non-covalent)
- 3 x GOL: GLYCEROL(Non-functional Binders)
- 12 x SO4: SULFATE ION(Non-functional Binders)
- 4 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Mori, T. et al., C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes. Nat Commun (2021)
- Release Date
- 2021-11-03
- Peptides
- AP_endonuc_2 domain-containing protein: ADF
DgpB: BCE - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
EF
GB
BC
DE
F