SMTL ID : 4zal.1

Structure of UbiX E49Q mutant in complex with reduced FMN and dimethylallyl monophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-12-mer

Ligands

12 x 4LR: Dimethylallyl monophosphate(Non-covalent)

4LR.1: 13 residues within 4Å: Chain A: Y.169, R.185, W.200 Chain C: R.139, E.140 Chain E: W.84, A.89, S.90, G.91, S.92, R.122, K.129 Ligands: FNR.2 15 PLIP interactions: 7 interactions with chain A, 5 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: A:Y.169, A:W.200, A:W.200, E:A.89 Hydrogen bonds: A:Y.169, E:G.91, E:S.92, C:E.140, C:E.140 Water bridges: A:R.185, A:R.185 Salt bridges: A:R.185, E:R.122, E:K.129, C:R.139 4LR.5: 13 residues within 4Å: Chain B: Y.169, R.185, W.200 Chain D: R.139, E.140 Chain G: W.84, A.89, S.90, G.91, S.92, R.122, K.129 Ligands: FNR.6 15 PLIP interactions: 7 interactions with chain B, 3 interactions with chain D, 5 interactions with chain G Hydrophobic interactions: B:Y.169, B:W.200, B:W.200, G:A.89 Hydrogen bonds: B:Y.169, D:E.140, D:E.140, G:G.91, G:S.92 Water bridges: B:R.185, B:R.185 Salt bridges: B:R.185, D:R.139, G:R.122, G:K.129 4LR.9: 13 residues within 4Å: Chain A: R.139, E.140 Chain C: Y.169, R.185, W.200 Chain H: W.84, A.89, S.90, G.91, S.92, R.122, K.129 Ligands: FNR.10 14 PLIP interactions: 5 interactions with chain H, 4 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: H:A.89, C:Y.169, C:W.200, C:W.200 Hydrogen bonds: H:G.91, H:S.92, A:E.140, A:E.140 Salt bridges: H:R.122, H:K.129, A:R.139, C:R.185 Water bridges: A:A.141, C:R.185 4LR.13: 13 residues within 4Å: Chain B: R.139, E.140 Chain D: Y.169, R.185, W.200 Chain F: W.84, A.89, S.90, G.91, S.92, R.122, K.129 Ligands: FNR.14 14 PLIP interactions: 4 interactions with chain B, 5 interactions with chain F, 5 interactions with chain D Hydrogen bonds: B:E.140, B:E.140, F:G.91, F:S.92 Water bridges: B:A.141, D:R.185 Salt bridges: B:R.139, F:R.122, F:K.129, D:R.185 Hydrophobic interactions: F:A.89, D:Y.169, D:W.200, D:W.200 4LR.17: 13 residues within 4Å: Chain E: Y.169, R.185, W.200 Chain G: R.139, E.140 Chain I: W.84, A.89, S.90, G.91, S.92, R.122, K.129 Ligands: FNR.18 15 PLIP interactions: 5 interactions with chain I, 6 interactions with chain E, 4 interactions with chain G Hydrophobic interactions: I:A.89, E:Y.169, E:W.200, E:W.200 Hydrogen bonds: I:G.91, I:S.92, E:Y.169, G:E.140, G:E.140 Salt bridges: I:R.122, I:K.129, E:R.185, G:R.139 Water bridges: E:R.185, G:A.141 4LR.21: 13 residues within 4Å: Chain F: Y.169, R.185, W.200 Chain H: R.139, E.140 Chain K: W.84, A.89, S.90, G.91, S.92, R.122, K.129 Ligands: FNR.22 14 PLIP interactions: 5 interactions with chain K, 6 interactions with chain F, 3 interactions with chain H Hydrophobic interactions: K:A.89, F:Y.169, F:W.200, F:W.200 Hydrogen bonds: K:G.91, K:S.92, H:E.140, H:E.140 Salt bridges: K:R.122, K:K.129, F:R.185, H:R.139 Water bridges: F:R.185, F:R.185 4LR.25: 13 residues within 4Å: Chain E: R.139, E.140 Chain G: Y.169, R.185, W.200 Chain L: W.84, A.89, S.90, G.91, S.92, R.122, K.129 Ligands: FNR.26 15 PLIP interactions: 5 interactions with chain L, 6 interactions with chain G, 4 interactions with chain E Hydrophobic interactions: L:A.89, G:Y.169, G:W.200, G:W.200 Hydrogen bonds: L:G.91, L:S.92, G:Y.169, E:E.140, E:E.140 Salt bridges: L:R.122, L:K.129, G:R.185, E:R.139 Water bridges: G:R.185, E:A.141 4LR.29: 13 residues within 4Å: Chain F: R.139, E.140 Chain H: Y.169, R.185, W.200 Chain J: W.84, A.89, S.90, G.91, S.92, R.122, K.129 Ligands: FNR.30 14 PLIP interactions: 3 interactions with chain F, 6 interactions with chain H, 5 interactions with chain J Hydrogen bonds: F:E.140, F:E.140, J:G.91, J:S.92 Salt bridges: F:R.139, H:R.185, J:R.122, J:K.129 Hydrophobic interactions: H:Y.169, H:W.200, H:W.200, J:A.89 Water bridges: H:R.185, H:R.185 4LR.33: 13 residues within 4Å: Chain A: W.84, A.89, S.90, G.91, S.92, R.122, K.129 Chain I: Y.169, R.185, W.200 Chain K: R.139, E.140 Ligands: FNR.34 15 PLIP interactions: 5 interactions with chain A, 3 interactions with chain K, 7 interactions with chain I Hydrophobic interactions: A:A.89, I:Y.169, I:W.200, I:W.200 Hydrogen bonds: A:G.91, A:S.92, K:E.140, K:E.140, I:Y.169 Salt bridges: A:R.122, A:K.129, K:R.139, I:R.185 Water bridges: I:R.185, I:R.185 4LR.37: 13 residues within 4Å: Chain C: W.84, A.89, S.90, G.91, S.92, R.122, K.129 Chain J: Y.169, R.185, W.200 Chain L: R.139, E.140 Ligands: FNR.38 14 PLIP interactions: 5 interactions with chain C, 5 interactions with chain J, 4 interactions with chain L Hydrophobic interactions: C:A.89, J:Y.169, J:W.200, J:W.200 Hydrogen bonds: C:G.91, C:S.92, L:E.140, L:E.140 Salt bridges: C:R.122, C:K.129, J:R.185, L:R.139 Water bridges: J:R.185, L:A.141 4LR.41: 13 residues within 4Å: Chain D: W.84, A.89, S.90, G.91, S.92, R.122, K.129 Chain I: R.139, E.140 Chain K: Y.169, R.185, W.200 Ligands: FNR.42 14 PLIP interactions: 5 interactions with chain D, 5 interactions with chain K, 4 interactions with chain I Hydrophobic interactions: D:A.89, K:Y.169, K:W.200, K:W.200 Hydrogen bonds: D:G.91, D:S.92, I:E.140, I:E.140 Salt bridges: D:R.122, D:K.129, K:R.185, I:R.139 Water bridges: K:R.185, I:A.141 4LR.45: 13 residues within 4Å: Chain B: W.84, A.89, S.90, G.91, S.92, R.122, K.129 Chain J: R.139, E.140 Chain L: Y.169, R.185, W.200 Ligands: FNR.46 15 PLIP interactions: 3 interactions with chain J, 7 interactions with chain L, 5 interactions with chain B Hydrogen bonds: J:E.140, J:E.140, L:Y.169, B:G.91, B:S.92 Salt bridges: J:R.139, L:R.185, B:R.122, B:K.129 Hydrophobic interactions: L:Y.169, L:W.200, L:W.200, B:A.89 Water bridges: L:R.185, L:R.185

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: 17 residues within 4Å: Chain C: T.12, G.13, A.14, S.15, S.39, A.41, V.45, Q.49, S.104, T.105, T.107, R.139, E.140 Chain E: W.84, C.116, R.122 Ligands: 4LR.1 24 PLIP interactions: 4 interactions with chain E, 20 interactions with chain C Hydrophobic interactions: E:W.84, C:V.45 Hydrogen bonds: E:R.122, C:G.13, C:G.13, C:S.15, C:S.39, C:S.39, C:S.104, C:T.105, C:T.107, C:R.139, C:R.139, C:E.140 Water bridges: E:C.116, E:N.117, C:K.40, C:A.41, C:S.104, C:G.106, C:G.106, C:E.121, C:E.121, C:R.139 FNR.6: 17 residues within 4Å: Chain D: T.12, G.13, A.14, S.15, S.39, A.41, V.45, Q.49, S.104, T.105, T.107, R.139, E.140 Chain G: W.84, C.116, R.122 Ligands: 4LR.5 24 PLIP interactions: 20 interactions with chain D, 4 interactions with chain G Hydrophobic interactions: D:V.45, G:W.84 Hydrogen bonds: D:G.13, D:G.13, D:S.15, D:S.39, D:S.39, D:S.104, D:T.105, D:T.107, D:R.139, D:R.139, D:E.140, G:R.122 Water bridges: D:K.40, D:A.41, D:S.104, D:G.106, D:G.106, D:E.121, D:E.121, D:R.139, G:C.116, G:N.117 FNR.10: 17 residues within 4Å: Chain A: T.12, G.13, A.14, S.15, S.39, A.41, V.45, Q.49, S.104, T.105, T.107, R.139, E.140 Chain H: W.84, C.116, R.122 Ligands: 4LR.9 24 PLIP interactions: 4 interactions with chain H, 20 interactions with chain A Hydrophobic interactions: H:W.84, A:V.45 Hydrogen bonds: H:R.122, A:G.13, A:G.13, A:S.15, A:S.39, A:S.39, A:S.104, A:T.105, A:T.107, A:T.107, A:R.139, A:R.139 Water bridges: H:C.116, H:N.117, A:K.40, A:A.41, A:S.104, A:G.106, A:G.106, A:T.107, A:N.118, A:R.139 FNR.14: 17 residues within 4Å: Chain B: T.12, G.13, A.14, S.15, S.39, A.41, V.45, Q.49, S.104, T.105, T.107, R.139, E.140 Chain F: W.84, C.116, R.122 Ligands: 4LR.13 24 PLIP interactions: 20 interactions with chain B, 4 interactions with chain F Hydrophobic interactions: B:V.45, F:W.84 Hydrogen bonds: B:G.13, B:G.13, B:S.15, B:S.39, B:S.39, B:S.104, B:T.105, B:T.107, B:T.107, B:R.139, B:R.139, F:R.122 Water bridges: B:K.40, B:A.41, B:S.104, B:G.106, B:G.106, B:T.107, B:N.118, B:R.139, F:C.116, F:N.117 FNR.18: 17 residues within 4Å: Chain G: T.12, G.13, A.14, S.15, S.39, A.41, V.45, Q.49, S.104, T.105, T.107, R.139, E.140 Chain I: W.84, C.116, R.122 Ligands: 4LR.17 24 PLIP interactions: 4 interactions with chain I, 20 interactions with chain G Hydrophobic interactions: I:W.84, G:V.45 Hydrogen bonds: I:R.122, G:G.13, G:G.13, G:S.15, G:S.39, G:S.39, G:S.104, G:T.105, G:T.107, G:T.107, G:R.139, G:R.139 Water bridges: I:C.116, I:N.117, G:K.40, G:A.41, G:S.104, G:G.106, G:G.106, G:E.121, G:E.121, G:R.139 FNR.22: 17 residues within 4Å: Chain H: T.12, G.13, A.14, S.15, S.39, A.41, V.45, Q.49, S.104, T.105, T.107, R.139, E.140 Chain K: W.84, C.116, R.122 Ligands: 4LR.21 24 PLIP interactions: 20 interactions with chain H, 4 interactions with chain K Hydrophobic interactions: H:V.45, K:W.84 Hydrogen bonds: H:G.13, H:G.13, H:S.15, H:S.39, H:S.39, H:S.104, H:T.105, H:T.107, H:R.139, H:R.139, H:E.140, K:R.122 Water bridges: H:K.40, H:A.41, H:S.104, H:G.106, H:G.106, H:T.107, H:N.118, H:R.139, K:C.116, K:N.117 FNR.26: 17 residues within 4Å: Chain E: T.12, G.13, A.14, S.15, S.39, A.41, V.45, Q.49, S.104, T.105, T.107, R.139, E.140 Chain L: W.84, C.116, R.122 Ligands: 4LR.25 24 PLIP interactions: 4 interactions with chain L, 20 interactions with chain E Hydrophobic interactions: L:W.84, E:V.45 Hydrogen bonds: L:R.122, E:G.13, E:G.13, E:S.15, E:S.39, E:S.39, E:S.104, E:T.105, E:T.107, E:T.107, E:R.139, E:R.139 Water bridges: L:C.116, L:N.117, E:K.40, E:A.41, E:S.104, E:G.106, E:G.106, E:E.121, E:E.121, E:R.139 FNR.30: 17 residues within 4Å: Chain F: T.12, G.13, A.14, S.15, S.39, A.41, V.45, Q.49, S.104, T.105, T.107, R.139, E.140 Chain J: W.84, C.116, R.122 Ligands: 4LR.29 24 PLIP interactions: 4 interactions with chain J, 20 interactions with chain F Hydrophobic interactions: J:W.84, F:V.45 Hydrogen bonds: J:R.122, F:G.13, F:G.13, F:S.15, F:S.39, F:S.39, F:S.104, F:T.105, F:T.107, F:R.139, F:R.139, F:E.140 Water bridges: J:C.116, J:N.117, F:K.40, F:A.41, F:S.104, F:G.106, F:G.106, F:T.107, F:N.118, F:R.139 FNR.34: 17 residues within 4Å: Chain A: W.84, C.116, R.122 Chain K: T.12, G.13, A.14, S.15, S.39, A.41, V.45, Q.49, S.104, T.105, T.107, R.139, E.140 Ligands: 4LR.33 23 PLIP interactions: 19 interactions with chain K, 4 interactions with chain A Hydrophobic interactions: K:V.45, A:W.84 Hydrogen bonds: K:G.13, K:G.13, K:S.15, K:S.39, K:S.39, K:S.104, K:T.105, K:T.107, K:R.139, K:R.139, A:R.122 Water bridges: K:K.40, K:A.41, K:S.104, K:G.106, K:G.106, K:E.121, K:E.121, K:R.139, A:C.116, A:N.117 FNR.38: 17 residues within 4Å: Chain C: W.84, C.116, R.122 Chain L: T.12, G.13, A.14, S.15, S.39, A.41, V.45, Q.49, S.104, T.105, T.107, R.139, E.140 Ligands: 4LR.37 25 PLIP interactions: 21 interactions with chain L, 4 interactions with chain C Hydrophobic interactions: L:V.45, C:W.84 Hydrogen bonds: L:G.13, L:G.13, L:S.15, L:S.39, L:S.39, L:S.104, L:T.105, L:T.107, L:T.107, L:R.139, L:R.139, L:E.140, C:R.122 Water bridges: L:K.40, L:A.41, L:S.104, L:G.106, L:G.106, L:T.107, L:N.118, L:R.139, C:C.116, C:N.117 FNR.42: 17 residues within 4Å: Chain D: W.84, C.116, R.122 Chain I: T.12, G.13, A.14, S.15, S.39, A.41, V.45, Q.49, S.104, T.105, T.107, R.139, E.140 Ligands: 4LR.41 25 PLIP interactions: 21 interactions with chain I, 4 interactions with chain D Hydrophobic interactions: I:V.45, D:W.84 Hydrogen bonds: I:G.13, I:G.13, I:S.15, I:S.39, I:S.39, I:S.104, I:T.105, I:T.107, I:T.107, I:R.139, I:R.139, I:E.140, D:R.122 Water bridges: I:K.40, I:A.41, I:S.104, I:G.106, I:G.106, I:T.107, I:N.118, I:R.139, D:C.116, D:N.117 FNR.46: 17 residues within 4Å: Chain B: W.84, C.116, R.122 Chain J: T.12, G.13, A.14, S.15, S.39, A.41, V.45, Q.49, S.104, T.105, T.107, R.139, E.140 Ligands: 4LR.45 23 PLIP interactions: 19 interactions with chain J, 4 interactions with chain B Hydrophobic interactions: J:V.45, B:W.84 Hydrogen bonds: J:G.13, J:G.13, J:S.15, J:S.39, J:S.39, J:S.104, J:T.105, J:T.107, J:R.139, J:R.139, B:R.122 Water bridges: J:K.40, J:A.41, J:S.104, J:G.106, J:G.106, J:E.121, J:E.121, J:R.139, B:C.116, B:N.117

24 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.3: 3 residues within 4Å: Chain A: E.31, E.33, Q.75 Ligand excluded by PLIP SCN.4: 2 residues within 4Å: Chain A: R.131, R.132 Ligand excluded by PLIP SCN.7: 3 residues within 4Å: Chain B: E.31, E.33, Q.75 Ligand excluded by PLIP SCN.8: 2 residues within 4Å: Chain B: R.131, R.132 Ligand excluded by PLIP SCN.11: 3 residues within 4Å: Chain C: E.31, E.33, Q.75 Ligand excluded by PLIP SCN.12: 2 residues within 4Å: Chain C: R.131, R.132 Ligand excluded by PLIP SCN.15: 3 residues within 4Å: Chain D: E.31, E.33, Q.75 Ligand excluded by PLIP SCN.16: 2 residues within 4Å: Chain D: R.131, R.132 Ligand excluded by PLIP SCN.19: 3 residues within 4Å: Chain E: E.31, E.33, Q.75 Ligand excluded by PLIP SCN.20: 2 residues within 4Å: Chain E: R.131, R.132 Ligand excluded by PLIP SCN.23: 3 residues within 4Å: Chain F: E.31, E.33, Q.75 Ligand excluded by PLIP SCN.24: 2 residues within 4Å: Chain F: R.131, R.132 Ligand excluded by PLIP SCN.27: 3 residues within 4Å: Chain G: E.31, E.33, Q.75 Ligand excluded by PLIP SCN.28: 2 residues within 4Å: Chain G: R.131, R.132 Ligand excluded by PLIP SCN.31: 3 residues within 4Å: Chain H: E.31, E.33, Q.75 Ligand excluded by PLIP SCN.32: 2 residues within 4Å: Chain H: R.131, R.132 Ligand excluded by PLIP SCN.35: 3 residues within 4Å: Chain I: E.31, E.33, Q.75 Ligand excluded by PLIP SCN.36: 2 residues within 4Å: Chain I: R.131, R.132 Ligand excluded by PLIP SCN.39: 3 residues within 4Å: Chain J: E.31, E.33, Q.75 Ligand excluded by PLIP SCN.40: 2 residues within 4Å: Chain J: R.131, R.132 Ligand excluded by PLIP SCN.43: 3 residues within 4Å: Chain K: E.31, E.33, Q.75 Ligand excluded by PLIP SCN.44: 2 residues within 4Å: Chain K: R.131, R.132 Ligand excluded by PLIP SCN.47: 3 residues within 4Å: Chain L: E.31, E.33, Q.75 Ligand excluded by PLIP SCN.48: 2 residues within 4Å: Chain L: R.131, R.132 Ligand excluded by PLIP

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
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

I
A

J
A

K
A

L
A

UbiX

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