- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.40 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)
- 48 x SCN: THIOCYANATE ION(Non-functional Binders)
SCN.2: 5 residues within 4Å:- Chain A: P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.3: 4 residues within 4Å:- Chain A: H.170, M.196, L.197, P.198
Ligand excluded by PLIPSCN.4: 3 residues within 4Å:- Chain A: E.5, R.6
- Chain I: R.199
Ligand excluded by PLIPSCN.5: 2 residues within 4Å:- Chain A: Q.59, A.60
Ligand excluded by PLIPSCN.9: 5 residues within 4Å:- Chain B: P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.10: 4 residues within 4Å:- Chain B: H.170, M.196, L.197, P.198
Ligand excluded by PLIPSCN.11: 3 residues within 4Å:- Chain B: E.5, R.6
- Chain L: R.199
Ligand excluded by PLIPSCN.12: 2 residues within 4Å:- Chain B: Q.59, A.60
Ligand excluded by PLIPSCN.16: 5 residues within 4Å:- Chain C: P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.17: 4 residues within 4Å:- Chain C: H.170, M.196, L.197, P.198
Ligand excluded by PLIPSCN.18: 3 residues within 4Å:- Chain C: E.5, R.6
- Chain J: R.199
Ligand excluded by PLIPSCN.19: 2 residues within 4Å:- Chain C: Q.59, A.60
Ligand excluded by PLIPSCN.23: 5 residues within 4Å:- Chain D: P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.24: 4 residues within 4Å:- Chain D: H.170, M.196, L.197, P.198
Ligand excluded by PLIPSCN.25: 3 residues within 4Å:- Chain D: E.5, R.6
- Chain K: R.199
Ligand excluded by PLIPSCN.26: 2 residues within 4Å:- Chain D: Q.59, A.60
Ligand excluded by PLIPSCN.30: 5 residues within 4Å:- Chain E: P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.31: 4 residues within 4Å:- Chain E: H.170, M.196, L.197, P.198
Ligand excluded by PLIPSCN.32: 3 residues within 4Å:- Chain A: R.199
- Chain E: E.5, R.6
Ligand excluded by PLIPSCN.33: 2 residues within 4Å:- Chain E: Q.59, A.60
Ligand excluded by PLIPSCN.37: 5 residues within 4Å:- Chain F: P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.38: 4 residues within 4Å:- Chain F: H.170, M.196, L.197, P.198
Ligand excluded by PLIPSCN.39: 3 residues within 4Å:- Chain D: R.199
- Chain F: E.5, R.6
Ligand excluded by PLIPSCN.40: 2 residues within 4Å:- Chain F: Q.59, A.60
Ligand excluded by PLIPSCN.44: 5 residues within 4Å:- Chain G: P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.45: 4 residues within 4Å:- Chain G: H.170, M.196, L.197, P.198
Ligand excluded by PLIPSCN.46: 3 residues within 4Å:- Chain B: R.199
- Chain G: E.5, R.6
Ligand excluded by PLIPSCN.47: 2 residues within 4Å:- Chain G: Q.59, A.60
Ligand excluded by PLIPSCN.51: 5 residues within 4Å:- Chain H: P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.52: 4 residues within 4Å:- Chain H: H.170, M.196, L.197, P.198
Ligand excluded by PLIPSCN.53: 3 residues within 4Å:- Chain C: R.199
- Chain H: E.5, R.6
Ligand excluded by PLIPSCN.54: 2 residues within 4Å:- Chain H: Q.59, A.60
Ligand excluded by PLIPSCN.58: 5 residues within 4Å:- Chain I: P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.59: 4 residues within 4Å:- Chain I: H.170, M.196, L.197, P.198
Ligand excluded by PLIPSCN.60: 3 residues within 4Å:- Chain E: R.199
- Chain I: E.5, R.6
Ligand excluded by PLIPSCN.61: 2 residues within 4Å:- Chain I: Q.59, A.60
Ligand excluded by PLIPSCN.65: 5 residues within 4Å:- Chain J: P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.66: 4 residues within 4Å:- Chain J: H.170, M.196, L.197, P.198
Ligand excluded by PLIPSCN.67: 3 residues within 4Å:- Chain H: R.199
- Chain J: E.5, R.6
Ligand excluded by PLIPSCN.68: 2 residues within 4Å:- Chain J: Q.59, A.60
Ligand excluded by PLIPSCN.72: 5 residues within 4Å:- Chain K: P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.73: 4 residues within 4Å:- Chain K: H.170, M.196, L.197, P.198
Ligand excluded by PLIPSCN.74: 3 residues within 4Å:- Chain F: R.199
- Chain K: E.5, R.6
Ligand excluded by PLIPSCN.75: 2 residues within 4Å:- Chain K: Q.59, A.60
Ligand excluded by PLIPSCN.79: 5 residues within 4Å:- Chain L: P.95, N.96, A.97, R.132, P.133
Ligand excluded by PLIPSCN.80: 4 residues within 4Å:- Chain L: H.170, M.196, L.197, P.198
Ligand excluded by PLIPSCN.81: 3 residues within 4Å:- Chain G: R.199
- Chain L: E.5, R.6
Ligand excluded by PLIPSCN.82: 2 residues within 4Å:- Chain L: Q.59, A.60
Ligand excluded by PLIP- 12 x NA: SODIUM ION(Non-functional Binders)
NA.6: 3 residues within 4Å:- Chain A: E.121
- Chain H: A.115, N.117
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain H- Hydrogen bonds: A:E.121
- Water bridges: H:N.117
NA.13: 3 residues within 4Å:- Chain B: E.121
- Chain F: A.115, N.117
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain F- Hydrogen bonds: B:E.121
- Water bridges: F:N.117
NA.20: 3 residues within 4Å:- Chain C: E.121
- Chain E: A.115, N.117
2 PLIP interactions:1 interactions with chain E, 1 interactions with chain C- Hydrogen bonds: E:N.117, C:E.121
NA.27: 3 residues within 4Å:- Chain D: E.121
- Chain G: A.115, N.117
2 PLIP interactions:1 interactions with chain D, 1 interactions with chain G- Hydrogen bonds: D:E.121, G:N.117
NA.34: 3 residues within 4Å:- Chain E: E.121
- Chain L: A.115, N.117
2 PLIP interactions:1 interactions with chain L, 1 interactions with chain E- Water bridges: L:N.117
- Hydrogen bonds: E:E.121
NA.41: 3 residues within 4Å:- Chain F: E.121
- Chain J: A.115, N.117
2 PLIP interactions:1 interactions with chain F, 1 interactions with chain J- Hydrogen bonds: F:E.121, J:N.117
NA.48: 3 residues within 4Å:- Chain G: E.121
- Chain I: A.115, N.117
2 PLIP interactions:1 interactions with chain I, 1 interactions with chain G- Water bridges: I:N.117
- Hydrogen bonds: G:E.121
NA.55: 3 residues within 4Å:- Chain H: E.121
- Chain K: A.115, N.117
2 PLIP interactions:1 interactions with chain K, 1 interactions with chain H- Hydrogen bonds: K:N.117, H:E.121
NA.62: 3 residues within 4Å:- Chain D: A.115, N.117
- Chain I: E.121
2 PLIP interactions:1 interactions with chain I, 1 interactions with chain D- Hydrogen bonds: I:E.121
- Water bridges: D:N.117
NA.69: 3 residues within 4Å:- Chain B: A.115, N.117
- Chain J: E.121
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain J- Hydrogen bonds: B:N.117, J:E.121
NA.76: 3 residues within 4Å:- Chain A: A.115, N.117
- Chain K: E.121
2 PLIP interactions:1 interactions with chain K, 1 interactions with chain A- Hydrogen bonds: K:E.121, A:N.117
NA.83: 3 residues within 4Å:- Chain C: A.115, N.117
- Chain L: E.121
2 PLIP interactions:1 interactions with chain L, 1 interactions with chain C- Hydrogen bonds: L:E.121
- Water bridges: C:N.117
- 12 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.7: 10 residues within 4Å:- Chain A: Y.169, R.185
- Chain C: R.139, E.140
- Chain E: S.90, G.91, S.92, R.122, K.129
- Ligands: 4LS.1
11 PLIP interactions:2 interactions with chain A, 5 interactions with chain C, 4 interactions with chain E- Hydrogen bonds: A:Y.169, C:E.140, C:E.140, E:G.91, E:S.92
- Salt bridges: A:R.185, C:R.139, E:R.122, E:K.129
- Water bridges: C:R.139, C:A.141
PO4.14: 10 residues within 4Å:- Chain B: Y.169, R.185
- Chain D: R.139, E.140
- Chain G: S.90, G.91, S.92, R.122, K.129
- Ligands: 4LS.8
11 PLIP interactions:4 interactions with chain G, 5 interactions with chain D, 2 interactions with chain B- Hydrogen bonds: G:G.91, G:S.92, D:E.140, D:E.140, B:Y.169
- Salt bridges: G:R.122, G:K.129, D:R.139, B:R.185
- Water bridges: D:R.139, D:A.141
PO4.21: 10 residues within 4Å:- Chain A: R.139, E.140
- Chain C: Y.169, R.185
- Chain H: S.90, G.91, S.92, R.122, K.129
- Ligands: 4LS.15
10 PLIP interactions:5 interactions with chain A, 4 interactions with chain H, 1 interactions with chain C- Hydrogen bonds: A:E.140, A:E.140, H:G.91, H:S.92
- Water bridges: A:R.139, A:A.141
- Salt bridges: A:R.139, H:R.122, H:K.129, C:R.185
PO4.28: 10 residues within 4Å:- Chain B: R.139, E.140
- Chain D: Y.169, R.185
- Chain F: S.90, G.91, S.92, R.122, K.129
- Ligands: 4LS.22
10 PLIP interactions:4 interactions with chain F, 5 interactions with chain B, 1 interactions with chain D- Hydrogen bonds: F:G.91, F:S.92, B:E.140, B:E.140
- Salt bridges: F:R.122, F:K.129, B:R.139, D:R.185
- Water bridges: B:R.139, B:A.141
PO4.35: 10 residues within 4Å:- Chain E: Y.169, R.185
- Chain G: R.139, E.140
- Chain I: S.90, G.91, S.92, R.122, K.129
- Ligands: 4LS.29
11 PLIP interactions:2 interactions with chain E, 5 interactions with chain G, 4 interactions with chain I- Hydrogen bonds: E:Y.169, G:E.140, G:E.140, I:G.91, I:S.92
- Salt bridges: E:R.185, G:R.139, I:R.122, I:K.129
- Water bridges: G:R.139, G:A.141
PO4.42: 10 residues within 4Å:- Chain F: Y.169, R.185
- Chain H: R.139, E.140
- Chain K: S.90, G.91, S.92, R.122, K.129
- Ligands: 4LS.36
10 PLIP interactions:4 interactions with chain K, 5 interactions with chain H, 1 interactions with chain F- Hydrogen bonds: K:G.91, K:S.92, H:E.140, H:E.140
- Salt bridges: K:R.122, K:K.129, H:R.139, F:R.185
- Water bridges: H:R.139, H:A.141
PO4.49: 10 residues within 4Å:- Chain E: R.139, E.140
- Chain G: Y.169, R.185
- Chain L: S.90, G.91, S.92, R.122, K.129
- Ligands: 4LS.43
11 PLIP interactions:2 interactions with chain G, 4 interactions with chain L, 5 interactions with chain E- Hydrogen bonds: G:Y.169, L:G.91, L:S.92, E:E.140, E:E.140
- Salt bridges: G:R.185, L:R.122, L:K.129, E:R.139
- Water bridges: E:R.139, E:A.141
PO4.56: 10 residues within 4Å:- Chain F: R.139, E.140
- Chain H: Y.169, R.185
- Chain J: S.90, G.91, S.92, R.122, K.129
- Ligands: 4LS.50
10 PLIP interactions:5 interactions with chain F, 1 interactions with chain H, 4 interactions with chain J- Hydrogen bonds: F:E.140, F:E.140, J:G.91, J:S.92
- Water bridges: F:R.139, F:A.141
- Salt bridges: F:R.139, H:R.185, J:R.122, J:K.129
PO4.63: 10 residues within 4Å:- Chain A: S.90, G.91, S.92, R.122, K.129
- Chain I: Y.169, R.185
- Chain K: R.139, E.140
- Ligands: 4LS.57
11 PLIP interactions:2 interactions with chain I, 4 interactions with chain A, 5 interactions with chain K- Hydrogen bonds: I:Y.169, A:G.91, A:S.92, K:E.140, K:E.140
- Salt bridges: I:R.185, A:R.122, A:K.129, K:R.139
- Water bridges: K:R.139, K:A.141
PO4.70: 10 residues within 4Å:- Chain C: S.90, G.91, S.92, R.122, K.129
- Chain J: Y.169, R.185
- Chain L: R.139, E.140
- Ligands: 4LS.64
10 PLIP interactions:5 interactions with chain L, 4 interactions with chain C, 1 interactions with chain J- Hydrogen bonds: L:E.140, L:E.140, C:G.91, C:S.92
- Water bridges: L:R.139, L:A.141
- Salt bridges: L:R.139, C:R.122, C:K.129, J:R.185
PO4.77: 10 residues within 4Å:- Chain D: S.90, G.91, S.92, R.122, K.129
- Chain I: R.139, E.140
- Chain K: Y.169, R.185
- Ligands: 4LS.71
10 PLIP interactions:5 interactions with chain I, 4 interactions with chain D, 1 interactions with chain K- Hydrogen bonds: I:E.140, I:E.140, D:G.91, D:S.92
- Water bridges: I:R.139, I:A.141
- Salt bridges: I:R.139, D:R.122, D:K.129, K:R.185
PO4.84: 10 residues within 4Å:- Chain B: S.90, G.91, S.92, R.122, K.129
- Chain J: R.139, E.140
- Chain L: Y.169, R.185
- Ligands: 4LS.78
11 PLIP interactions:2 interactions with chain L, 4 interactions with chain B, 5 interactions with chain J- Hydrogen bonds: L:Y.169, B:G.91, B:S.92, J:E.140, J:E.140
- Salt bridges: L:R.185, B:R.122, B:K.129, J:R.139
- Water bridges: J:R.139, J:A.141
- 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 1.40 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)
- 48 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