- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 Å
- Oligo State
- homo-12-mer
- Ligands
- 12 x DMA: DIMETHYLALLYL DIPHOSPHATE(Non-covalent)
- 12 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)
FMN.2: 20 residues within 4Å:- Chain A: M.106, A.107, C.138, D.139, R.144
- Chain J: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162
- Chain L: W.222, W.225
- Ligands: DMA.1
20 PLIP interactions:15 interactions with chain J, 2 interactions with chain L, 3 interactions with chain A- Hydrogen bonds: J:G.49, J:G.49, J:T.51, J:S.75, J:S.126, J:M.127, J:T.129, J:R.161, J:R.161, J:E.162, A:R.144, A:R.144
- Water bridges: J:K.76, J:K.76, J:S.126, J:K.128
- Salt bridges: J:K.128
- Hydrophobic interactions: L:W.222, L:W.225, A:A.107
FMN.3: 20 residues within 4Å:- Chain A: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162
- Chain B: W.222, W.225
- Chain C: M.106, A.107, C.138, D.139, R.144
- Ligands: DMA.8
22 PLIP interactions:15 interactions with chain A, 3 interactions with chain B, 4 interactions with chain C- Hydrogen bonds: A:G.49, A:G.49, A:T.51, A:S.75, A:S.75, A:S.126, A:M.127, A:T.129, A:T.129, A:R.161, A:R.161, C:R.144, C:R.144, C:R.144
- Water bridges: A:K.76, A:W.77, A:K.128
- Salt bridges: A:K.128
- Hydrophobic interactions: B:W.222, B:W.225, B:W.225, C:A.107
FMN.7: 19 residues within 4Å:- Chain A: W.225
- Chain B: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162
- Chain E: M.106, A.107, C.138, D.139, R.144
- Ligands: DMA.4
21 PLIP interactions:15 interactions with chain B, 2 interactions with chain A, 4 interactions with chain E- Hydrogen bonds: B:G.49, B:G.49, B:T.51, B:S.75, B:S.75, B:S.126, B:M.127, B:T.129, B:T.129, B:R.161, B:R.161, E:R.144, E:R.144, E:R.144
- Water bridges: B:K.76, B:W.77, B:K.128
- Salt bridges: B:K.128
- Hydrophobic interactions: A:W.225, A:W.225, E:A.107
FMN.11: 20 residues within 4Å:- Chain C: W.222, W.225
- Chain D: M.106, A.107, C.138, D.139, R.144
- Chain I: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162
- Ligands: DMA.9
21 PLIP interactions:15 interactions with chain I, 3 interactions with chain D, 3 interactions with chain C- Hydrogen bonds: I:G.49, I:G.49, I:T.51, I:S.75, I:S.75, I:S.126, I:M.127, I:T.129, I:R.161, I:R.161, D:R.144, D:R.144
- Water bridges: I:K.76, I:W.77, I:S.126, I:K.128
- Salt bridges: I:K.128
- Hydrophobic interactions: D:A.107, C:W.222, C:W.225, C:W.225
FMN.13: 19 residues within 4Å:- Chain E: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162
- Chain F: M.106, A.107, C.138, D.139, R.144
- Chain K: W.222
- Ligands: DMA.15
20 PLIP interactions:15 interactions with chain E, 4 interactions with chain F, 1 interactions with chain K- Hydrogen bonds: E:G.49, E:G.49, E:T.51, E:S.75, E:S.75, E:S.126, E:M.127, E:T.129, E:T.129, E:R.161, E:R.161, E:E.162, F:R.144, F:R.144, F:R.144
- Water bridges: E:W.77, E:K.128
- Salt bridges: E:K.128
- Hydrophobic interactions: F:A.107, K:W.222
FMN.14: 20 residues within 4Å:- Chain B: M.106, A.107, C.138, D.139, R.144
- Chain D: W.222, W.225
- Chain F: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162
- Ligands: DMA.10
20 PLIP interactions:14 interactions with chain F, 4 interactions with chain B, 2 interactions with chain D- Hydrogen bonds: F:G.49, F:G.49, F:T.51, F:S.75, F:S.126, F:M.127, F:T.129, F:R.161, F:R.161, F:E.162, B:R.144, B:R.144, B:R.144
- Water bridges: F:K.76, F:K.76, F:K.128
- Salt bridges: F:K.128
- Hydrophobic interactions: B:A.107, D:W.222, D:W.225
FMN.17: 20 residues within 4Å:- Chain D: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162
- Chain F: W.222, W.225
- Chain G: M.106, A.107, C.138, D.139, R.144
- Ligands: DMA.16
20 PLIP interactions:2 interactions with chain F, 15 interactions with chain D, 3 interactions with chain G- Hydrophobic interactions: F:W.222, F:W.225, G:A.107
- Hydrogen bonds: D:G.49, D:G.49, D:T.51, D:S.75, D:S.126, D:M.127, D:T.129, D:T.129, D:R.161, D:R.161, G:R.144, G:R.144
- Water bridges: D:K.76, D:K.76, D:S.126, D:K.128
- Salt bridges: D:K.128
FMN.18: 20 residues within 4Å:- Chain G: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162
- Chain H: W.222, W.225
- Chain I: M.106, A.107, C.138, D.139, R.144
- Ligands: DMA.23
21 PLIP interactions:14 interactions with chain G, 3 interactions with chain H, 4 interactions with chain I- Hydrogen bonds: G:G.49, G:G.49, G:T.51, G:S.75, G:S.75, G:S.126, G:M.127, G:T.129, G:R.161, G:R.161, I:R.144, I:R.144, I:R.144
- Water bridges: G:K.76, G:W.77, G:K.128
- Salt bridges: G:K.128
- Hydrophobic interactions: H:W.222, H:W.225, H:W.225, I:A.107
FMN.22: 19 residues within 4Å:- Chain G: W.225
- Chain H: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162
- Chain K: M.106, A.107, C.138, D.139, R.144
- Ligands: DMA.19
21 PLIP interactions:15 interactions with chain H, 2 interactions with chain G, 4 interactions with chain K- Hydrogen bonds: H:G.49, H:G.49, H:T.51, H:S.75, H:S.75, H:S.126, H:M.127, H:T.129, H:R.161, H:R.161, H:E.162, K:R.144, K:R.144, K:R.144
- Water bridges: H:K.76, H:W.77, H:K.128
- Salt bridges: H:K.128
- Hydrophobic interactions: G:W.225, G:W.225, K:A.107
FMN.26: 20 residues within 4Å:- Chain C: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162
- Chain I: W.222, W.225
- Chain J: M.106, A.107, C.138, D.139, R.144
- Ligands: DMA.24
23 PLIP interactions:17 interactions with chain C, 3 interactions with chain I, 3 interactions with chain J- Hydrogen bonds: C:G.49, C:G.49, C:T.51, C:S.75, C:S.75, C:S.126, C:M.127, C:T.129, C:T.129, C:R.161, C:R.161, C:E.162, J:R.144, J:R.144
- Water bridges: C:K.76, C:W.77, C:S.126, C:K.128
- Salt bridges: C:K.128
- Hydrophobic interactions: I:W.222, I:W.225, I:W.225, J:A.107
FMN.28: 19 residues within 4Å:- Chain E: W.222
- Chain K: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162
- Chain L: M.106, A.107, C.138, D.139, R.144
- Ligands: DMA.30
18 PLIP interactions:13 interactions with chain K, 4 interactions with chain L, 1 interactions with chain E- Hydrogen bonds: K:G.49, K:G.49, K:T.51, K:S.75, K:S.75, K:S.126, K:M.127, K:T.129, K:R.161, K:R.161, L:R.144, L:R.144, L:R.144
- Water bridges: K:W.77, K:K.128
- Salt bridges: K:K.128
- Hydrophobic interactions: L:A.107, E:W.222
FMN.29: 20 residues within 4Å:- Chain H: M.106, A.107, C.138, D.139, R.144
- Chain J: W.222, W.225
- Chain L: T.48, G.49, A.50, T.51, S.75, W.77, S.126, M.127, K.128, T.129, R.161, E.162
- Ligands: DMA.25
20 PLIP interactions:14 interactions with chain L, 2 interactions with chain J, 4 interactions with chain H- Hydrogen bonds: L:G.49, L:G.49, L:T.51, L:S.75, L:S.126, L:M.127, L:T.129, L:T.129, L:R.161, L:R.161, H:R.144, H:R.144, H:R.144
- Water bridges: L:K.76, L:K.76, L:K.128
- Salt bridges: L:K.128
- Hydrophobic interactions: J:W.222, J:W.225, H:A.107
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
- 4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.6: 9 residues within 4Å:- Chain A: P.188, F.190, L.200
- Chain B: P.186, P.188, F.190, L.200, I.201, S.204
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:S.204, B:S.204
- Water bridges: A:L.200
PEG.12: 7 residues within 4Å:- Chain D: P.188, L.200, I.201, S.204
- Chain F: P.188, F.190, L.200
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:S.204, D:S.204
PEG.21: 9 residues within 4Å:- Chain G: P.188, F.190, L.200
- Chain H: P.186, P.188, F.190, L.200, I.201, S.204
3 PLIP interactions:2 interactions with chain H, 1 interactions with chain G- Hydrogen bonds: H:S.204, H:S.204
- Water bridges: G:L.200
PEG.27: 7 residues within 4Å:- Chain J: P.188, L.200, I.201, S.204
- Chain L: P.188, F.190, L.200
2 PLIP interactions:2 interactions with chain J- Hydrogen bonds: J:S.204, J:S.204
- 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 PAD1, mitochondrial: ABCDEFGHIJKL
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
AC
BD
DE
EF
FG
CH
AI
BJ
DK
EL
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 Å
- Oligo State
- homo-12-mer
- Ligands
- 12 x DMA: DIMETHYLALLYL DIPHOSPHATE(Non-covalent)
- 12 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
- 4 x PEG: DI(HYDROXYETHYL)ETHER(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 PAD1, mitochondrial: ABCDEFGHIJKL
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
AC
BD
DE
EF
FG
CH
AI
BJ
DK
EL
F