- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.56 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: 18 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, M.106, C.137, R.143
- Ligands: 4LR.1, SO4.4
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: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:G.127, A:G.127, A:E.142, A:E.142, A:E.142
FNR.6: 18 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, M.106, C.137, R.143
- Ligands: 4LR.5, SO4.8
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:S.125, B:T.126, B:T.128, B:R.160, B:R.160
- Water bridges: B:K.61, B:A.62, B:G.127, B:G.127, B:E.142, B:E.142, B:E.142
FNR.10: 18 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, M.106, C.137, R.143
- Ligands: 4LR.9, SO4.12
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: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:G.127, C:G.127, C:T.128
FNR.14: 18 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, M.106, C.137, R.143
- Ligands: 4LR.13, SO4.16
20 PLIP interactions:18 interactions with chain D, 2 interactions with chain J- Hydrophobic interactions: D:V.66, J:W.105
- Hydrogen bonds: D:G.34, D:G.34, D:S.36, D:S.60, D:S.125, D:S.125, D:T.126, D:T.128, D:T.128, D:R.160, D:R.160, D:E.161, J:R.143
- Water bridges: D:K.61, D:A.62, D:G.127, D:G.127, D:T.128
FNR.18: 18 residues within 4Å:- Chain D: W.105, M.106, 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.17, SO4.20
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: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:G.127, E:G.127, E:E.142, E:E.142, E:E.142
FNR.22: 18 residues within 4Å:- Chain A: W.105, M.106, 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.21, SO4.24
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: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:G.127, F:G.127, F:T.128
FNR.26: 18 residues within 4Å:- Chain C: W.105, M.106, 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.25, SO4.28
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: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:G.127, G:G.127, G:E.142, G:E.142, G:E.142
FNR.30: 18 residues within 4Å:- Chain B: W.105, M.106, 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.29, SO4.32
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: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:G.127, H:G.127, H:T.128
FNR.34: 18 residues within 4Å:- Chain H: W.105, M.106, 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.33, SO4.36
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: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:G.127, I:G.127, I:T.128
FNR.38: 18 residues within 4Å:- Chain E: W.105, M.106, 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.37, SO4.40
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: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:G.127, J:G.127, J:E.142, J:E.142, J:E.142
FNR.42: 18 residues within 4Å:- Chain G: W.105, M.106, 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.41, SO4.44
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: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:G.127, K:G.127, K:E.142, K:E.142, K:E.142
FNR.46: 18 residues within 4Å:- Chain F: W.105, M.106, 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.45, SO4.48
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: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:G.127, L:G.127, L:T.128
- 12 x NA: SODIUM ION(Non-functional Binders)
NA.3: 2 residues within 4Å:- Chain L: C.137, N.138
1 PLIP interactions:1 interactions with chain L- Hydrogen bonds: L:N.138
NA.7: 2 residues within 4Å:- Chain I: C.137, N.138
1 PLIP interactions:1 interactions with chain I- Hydrogen bonds: I:C.137
NA.11: 2 residues within 4Å:- Chain K: C.137, N.138
1 PLIP interactions:1 interactions with chain K- Hydrogen bonds: K:C.137
NA.15: 2 residues within 4Å:- Chain J: C.137, N.138
1 PLIP interactions:1 interactions with chain J- Hydrogen bonds: J:N.138
NA.19: 2 residues within 4Å:- Chain D: C.137, N.138
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:N.138
NA.23: 2 residues within 4Å:- Chain A: C.137, N.138
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.138
NA.27: 2 residues within 4Å:- Chain C: C.137, N.138
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:C.137
NA.31: 2 residues within 4Å:- Chain B: C.137, N.138
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:C.137
NA.35: 2 residues within 4Å:- Chain H: C.137, N.138
1 PLIP interactions:1 interactions with chain H- Water bridges: H:N.138
NA.39: 2 residues within 4Å:- Chain E: C.137, N.138
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:C.137
NA.43: 2 residues within 4Å:- Chain G: C.137, N.138
1 PLIP interactions:1 interactions with chain G- Hydrogen bonds: G:C.137
NA.47: 2 residues within 4Å:- Chain F: C.137, N.138
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:C.137
- 12 x SO4: SULFATE ION(Non-functional Binders)
SO4.4: 5 residues within 4Å:- Chain A: S.60, K.61, Q.102, N.139
- Ligands: FNR.2
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:K.61, A:Q.102, A:N.139
- Water bridges: A:A.62, A:A.62, A:E.142
SO4.8: 5 residues within 4Å:- Chain B: S.60, K.61, Q.102, N.139
- Ligands: FNR.6
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:K.61, B:Q.102, B:N.139
- Water bridges: B:A.62, B:A.62, B:E.142
SO4.12: 5 residues within 4Å:- Chain C: S.60, K.61, Q.102, N.139
- Ligands: FNR.10
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:K.61, C:Q.102, C:N.139
- Water bridges: C:A.62, C:A.62
SO4.16: 5 residues within 4Å:- Chain D: S.60, K.61, Q.102, N.139
- Ligands: FNR.14
5 PLIP interactions:5 interactions with chain D- Hydrogen bonds: D:K.61, D:Q.102, D:N.139
- Water bridges: D:A.62, D:A.62
SO4.20: 5 residues within 4Å:- Chain E: S.60, K.61, Q.102, N.139
- Ligands: FNR.18
6 PLIP interactions:6 interactions with chain E- Hydrogen bonds: E:K.61, E:Q.102, E:N.139
- Water bridges: E:A.62, E:A.62, E:E.142
SO4.24: 5 residues within 4Å:- Chain F: S.60, K.61, Q.102, N.139
- Ligands: FNR.22
5 PLIP interactions:5 interactions with chain F- Hydrogen bonds: F:K.61, F:Q.102, F:N.139
- Water bridges: F:A.62, F:A.62
SO4.28: 5 residues within 4Å:- Chain G: S.60, K.61, Q.102, N.139
- Ligands: FNR.26
6 PLIP interactions:6 interactions with chain G- Hydrogen bonds: G:K.61, G:Q.102, G:N.139
- Water bridges: G:A.62, G:A.62, G:E.142
SO4.32: 5 residues within 4Å:- Chain H: S.60, K.61, Q.102, N.139
- Ligands: FNR.30
5 PLIP interactions:5 interactions with chain H- Hydrogen bonds: H:K.61, H:Q.102, H:N.139
- Water bridges: H:A.62, H:A.62
SO4.36: 5 residues within 4Å:- Chain I: S.60, K.61, Q.102, N.139
- Ligands: FNR.34
5 PLIP interactions:5 interactions with chain I- Hydrogen bonds: I:K.61, I:Q.102, I:N.139
- Water bridges: I:A.62, I:A.62
SO4.40: 5 residues within 4Å:- Chain J: S.60, K.61, Q.102, N.139
- Ligands: FNR.38
6 PLIP interactions:6 interactions with chain J- Hydrogen bonds: J:K.61, J:Q.102, J:N.139
- Water bridges: J:A.62, J:A.62, J:E.142
SO4.44: 5 residues within 4Å:- Chain K: S.60, K.61, Q.102, N.139
- Ligands: FNR.42
6 PLIP interactions:6 interactions with chain K- Hydrogen bonds: K:K.61, K:Q.102, K:N.139
- Water bridges: K:A.62, K:A.62, K:E.142
SO4.48: 5 residues within 4Å:- Chain L: S.60, K.61, Q.102, N.139
- Ligands: FNR.46
5 PLIP interactions:5 interactions with chain L- Hydrogen bonds: L:K.61, L:Q.102, L:N.139
- Water bridges: L:A.62, L:A.62
- 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 1.56 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)
- 12 x SO4: SULFATE 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