SMTL ID : 4zag.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-12-mer

Ligands

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

4LR.1: 12 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, R.122, K.129 Ligands: FMN.2 15 PLIP interactions: 5 interactions with chain A, 5 interactions with chain C, 5 interactions with chain E Hydrophobic interactions: A:Y.169, A:W.200, A:W.200, E:A.89 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:A.141, C:A.141 4LR.5: 12 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, R.122, K.129 Ligands: FMN.6 15 PLIP interactions: 5 interactions with chain G, 5 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: G:A.89, B:Y.169, B:W.200, B:W.200 Hydrogen bonds: G:G.91, G:S.92, B:Y.169, D:E.140, D:E.140 Salt bridges: G:R.122, G:K.129, B:R.185, D:R.139 Water bridges: D:A.141, D:A.141 4LR.9: 12 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, R.122, K.129 Ligands: FMN.10 14 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C, 5 interactions with chain H Hydrogen bonds: A:E.140, A:E.140, H:G.91, H:S.92 Water bridges: A:A.141, A:A.141 Salt bridges: A:R.139, C:R.185, H:R.122, H:K.129 Hydrophobic interactions: C:Y.169, C:W.200, C:W.200, H:A.89 4LR.13: 12 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, R.122, K.129 Ligands: FMN.14 14 PLIP interactions: 4 interactions with chain D, 5 interactions with chain F, 5 interactions with chain B Hydrophobic interactions: D:Y.169, D:W.200, D:W.200, F:A.89 Salt bridges: D:R.185, F:R.122, F:K.129, B:R.139 Hydrogen bonds: F:G.91, F:S.92, B:E.140, B:E.140 Water bridges: B:A.141, B:A.141 4LR.17: 12 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, R.122, K.129 Ligands: FMN.18 15 PLIP interactions: 5 interactions with chain G, 5 interactions with chain E, 5 interactions with chain I Hydrogen bonds: G:E.140, G:E.140, E:Y.169, I:G.91, I:S.92 Water bridges: G:A.141, G:A.141 Salt bridges: G:R.139, E:R.185, I:R.122, I:K.129 Hydrophobic interactions: E:Y.169, E:W.200, E:W.200, I:A.89 4LR.21: 12 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, R.122, K.129 Ligands: FMN.22 14 PLIP interactions: 4 interactions with chain F, 5 interactions with chain K, 5 interactions with chain H Hydrophobic interactions: F:Y.169, F:W.200, F:W.200, K:A.89 Salt bridges: F:R.185, K:R.122, K:K.129, H:R.139 Hydrogen bonds: K:G.91, K:S.92, H:E.140, H:E.140 Water bridges: H:A.141, H:A.141 4LR.25: 12 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, R.122, K.129 Ligands: FMN.26 15 PLIP interactions: 5 interactions with chain E, 5 interactions with chain L, 5 interactions with chain G Hydrogen bonds: E:E.140, E:E.140, L:G.91, L:S.92, G:Y.169 Water bridges: E:A.141, E:A.141 Salt bridges: E:R.139, L:R.122, L:K.129, G:R.185 Hydrophobic interactions: L:A.89, G:Y.169, G:W.200, G:W.200 4LR.29: 12 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, R.122, K.129 Ligands: FMN.30 14 PLIP interactions: 4 interactions with chain H, 5 interactions with chain J, 5 interactions with chain F Hydrophobic interactions: H:Y.169, H:W.200, H:W.200, J:A.89 Salt bridges: H:R.185, J:R.122, J:K.129, F:R.139 Hydrogen bonds: J:G.91, J:S.92, F:E.140, F:E.140 Water bridges: F:A.141, F:A.141 4LR.33: 12 residues within 4Å: Chain A: W.84, A.89, S.90, G.91, R.122, K.129 Chain I: Y.169, R.185, W.200 Chain K: R.139, E.140 Ligands: FMN.34 15 PLIP interactions: 5 interactions with chain A, 5 interactions with chain I, 5 interactions with chain K Hydrophobic interactions: A:A.89, I:Y.169, I:W.200, I:W.200 Hydrogen bonds: A:G.91, A:S.92, I:Y.169, K:E.140, K:E.140 Salt bridges: A:R.122, A:K.129, I:R.185, K:R.139 Water bridges: K:A.141, K:A.141 4LR.37: 12 residues within 4Å: Chain C: W.84, A.89, S.90, G.91, R.122, K.129 Chain J: Y.169, R.185, W.200 Chain L: R.139, E.140 Ligands: FMN.38 14 PLIP interactions: 5 interactions with chain L, 4 interactions with chain J, 5 interactions with chain C Hydrogen bonds: L:E.140, L:E.140, C:G.91, C:S.92 Water bridges: L:A.141, L:A.141 Salt bridges: L:R.139, J:R.185, C:R.122, C:K.129 Hydrophobic interactions: J:Y.169, J:W.200, J:W.200, C:A.89 4LR.41: 12 residues within 4Å: Chain D: W.84, A.89, S.90, G.91, R.122, K.129 Chain I: R.139, E.140 Chain K: Y.169, R.185, W.200 Ligands: FMN.42 14 PLIP interactions: 4 interactions with chain K, 5 interactions with chain I, 5 interactions with chain D Hydrophobic interactions: K:Y.169, K:W.200, K:W.200, D:A.89 Salt bridges: K:R.185, I:R.139, D:R.122, D:K.129 Hydrogen bonds: I:E.140, I:E.140, D:G.91, D:S.92 Water bridges: I:A.141, I:A.141 4LR.45: 12 residues within 4Å: Chain B: W.84, A.89, S.90, G.91, R.122, K.129 Chain J: R.139, E.140 Chain L: Y.169, R.185, W.200 Ligands: FMN.46 15 PLIP interactions: 5 interactions with chain L, 5 interactions with chain J, 5 interactions with chain B Hydrophobic interactions: L:Y.169, L:W.200, L:W.200, B:A.89 Hydrogen bonds: L:Y.169, J:E.140, J:E.140, B:G.91, B:S.92 Salt bridges: L:R.185, J:R.139, B:R.122, B:K.129 Water bridges: J:A.141, J:A.141

12 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.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 26 PLIP interactions: 21 interactions with chain C, 5 interactions with chain E Hydrophobic interactions: C:V.45, E:W.84 Hydrogen bonds: 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, E:R.122 Water bridges: C:K.40, C:A.41, C:S.104, C:G.106, C:G.106, C:T.107, C:T.107, C:E.121, C:R.139, E:C.116, E:N.117, E:N.118 FMN.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 26 PLIP interactions: 5 interactions with chain G, 21 interactions with chain D Hydrophobic interactions: G:W.84, D:V.45 Hydrogen bonds: G:R.122, 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 Water bridges: G:C.116, G:N.117, G:N.118, D:K.40, D:A.41, D:S.104, D:G.106, D:G.106, D:T.107, D:T.107, D:E.121, D:R.139 FMN.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: 19 interactions with chain A, 5 interactions with chain H Hydrophobic interactions: A:V.45, H:W.84 Hydrogen bonds: 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, H:R.122 Water bridges: A:K.40, A:A.41, A:S.104, A:G.106, A:G.106, A:N.118, A:R.139, H:C.116, H:N.117, H:N.118 FMN.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: 19 interactions with chain B, 5 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:N.118, B:R.139, F:C.116, F:N.117, F:N.118 FMN.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: 5 interactions with chain I, 19 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, I:N.118, G:K.40, G:A.41, G:S.104, G:G.106, G:G.106, G:E.121, G:R.139 FMN.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 26 PLIP interactions: 21 interactions with chain H, 5 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:T.107, H:N.118, H:R.139, K:C.116, K:N.117, K:N.118 FMN.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: 19 interactions with chain E, 5 interactions with chain L Hydrophobic interactions: E:V.45, L:W.84 Hydrogen bonds: 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, L:R.122 Water bridges: E:K.40, E:A.41, E:S.104, E:G.106, E:G.106, E:E.121, E:R.139, L:C.116, L:N.117, L:N.118 FMN.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 26 PLIP interactions: 21 interactions with chain F, 5 interactions with chain J Hydrophobic interactions: F:V.45, J:W.84 Hydrogen bonds: 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, J:R.122 Water bridges: F:K.40, F:A.41, F:S.104, F:G.106, F:G.106, F:T.107, F:T.107, F:N.118, F:R.139, J:C.116, J:N.117, J:N.118 FMN.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 25 PLIP interactions: 20 interactions with chain K, 5 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:T.107, K:T.107, K:E.121, K:R.139, A:C.116, A:N.117, A:N.118 FMN.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: 5 interactions with chain C, 20 interactions with chain L Hydrophobic interactions: C:W.84, L:V.45 Hydrogen bonds: C:R.122, 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 Water bridges: C:C.116, C:N.117, C:N.118, L:K.40, L:A.41, L:S.104, L:G.106, L:G.106, L:N.118, L:R.139 FMN.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: 20 interactions with chain I, 5 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:N.118, I:R.139, D:C.116, D:N.117, D:N.118 FMN.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 25 PLIP interactions: 5 interactions with chain B, 20 interactions with chain J Hydrophobic interactions: B:W.84, J:V.45 Hydrogen bonds: B:R.122, 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 Water bridges: B:C.116, B:N.117, B:N.118, J:K.40, J:A.41, J:S.104, J:G.106, J:G.106, J:T.107, J:T.107, J:E.121, J:R.139

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

SCN.3: 6 residues within 4Å: Chain A: P.4, P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.7: 6 residues within 4Å: Chain B: P.4, P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.11: 6 residues within 4Å: Chain C: P.4, P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.15: 6 residues within 4Å: Chain D: P.4, P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.19: 6 residues within 4Å: Chain E: P.4, P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.23: 6 residues within 4Å: Chain F: P.4, P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.27: 6 residues within 4Å: Chain G: P.4, P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.31: 6 residues within 4Å: Chain H: P.4, P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.35: 6 residues within 4Å: Chain I: P.4, P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.39: 6 residues within 4Å: Chain J: P.4, P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.43: 6 residues within 4Å: Chain K: P.4, P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.47: 6 residues within 4Å: Chain L: P.4, P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP)

12 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: S.15, V.45, Q.49 Chain C: F.168, Y.169 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.15, H2O.5 K.8: 5 residues within 4Å: Chain B: S.15, V.45, Q.49 Chain D: F.168, Y.169 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.15, H2O.10 K.12: 5 residues within 4Å: Chain A: F.168, Y.169 Chain C: S.15, V.45, Q.49 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.15, H2O.15 K.16: 5 residues within 4Å: Chain B: F.168, Y.169 Chain D: S.15, V.45, Q.49 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.15, H2O.21 K.20: 5 residues within 4Å: Chain E: S.15, V.45, Q.49 Chain G: F.168, Y.169 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:S.15, H2O.26 K.24: 5 residues within 4Å: Chain F: S.15, V.45, Q.49 Chain H: F.168, Y.169 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:S.15, H2O.32 K.28: 5 residues within 4Å: Chain E: F.168, Y.169 Chain G: S.15, V.45, Q.49 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:S.15, H2O.37 K.32: 5 residues within 4Å: Chain F: F.168, Y.169 Chain H: S.15, V.45, Q.49 2 PLIP interactions: 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:S.15, H2O.43 K.36: 5 residues within 4Å: Chain I: S.15, V.45, Q.49 Chain K: F.168, Y.169 2 PLIP interactions: 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:S.15, H2O.48 K.40: 5 residues within 4Å: Chain J: S.15, V.45, Q.49 Chain L: F.168, Y.169 2 PLIP interactions: 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:S.15, H2O.53 K.44: 5 residues within 4Å: Chain I: F.168, Y.169 Chain K: S.15, V.45, Q.49 2 PLIP interactions: 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:S.15, H2O.59 K.48: 5 residues within 4Å: Chain J: F.168, Y.169 Chain L: S.15, V.45, Q.49 2 PLIP interactions: 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:S.15, H2O.64

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

Probable aromatic acid decarboxylase: 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

Probable aromatic acid decarboxylase

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