- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.57 Å
- Oligo State
- homo-12-mer
- Ligands
- 12 x NA: SODIUM ION(Non-functional Binders)
- 12 x IP8: Isopentenyl phosphate(Non-covalent)
IP8.2: 13 residues within 4Å:- Chain A: R.160, E.161
- Chain C: Y.190, R.206, W.221
- Chain L: W.105, A.110, S.111, G.112, S.113, R.143, K.150
- Ligands: FNR.3
13 PLIP interactions:5 interactions with chain C, 3 interactions with chain A, 5 interactions with chain L- Hydrophobic interactions: C:Y.190, C:W.221, C:W.221, L:A.110
- Hydrogen bonds: C:Y.190, L:G.112, L:S.113
- Salt bridges: C:R.206, A:R.160, L:R.143, L:K.150
- Water bridges: A:A.162, A:A.162
IP8.5: 13 residues within 4Å:- Chain B: R.160, E.161
- Chain D: Y.190, R.206, W.221
- Chain I: W.105, A.110, S.111, G.112, S.113, R.143, K.150
- Ligands: FNR.6
13 PLIP interactions:3 interactions with chain B, 5 interactions with chain I, 5 interactions with chain D- Water bridges: B:A.162, B:A.162
- Salt bridges: B:R.160, I:R.143, I:K.150, D:R.206
- Hydrophobic interactions: I:A.110, D:Y.190, D:W.221, D:W.221
- Hydrogen bonds: I:G.112, I:S.113, D:Y.190
IP8.8: 13 residues within 4Å:- Chain A: Y.190, R.206, W.221
- Chain C: R.160, E.161
- Chain K: W.105, A.110, S.111, G.112, S.113, R.143, K.150
- Ligands: FNR.9
12 PLIP interactions:5 interactions with chain K, 3 interactions with chain C, 4 interactions with chain A- Hydrophobic interactions: K:A.110, A:Y.190, A:W.221, A:W.221
- Hydrogen bonds: K:G.112, K:S.113
- Salt bridges: K:R.143, K:K.150, C:R.160, A:R.206
- Water bridges: C:A.162, C:A.162
IP8.11: 13 residues within 4Å:- Chain B: Y.190, R.206, W.221
- Chain D: R.160, E.161
- Chain J: W.105, A.110, S.111, G.112, S.113, R.143, K.150
- Ligands: FNR.12
12 PLIP interactions:5 interactions with chain J, 3 interactions with chain D, 4 interactions with chain B- Hydrophobic interactions: J:A.110, B:Y.190, B:W.221, B:W.221
- Hydrogen bonds: J:G.112, J:S.113
- Salt bridges: J:R.143, J:K.150, D:R.160, B:R.206
- Water bridges: D:A.162, D:A.162
IP8.14: 13 residues within 4Å:- Chain D: W.105, A.110, S.111, G.112, S.113, R.143, K.150
- Chain E: R.160, E.161
- Chain G: Y.190, R.206, W.221
- Ligands: FNR.15
13 PLIP interactions:3 interactions with chain E, 5 interactions with chain D, 5 interactions with chain G- Water bridges: E:A.162, E:A.162
- Salt bridges: E:R.160, D:R.143, D:K.150, G:R.206
- Hydrophobic interactions: D:A.110, G:Y.190, G:W.221, G:W.221
- Hydrogen bonds: D:G.112, D:S.113, G:Y.190
IP8.17: 13 residues within 4Å:- Chain A: W.105, A.110, S.111, G.112, S.113, R.143, K.150
- Chain F: R.160, E.161
- Chain H: Y.190, R.206, W.221
- Ligands: FNR.18
12 PLIP interactions:4 interactions with chain H, 5 interactions with chain A, 3 interactions with chain F- Hydrophobic interactions: H:Y.190, H:W.221, H:W.221, A:A.110
- Salt bridges: H:R.206, A:R.143, A:K.150, F:R.160
- Hydrogen bonds: A:G.112, A:S.113
- Water bridges: F:A.162, F:A.162
IP8.20: 13 residues within 4Å:- Chain C: W.105, A.110, S.111, G.112, S.113, R.143, K.150
- Chain E: Y.190, R.206, W.221
- Chain G: R.160, E.161
- Ligands: FNR.21
13 PLIP interactions:5 interactions with chain E, 5 interactions with chain C, 3 interactions with chain G- Hydrophobic interactions: E:Y.190, E:W.221, E:W.221, C:A.110
- Hydrogen bonds: E:Y.190, C:G.112, C:S.113
- Salt bridges: E:R.206, C:R.143, C:K.150, G:R.160
- Water bridges: G:A.162, G:A.162
IP8.23: 13 residues within 4Å:- Chain B: W.105, A.110, S.111, G.112, S.113, R.143, K.150
- Chain F: Y.190, R.206, W.221
- Chain H: R.160, E.161
- Ligands: FNR.24
12 PLIP interactions:3 interactions with chain H, 5 interactions with chain B, 4 interactions with chain F- Water bridges: H:A.162, H:A.162
- Salt bridges: H:R.160, B:R.143, B:K.150, F:R.206
- Hydrophobic interactions: B:A.110, F:Y.190, F:W.221, F:W.221
- Hydrogen bonds: B:G.112, B:S.113
IP8.26: 13 residues within 4Å:- Chain H: W.105, A.110, S.111, G.112, S.113, R.143, K.150
- Chain I: R.160, E.161
- Chain K: Y.190, R.206, W.221
- Ligands: FNR.27
12 PLIP interactions:3 interactions with chain I, 5 interactions with chain H, 4 interactions with chain K- Water bridges: I:A.162, I:A.162
- Salt bridges: I:R.160, H:R.143, H:K.150, K:R.206
- Hydrophobic interactions: H:A.110, K:Y.190, K:W.221, K:W.221
- Hydrogen bonds: H:G.112, H:S.113
IP8.29: 13 residues within 4Å:- Chain E: W.105, A.110, S.111, G.112, S.113, R.143, K.150
- Chain J: R.160, E.161
- Chain L: Y.190, R.206, W.221
- Ligands: FNR.30
13 PLIP interactions:5 interactions with chain L, 3 interactions with chain J, 5 interactions with chain E- Hydrophobic interactions: L:Y.190, L:W.221, L:W.221, E:A.110
- Hydrogen bonds: L:Y.190, E:G.112, E:S.113
- Salt bridges: L:R.206, J:R.160, E:R.143, E:K.150
- Water bridges: J:A.162, J:A.162
IP8.32: 13 residues within 4Å:- Chain G: W.105, A.110, S.111, G.112, S.113, R.143, K.150
- Chain I: Y.190, R.206, W.221
- Chain K: R.160, E.161
- Ligands: FNR.33
13 PLIP interactions:5 interactions with chain G, 5 interactions with chain I, 3 interactions with chain K- Hydrophobic interactions: G:A.110, I:Y.190, I:W.221, I:W.221
- Hydrogen bonds: G:G.112, G:S.113, I:Y.190
- Salt bridges: G:R.143, G:K.150, I:R.206, K:R.160
- Water bridges: K:A.162, K:A.162
IP8.35: 13 residues within 4Å:- Chain F: W.105, A.110, S.111, G.112, S.113, R.143, K.150
- Chain J: Y.190, R.206, W.221
- Chain L: R.160, E.161
- Ligands: FNR.36
12 PLIP interactions:5 interactions with chain F, 4 interactions with chain J, 3 interactions with chain L- Hydrophobic interactions: F:A.110, J:Y.190, J:W.221, J:W.221
- Hydrogen bonds: F:G.112, F:S.113
- Salt bridges: F:R.143, F:K.150, J:R.206, L:R.160
- Water bridges: L:A.162, L:A.162
- 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.3: 17 residues within 4Å:- Chain A: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, S.125, T.126, T.128, R.160, E.161
- Chain L: W.105, C.137, R.143
- Ligands: IP8.2
23 PLIP interactions:21 interactions with chain A, 2 interactions with chain L- Hydrophobic interactions: A:L.65, A:V.66, L:W.105
- Hydrogen bonds: A:G.34, A:G.34, A:S.36, A:S.60, 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:T.128, A:E.142, A:E.142, A:E.142, A:R.160
FNR.6: 17 residues within 4Å:- Chain B: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, S.125, T.126, T.128, R.160, E.161
- Chain I: W.105, C.137, R.143
- Ligands: IP8.5
23 PLIP interactions:21 interactions with chain B, 2 interactions with chain I- Hydrophobic interactions: B:L.65, B:V.66, I:W.105
- Hydrogen bonds: B:G.34, B:G.34, B:S.36, B:S.60, B:S.60, B:S.125, B:T.126, B:T.128, B:R.160, B:R.160, I:R.143
- Water bridges: B:K.61, B:A.62, B:S.125, B:G.127, B:T.128, B:E.142, B:E.142, B:E.142, B:R.160
FNR.9: 17 residues within 4Å:- Chain C: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, S.125, T.126, T.128, R.160, E.161
- Chain K: W.105, C.137, R.143
- Ligands: IP8.8
23 PLIP interactions:21 interactions with chain C, 2 interactions with chain K- Hydrophobic interactions: C:L.65, C:V.66, K:W.105
- Hydrogen bonds: C:G.34, C:G.34, C:S.36, C:S.60, 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:T.128, C:N.139, C:R.160
FNR.12: 17 residues within 4Å:- Chain D: T.33, G.34, A.35, S.36, S.60, A.62, L.65, V.66, S.125, T.126, T.128, R.160, E.161
- Chain J: W.105, C.137, R.143
- Ligands: IP8.11
23 PLIP interactions:2 interactions with chain J, 21 interactions with chain D- Hydrophobic interactions: J:W.105, D:L.65, D:V.66
- Hydrogen bonds: J:R.143, D:G.34, D:G.34, D:S.36, D:S.60, 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:T.128, D:N.139, D:R.160
FNR.15: 17 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, L.65, V.66, S.125, T.126, T.128, R.160, E.161
- Ligands: IP8.14
24 PLIP interactions:22 interactions with chain E, 2 interactions with chain D- Hydrophobic interactions: E:L.65, E:V.66, D:W.105
- Hydrogen bonds: E:G.34, E:G.34, E:S.36, E:S.60, 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:T.128, E:E.142, E:E.142, E:E.142, E:R.160
FNR.18: 17 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, L.65, V.66, S.125, T.126, T.128, R.160, E.161
- Ligands: IP8.17
22 PLIP interactions:20 interactions with chain F, 2 interactions with chain A- Hydrophobic interactions: F:L.65, F:V.66, A:W.105
- Hydrogen bonds: F:G.34, F:G.34, F:S.36, F:S.60, 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:T.128, F:N.139, F:R.160
FNR.21: 17 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, L.65, V.66, S.125, T.126, T.128, R.160, E.161
- Ligands: IP8.20
24 PLIP interactions:22 interactions with chain G, 2 interactions with chain C- Hydrophobic interactions: G:L.65, G:V.66, C:W.105
- Hydrogen bonds: G:G.34, G:G.34, G:S.36, G:S.60, 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:T.128, G:E.142, G:E.142, G:E.142, G:R.160
FNR.24: 17 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, L.65, V.66, S.125, T.126, T.128, R.160, E.161
- Ligands: IP8.23
22 PLIP interactions:20 interactions with chain H, 2 interactions with chain B- Hydrophobic interactions: H:L.65, H:V.66, B:W.105
- Hydrogen bonds: H:G.34, H:G.34, H:S.36, H:S.60, 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:T.128, H:N.139, H:R.160
FNR.27: 17 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, L.65, V.66, S.125, T.126, T.128, R.160, E.161
- Ligands: IP8.26
22 PLIP interactions:2 interactions with chain H, 20 interactions with chain I- Hydrophobic interactions: H:W.105, I:L.65, I:V.66
- Hydrogen bonds: H:R.143, I:G.34, I:G.34, I:S.36, I:S.60, I:S.60, I:S.125, I:T.126, I:T.128, I:T.128, I:R.160, I:R.160
- Water bridges: I:K.61, I:A.62, I:S.125, I:G.127, I:T.128, I:N.139, I:R.160
FNR.30: 17 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, L.65, V.66, S.125, T.126, T.128, R.160, E.161
- Ligands: IP8.29
24 PLIP interactions:22 interactions with chain J, 2 interactions with chain E- Hydrophobic interactions: J:L.65, J:V.66, E:W.105
- Hydrogen bonds: J:G.34, J:G.34, J:S.36, J:S.60, J:S.60, J:S.125, J:T.126, J:T.128, J:R.160, J:R.160, J:E.161, E:R.143
- Water bridges: J:K.61, J:A.62, J:S.125, J:G.127, J:T.128, J:E.142, J:E.142, J:E.142, J:R.160
FNR.33: 17 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, L.65, V.66, S.125, T.126, T.128, R.160, E.161
- Ligands: IP8.32
24 PLIP interactions:22 interactions with chain K, 2 interactions with chain G- Hydrophobic interactions: K:L.65, K:V.66, G:W.105
- Hydrogen bonds: K:G.34, K:G.34, K:S.36, K:S.60, 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:T.128, K:E.142, K:E.142, K:E.142, K:R.160
FNR.36: 17 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, L.65, V.66, S.125, T.126, T.128, R.160, E.161
- Ligands: IP8.35
22 PLIP interactions:2 interactions with chain F, 20 interactions with chain L- Hydrophobic interactions: F:W.105, L:L.65, L:V.66
- Hydrogen bonds: F:R.143, L:G.34, L:G.34, L:S.36, L:S.60, L:S.60, L:S.125, L:T.126, L:T.128, L:T.128, L:R.160, L:R.160
- Water bridges: L:K.61, L:A.62, L:S.125, L:G.127, L:T.128, L:N.139, L:R.160
- 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 1.57 Å
- Oligo State
- homo-12-mer
- Ligands
- 12 x NA: SODIUM ION(Non-functional Binders)
- 12 x IP8: Isopentenyl phosphate(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)
- 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