- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.45 Å
- Oligo State
- homo-12-mer
- Ligands
- 12 x 4LS: 1-deoxy-1-[7,8-dimethyl-5-(3-methylbut-2-en-1-yl)-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol(Non-covalent)
- 36 x SCN: THIOCYANATE ION(Non-functional Binders)
SCN.2: 7 residues within 4Å:- Chain A: Q.62, T.66, A.71, A.72, G.74, Q.75, I.76
Ligand excluded by PLIPSCN.3: 2 residues within 4Å:- Chain A: Q.59, A.60
Ligand excluded by PLIPSCN.4: 6 residues within 4Å:- Chain A: P.4, P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.8: 7 residues within 4Å:- Chain B: Q.62, T.66, A.71, A.72, G.74, Q.75, I.76
Ligand excluded by PLIPSCN.9: 2 residues within 4Å:- Chain B: Q.59, A.60
Ligand excluded by PLIPSCN.10: 6 residues within 4Å:- Chain B: P.4, P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.14: 7 residues within 4Å:- Chain C: Q.62, T.66, A.71, A.72, G.74, Q.75, I.76
Ligand excluded by PLIPSCN.15: 2 residues within 4Å:- Chain C: Q.59, A.60
Ligand excluded by PLIPSCN.16: 6 residues within 4Å:- Chain C: P.4, P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.20: 7 residues within 4Å:- Chain D: Q.62, T.66, A.71, A.72, G.74, Q.75, I.76
Ligand excluded by PLIPSCN.21: 2 residues within 4Å:- Chain D: Q.59, A.60
Ligand excluded by PLIPSCN.22: 6 residues within 4Å:- Chain D: P.4, P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.26: 7 residues within 4Å:- Chain E: Q.62, T.66, A.71, A.72, G.74, Q.75, I.76
Ligand excluded by PLIPSCN.27: 2 residues within 4Å:- Chain E: Q.59, A.60
Ligand excluded by PLIPSCN.28: 6 residues within 4Å:- Chain E: P.4, P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.32: 7 residues within 4Å:- Chain F: Q.62, T.66, A.71, A.72, G.74, Q.75, I.76
Ligand excluded by PLIPSCN.33: 2 residues within 4Å:- Chain F: Q.59, A.60
Ligand excluded by PLIPSCN.34: 6 residues within 4Å:- Chain F: P.4, P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.38: 7 residues within 4Å:- Chain G: Q.62, T.66, A.71, A.72, G.74, Q.75, I.76
Ligand excluded by PLIPSCN.39: 2 residues within 4Å:- Chain G: Q.59, A.60
Ligand excluded by PLIPSCN.40: 6 residues within 4Å:- Chain G: P.4, P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.44: 7 residues within 4Å:- Chain H: Q.62, T.66, A.71, A.72, G.74, Q.75, I.76
Ligand excluded by PLIPSCN.45: 2 residues within 4Å:- Chain H: Q.59, A.60
Ligand excluded by PLIPSCN.46: 6 residues within 4Å:- Chain H: P.4, P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.50: 7 residues within 4Å:- Chain I: Q.62, T.66, A.71, A.72, G.74, Q.75, I.76
Ligand excluded by PLIPSCN.51: 2 residues within 4Å:- Chain I: Q.59, A.60
Ligand excluded by PLIPSCN.52: 6 residues within 4Å:- Chain I: P.4, P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.56: 7 residues within 4Å:- Chain J: Q.62, T.66, A.71, A.72, G.74, Q.75, I.76
Ligand excluded by PLIPSCN.57: 2 residues within 4Å:- Chain J: Q.59, A.60
Ligand excluded by PLIPSCN.58: 6 residues within 4Å:- Chain J: P.4, P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.62: 7 residues within 4Å:- Chain K: Q.62, T.66, A.71, A.72, G.74, Q.75, I.76
Ligand excluded by PLIPSCN.63: 2 residues within 4Å:- Chain K: Q.59, A.60
Ligand excluded by PLIPSCN.64: 6 residues within 4Å:- Chain K: P.4, P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.68: 7 residues within 4Å:- Chain L: Q.62, T.66, A.71, A.72, G.74, Q.75, I.76
Ligand excluded by PLIPSCN.69: 2 residues within 4Å:- Chain L: Q.59, A.60
Ligand excluded by PLIPSCN.70: 6 residues within 4Å:- Chain L: P.4, P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIP- 12 x NA: SODIUM ION(Non-functional Binders)
NA.5: 2 residues within 4Å:- Chain A: S.39, K.40
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.40
- Water bridges: A:S.39, A:A.41
NA.11: 2 residues within 4Å:- Chain B: S.39, K.40
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:K.40
- Water bridges: B:S.39, B:A.41
NA.17: 2 residues within 4Å:- Chain C: S.39, K.40
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:K.40
- Water bridges: C:S.39, C:A.41, C:Q.81
NA.23: 2 residues within 4Å:- Chain D: S.39, K.40
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:K.40
- Water bridges: D:S.39, D:A.41
NA.29: 2 residues within 4Å:- Chain E: S.39, K.40
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:K.40
- Water bridges: E:A.41
NA.35: 2 residues within 4Å:- Chain F: S.39, K.40
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:K.40
- Water bridges: F:S.39, F:A.41
NA.41: 2 residues within 4Å:- Chain G: S.39, K.40
3 PLIP interactions:3 interactions with chain G- Hydrogen bonds: G:K.40
- Water bridges: G:S.39, G:A.41
NA.47: 2 residues within 4Å:- Chain H: S.39, K.40
2 PLIP interactions:2 interactions with chain H- Hydrogen bonds: H:K.40
- Water bridges: H:A.41
NA.53: 2 residues within 4Å:- Chain I: S.39, K.40
3 PLIP interactions:3 interactions with chain I- Hydrogen bonds: I:K.40
- Water bridges: I:S.39, I:A.41
NA.59: 2 residues within 4Å:- Chain J: S.39, K.40
3 PLIP interactions:3 interactions with chain J- Hydrogen bonds: J:K.40
- Water bridges: J:S.39, J:A.41
NA.65: 2 residues within 4Å:- Chain K: S.39, K.40
3 PLIP interactions:3 interactions with chain K- Hydrogen bonds: K:K.40
- Water bridges: K:S.39, K:A.41
NA.71: 2 residues within 4Å:- Chain L: S.39, K.40
3 PLIP interactions:3 interactions with chain L- Hydrogen bonds: L:K.40
- Water bridges: L:S.39, L:A.41
- 12 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.6: 9 residues within 4Å:- Chain A: F.169, R.185
- Chain C: R.139, E.140
- Chain E: S.90, G.91, R.122, K.129
- Ligands: 4LS.1
7 PLIP interactions:3 interactions with chain E, 3 interactions with chain C, 1 interactions with chain A- Hydrogen bonds: E:G.91
- Salt bridges: E:R.122, E:K.129, C:R.139, A:R.185
- Water bridges: C:R.139, C:A.141
PO4.12: 9 residues within 4Å:- Chain B: F.169, R.185
- Chain D: R.139, E.140
- Chain G: S.90, G.91, R.122, K.129
- Ligands: 4LS.7
7 PLIP interactions:3 interactions with chain D, 3 interactions with chain G, 1 interactions with chain B- Water bridges: D:R.139, D:A.141
- Salt bridges: D:R.139, G:R.122, G:K.129, B:R.185
- Hydrogen bonds: G:G.91
PO4.18: 9 residues within 4Å:- Chain A: R.139, E.140
- Chain C: F.169, R.185
- Chain H: S.90, G.91, R.122, K.129
- Ligands: 4LS.13
7 PLIP interactions:3 interactions with chain A, 3 interactions with chain H, 1 interactions with chain C- Water bridges: A:R.139, A:A.141
- Salt bridges: A:R.139, H:R.122, H:K.129, C:R.185
- Hydrogen bonds: H:G.91
PO4.24: 9 residues within 4Å:- Chain B: R.139, E.140
- Chain D: F.169, R.185
- Chain F: S.90, G.91, R.122, K.129
- Ligands: 4LS.19
7 PLIP interactions:3 interactions with chain F, 3 interactions with chain B, 1 interactions with chain D- Hydrogen bonds: F:G.91
- Salt bridges: F:R.122, F:K.129, B:R.139, D:R.185
- Water bridges: B:R.139, B:A.141
PO4.30: 9 residues within 4Å:- Chain E: F.169, R.185
- Chain G: R.139, E.140
- Chain I: S.90, G.91, R.122, K.129
- Ligands: 4LS.25
7 PLIP interactions:3 interactions with chain I, 1 interactions with chain E, 3 interactions with chain G- Hydrogen bonds: I:G.91
- Salt bridges: I:R.122, I:K.129, E:R.185, G:R.139
- Water bridges: G:R.139, G:A.141
PO4.36: 9 residues within 4Å:- Chain F: F.169, R.185
- Chain H: R.139, E.140
- Chain K: S.90, G.91, R.122, K.129
- Ligands: 4LS.31
7 PLIP interactions:3 interactions with chain H, 3 interactions with chain K, 1 interactions with chain F- Water bridges: H:R.139, H:A.141
- Salt bridges: H:R.139, K:R.122, K:K.129, F:R.185
- Hydrogen bonds: K:G.91
PO4.42: 9 residues within 4Å:- Chain E: R.139, E.140
- Chain G: F.169, R.185
- Chain L: S.90, G.91, R.122, K.129
- Ligands: 4LS.37
7 PLIP interactions:1 interactions with chain G, 3 interactions with chain L, 3 interactions with chain E- Salt bridges: G:R.185, L:R.122, L:K.129, E:R.139
- Hydrogen bonds: L:G.91
- Water bridges: E:R.139, E:A.141
PO4.48: 9 residues within 4Å:- Chain F: R.139, E.140
- Chain H: F.169, R.185
- Chain J: S.90, G.91, R.122, K.129
- Ligands: 4LS.43
7 PLIP interactions:3 interactions with chain F, 1 interactions with chain H, 3 interactions with chain J- Water bridges: F:R.139, F:A.141
- Salt bridges: F:R.139, H:R.185, J:R.122, J:K.129
- Hydrogen bonds: J:G.91
PO4.54: 9 residues within 4Å:- Chain A: S.90, G.91, R.122, K.129
- Chain I: F.169, R.185
- Chain K: R.139, E.140
- Ligands: 4LS.49
7 PLIP interactions:3 interactions with chain K, 3 interactions with chain A, 1 interactions with chain I- Water bridges: K:R.139, K:A.141
- Salt bridges: K:R.139, A:R.122, A:K.129, I:R.185
- Hydrogen bonds: A:G.91
PO4.60: 9 residues within 4Å:- Chain C: S.90, G.91, R.122, K.129
- Chain J: F.169, R.185
- Chain L: R.139, E.140
- Ligands: 4LS.55
7 PLIP interactions:3 interactions with chain C, 3 interactions with chain L, 1 interactions with chain J- Hydrogen bonds: C:G.91
- Salt bridges: C:R.122, C:K.129, L:R.139, J:R.185
- Water bridges: L:R.139, L:A.141
PO4.66: 9 residues within 4Å:- Chain D: S.90, G.91, R.122, K.129
- Chain I: R.139, E.140
- Chain K: F.169, R.185
- Ligands: 4LS.61
7 PLIP interactions:3 interactions with chain I, 3 interactions with chain D, 1 interactions with chain K- Water bridges: I:R.139, I:A.141
- Salt bridges: I:R.139, D:R.122, D:K.129, K:R.185
- Hydrogen bonds: D:G.91
PO4.72: 9 residues within 4Å:- Chain B: S.90, G.91, R.122, K.129
- Chain J: R.139, E.140
- Chain L: F.169, R.185
- Ligands: 4LS.67
7 PLIP interactions:1 interactions with chain L, 3 interactions with chain J, 3 interactions with chain B- Salt bridges: L:R.185, J:R.139, B:R.122, B:K.129
- Water bridges: J:R.139, J:A.141
- Hydrogen bonds: B:G.91
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- White, M.D. et al., UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis. Nature (2015)
- Release Date
- 2015-06-17
- Peptides
- 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 1.45 Å
- Oligo State
- homo-12-mer
- Ligands
- 12 x 4LS: 1-deoxy-1-[7,8-dimethyl-5-(3-methylbut-2-en-1-yl)-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol(Non-covalent)
- 36 x SCN: THIOCYANATE ION(Non-functional Binders)
- 12 x NA: SODIUM ION(Non-functional Binders)
- 12 x PO4: PHOSPHATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- White, M.D. et al., UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis. Nature (2015)
- Release Date
- 2015-06-17
- Peptides
- UbiX: ABCDEFGHIJKL
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
AE
AF
AG
AH
AI
AJ
AK
AL
A