- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.99 Å
- Oligo State
- homo-12-mer
- Ligands
- 12 x 4LR: Dimethylallyl monophosphate(Non-covalent)
- 12 x FNR: 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL(Non-covalent)
FNR.2: 16 residues within 4Å:- Chain A: T.33, G.34, A.35, S.36, S.60, A.62, V.66, S.125, T.126, T.128, R.160, E.161
- Chain L: W.105, C.137, R.143
- Ligands: 4LR.1
20 PLIP interactions:18 interactions with chain A, 2 interactions with chain L- Hydrophobic interactions: A:V.66, L:W.105
- Hydrogen bonds: A:G.34, A:G.34, A:S.36, A:S.60, A:S.125, A:T.126, A:T.128, A:R.160, A:R.160, L:R.143
- Water bridges: A:K.61, A:A.62, A:S.125, A:G.127, A:G.127, A:T.128, A:E.142, A:E.142
FNR.5: 16 residues within 4Å:- Chain B: T.33, G.34, A.35, S.36, S.60, A.62, V.66, S.125, T.126, T.128, R.160, E.161
- Chain I: W.105, C.137, R.143
- Ligands: 4LR.4
20 PLIP interactions:2 interactions with chain I, 18 interactions with chain B- Hydrophobic interactions: I:W.105, B:V.66
- Hydrogen bonds: I:R.143, B:G.34, B:G.34, B:S.36, B:S.60, B:S.125, B:T.126, B:T.128, B:R.160, B:R.160
- Water bridges: B:K.61, B:A.62, B:S.125, B:G.127, B:G.127, B:T.128, B:E.142, B:E.142
FNR.8: 16 residues within 4Å:- Chain C: T.33, G.34, A.35, S.36, S.60, A.62, V.66, S.125, T.126, T.128, R.160, E.161
- Chain K: W.105, C.137, R.143
- Ligands: 4LR.7
20 PLIP interactions:18 interactions with chain C, 2 interactions with chain K- Hydrophobic interactions: C:V.66, K:W.105
- Hydrogen bonds: C:G.34, C:G.34, C:S.36, C:S.60, C:S.125, C:T.126, C:T.128, C:T.128, C:R.160, C:R.160, C:E.161, K:R.143
- Water bridges: C:K.61, C:A.62, C:S.125, C:G.127, C:G.127, C:T.128
FNR.11: 16 residues within 4Å:- Chain D: T.33, G.34, A.35, S.36, S.60, A.62, V.66, S.125, T.126, T.128, R.160, E.161
- Chain J: W.105, C.137, R.143
- Ligands: 4LR.10
20 PLIP interactions:2 interactions with chain J, 18 interactions with chain D- Hydrophobic interactions: J:W.105, D:V.66
- Hydrogen bonds: J:R.143, D:G.34, D:G.34, D:S.36, D:S.60, D:S.125, D:T.126, D:T.128, D:T.128, D:R.160, D:R.160, D:E.161
- Water bridges: D:K.61, D:A.62, D:S.125, D:G.127, D:G.127, D:T.128
FNR.14: 16 residues within 4Å:- Chain D: W.105, C.137, R.143
- Chain E: T.33, G.34, A.35, S.36, S.60, A.62, V.66, S.125, T.126, T.128, R.160, E.161
- Ligands: 4LR.13
21 PLIP interactions:19 interactions with chain E, 2 interactions with chain D- Hydrophobic interactions: E:V.66, D:W.105
- Hydrogen bonds: E:G.34, E:G.34, E:S.36, E:S.60, E:S.125, E:T.126, E:T.128, E:T.128, E:R.160, E:R.160, D:R.143
- Water bridges: E:K.61, E:A.62, E:S.125, E:G.127, E:G.127, E:T.128, E:E.142, E:E.142
FNR.17: 16 residues within 4Å:- Chain A: W.105, C.137, R.143
- Chain F: T.33, G.34, A.35, S.36, S.60, A.62, V.66, S.125, T.126, T.128, R.160, E.161
- Ligands: 4LR.16
19 PLIP interactions:17 interactions with chain F, 2 interactions with chain A- Hydrophobic interactions: F:V.66, A:W.105
- Hydrogen bonds: F:G.34, F:G.34, F:S.36, F:S.60, F:S.125, F:T.126, F:T.128, F:R.160, F:R.160, F:E.161, A:R.143
- Water bridges: F:K.61, F:A.62, F:S.125, F:G.127, F:G.127, F:T.128
FNR.20: 16 residues within 4Å:- Chain C: W.105, C.137, R.143
- Chain G: T.33, G.34, A.35, S.36, S.60, A.62, V.66, S.125, T.126, T.128, R.160, E.161
- Ligands: 4LR.19
21 PLIP interactions:19 interactions with chain G, 2 interactions with chain C- Hydrophobic interactions: G:V.66, C:W.105
- Hydrogen bonds: G:G.34, G:G.34, G:S.36, G:S.60, G:S.125, G:T.126, G:T.128, G:T.128, G:R.160, G:R.160, C:R.143
- Water bridges: G:K.61, G:A.62, G:S.125, G:G.127, G:G.127, G:T.128, G:E.142, G:E.142
FNR.23: 16 residues within 4Å:- Chain B: W.105, C.137, R.143
- Chain H: T.33, G.34, A.35, S.36, S.60, A.62, V.66, S.125, T.126, T.128, R.160, E.161
- Ligands: 4LR.22
19 PLIP interactions:17 interactions with chain H, 2 interactions with chain B- Hydrophobic interactions: H:V.66, B:W.105
- Hydrogen bonds: H:G.34, H:G.34, H:S.36, H:S.60, H:S.125, H:T.126, H:T.128, H:R.160, H:R.160, H:E.161, B:R.143
- Water bridges: H:K.61, H:A.62, H:S.125, H:G.127, H:G.127, H:T.128
FNR.26: 16 residues within 4Å:- Chain H: W.105, C.137, R.143
- Chain I: T.33, G.34, A.35, S.36, S.60, A.62, V.66, S.125, T.126, T.128, R.160, E.161
- Ligands: 4LR.25
19 PLIP interactions:17 interactions with chain I, 2 interactions with chain H- Hydrophobic interactions: I:V.66, H:W.105
- Hydrogen bonds: I:G.34, I:G.34, I:S.36, I:S.60, I:S.125, I:T.126, I:T.128, I:T.128, I:R.160, I:R.160, H:R.143
- Water bridges: I:K.61, I:A.62, I:S.125, I:G.127, I:G.127, I:T.128
FNR.29: 16 residues within 4Å:- Chain E: W.105, C.137, R.143
- Chain J: T.33, G.34, A.35, S.36, S.60, A.62, V.66, S.125, T.126, T.128, R.160, E.161
- Ligands: 4LR.28
21 PLIP interactions:2 interactions with chain E, 19 interactions with chain J- Hydrophobic interactions: E:W.105, J:V.66
- Hydrogen bonds: E:R.143, J:G.34, J:G.34, J:S.36, J:S.60, J:S.125, J:T.126, J:T.128, J:R.160, J:R.160, J:E.161
- Water bridges: J:K.61, J:A.62, J:S.125, J:G.127, J:G.127, J:T.128, J:E.142, J:E.142
FNR.32: 16 residues within 4Å:- Chain G: W.105, C.137, R.143
- Chain K: T.33, G.34, A.35, S.36, S.60, A.62, V.66, S.125, T.126, T.128, R.160, E.161
- Ligands: 4LR.31
21 PLIP interactions:19 interactions with chain K, 2 interactions with chain G- Hydrophobic interactions: K:V.66, G:W.105
- Hydrogen bonds: K:G.34, K:G.34, K:S.36, K:S.60, K:S.125, K:T.126, K:T.128, K:R.160, K:R.160, K:E.161, G:R.143
- Water bridges: K:K.61, K:A.62, K:S.125, K:G.127, K:G.127, K:T.128, K:E.142, K:E.142
FNR.35: 16 residues within 4Å:- Chain F: W.105, C.137, R.143
- Chain L: T.33, G.34, A.35, S.36, S.60, A.62, V.66, S.125, T.126, T.128, R.160, E.161
- Ligands: 4LR.34
19 PLIP interactions:17 interactions with chain L, 2 interactions with chain F- Hydrophobic interactions: L:V.66, F:W.105
- Hydrogen bonds: L:G.34, L:G.34, L:S.36, L:S.60, L:S.125, L:T.126, L:T.128, L:T.128, L:R.160, L:R.160, F:R.143
- Water bridges: L:K.61, L:A.62, L:S.125, L:G.127, L:G.127, L:T.128
- 12 x NA: SODIUM ION(Non-functional Binders)
NA.3: 3 residues within 4Å:- Chain A: C.137, N.138
- Chain F: E.142
3 PLIP interactions:2 interactions with chain F, 1 interactions with chain A- Hydrogen bonds: F:E.142
- Water bridges: F:N.138, A:C.137
NA.6: 3 residues within 4Å:- Chain B: C.137, N.138
- Chain H: E.142
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain H- Hydrogen bonds: B:N.138
- Water bridges: B:C.137, H:N.138
NA.9: 3 residues within 4Å:- Chain C: C.137, N.138
- Chain G: E.142
3 PLIP interactions:1 interactions with chain G, 2 interactions with chain C- Water bridges: G:N.138, C:C.137
- Hydrogen bonds: C:N.138
NA.12: 3 residues within 4Å:- Chain D: C.137, N.138
- Chain E: E.142
3 PLIP interactions:2 interactions with chain D, 1 interactions with chain E- Hydrogen bonds: D:N.138
- Water bridges: D:C.137, E:N.138
NA.15: 3 residues within 4Å:- Chain E: C.137, N.138
- Chain J: E.142
3 PLIP interactions:2 interactions with chain E, 1 interactions with chain J- Hydrogen bonds: E:C.137
- Water bridges: E:C.137, J:N.138
NA.18: 3 residues within 4Å:- Chain F: C.137, N.138
- Chain L: E.142
3 PLIP interactions:1 interactions with chain F, 2 interactions with chain L- Water bridges: F:C.137, L:N.138
- Hydrogen bonds: L:E.142
NA.21: 3 residues within 4Å:- Chain G: C.137, N.138
- Chain K: E.142
3 PLIP interactions:2 interactions with chain K, 1 interactions with chain G- Hydrogen bonds: K:E.142
- Water bridges: K:N.138, G:C.137
NA.24: 3 residues within 4Å:- Chain H: C.137, N.138
- Chain I: E.142
3 PLIP interactions:2 interactions with chain H, 1 interactions with chain I- Hydrogen bonds: H:C.137
- Water bridges: H:C.137, I:N.138
NA.27: 3 residues within 4Å:- Chain B: E.142
- Chain I: C.137, N.138
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain I- Hydrogen bonds: B:E.142
- Water bridges: B:N.138, I:C.137
NA.30: 3 residues within 4Å:- Chain D: E.142
- Chain J: C.137, N.138
3 PLIP interactions:1 interactions with chain D, 2 interactions with chain J- Water bridges: D:N.138, J:C.137
- Hydrogen bonds: J:N.138
NA.33: 3 residues within 4Å:- Chain C: E.142
- Chain K: C.137, N.138
3 PLIP interactions:2 interactions with chain K, 1 interactions with chain C- Hydrogen bonds: K:N.138
- Water bridges: K:C.137, C:N.138
NA.36: 3 residues within 4Å:- Chain A: E.142
- Chain L: C.137, N.138
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain L- Hydrogen bonds: A:E.142
- Water bridges: A:N.138, L:C.137
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Marshall, S.A. et al., The UbiX flavin prenyltransferase reaction mechanism resembles class I terpene cyclase chemistry. Nat Commun (2019)
- Release Date
- 2019-06-05
- Peptides
- Flavin prenyltransferase UbiX: ABCDEFGHIJKL
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
AE
AF
AG
AH
AI
AJ
AK
AL
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.99 Å
- Oligo State
- homo-12-mer
- Ligands
- 12 x 4LR: Dimethylallyl monophosphate(Non-covalent)
- 12 x FNR: 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL(Non-covalent)
- 12 x NA: SODIUM ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Marshall, S.A. et al., The UbiX flavin prenyltransferase reaction mechanism resembles class I terpene cyclase chemistry. Nat Commun (2019)
- Release Date
- 2019-06-05
- Peptides
- Flavin prenyltransferase UbiX: ABCDEFGHIJKL
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
AE
AF
AG
AH
AI
AJ
AK
AL
A