SMTL ID : 4zaw.1

Structure of UbiX in complex with reduced prenylated FMN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-12-mer

Ligands

12 x 4LU: 1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-yl)-D-ribitol(Non-covalent)

4LU.1: 19 residues within 4Å: Chain A: Y.169, W.200 Chain C: T.12, G.13, A.14, S.15, S.39, A.41, V.45, E.49, S.104, T.105, T.107, R.139, E.140 Chain E: W.84, C.116, R.122 Ligands: PO4.4 23 PLIP interactions: 1 interactions with chain A, 19 interactions with chain C, 3 interactions with chain E Hydrophobic interactions: A:W.200, C:V.45, E:W.84 Hydrogen bonds: C:G.13, C:G.13, C:S.15, C:S.39, C:S.104, C:T.105, C:T.107, C:R.139, C:R.139, C:E.140, E:R.122, E:R.122 Water bridges: C:K.40, C:A.41, C:G.106, C:N.118, C:E.121, C:E.121, C:E.121, C:R.139 4LU.5: 19 residues within 4Å: Chain B: Y.169, W.200 Chain D: T.12, G.13, A.14, S.15, S.39, A.41, V.45, E.49, S.104, T.105, T.107, R.139, E.140 Chain G: W.84, C.116, R.122 Ligands: PO4.8 23 PLIP interactions: 19 interactions with chain D, 3 interactions with chain G, 1 interactions with chain B Hydrophobic interactions: D:V.45, G:W.84, B:W.200 Hydrogen bonds: D:G.13, D:G.13, D:S.15, D:S.39, D:S.104, D:T.105, D:T.107, D:R.139, D:R.139, D:E.140, G:R.122, G:R.122 Water bridges: D:K.40, D:A.41, D:G.106, D:N.118, D:E.121, D:E.121, D:E.121, D:R.139 4LU.9: 19 residues within 4Å: Chain A: T.12, G.13, A.14, S.15, S.39, A.41, V.45, E.49, S.104, T.105, T.107, R.139, E.140 Chain C: Y.169, W.200 Chain H: W.84, C.116, R.122 Ligands: PO4.12 22 PLIP interactions: 18 interactions with chain A, 1 interactions with chain C, 3 interactions with chain H Hydrophobic interactions: A:V.45, C:W.200, H:W.84 Hydrogen bonds: A:G.13, A:G.13, A:S.15, A:S.39, A:S.104, A:T.105, A:T.107, A:T.107, A:R.139, A:R.139, H:R.122, H:R.122 Water bridges: A:K.40, A:A.41, A:G.106, A:T.107, A:N.118, A:E.121, A:R.139 4LU.13: 19 residues within 4Å: Chain B: T.12, G.13, A.14, S.15, S.39, A.41, V.45, E.49, S.104, T.105, T.107, R.139, E.140 Chain D: Y.169, W.200 Chain F: W.84, C.116, R.122 Ligands: PO4.16 22 PLIP interactions: 1 interactions with chain D, 18 interactions with chain B, 3 interactions with chain F Hydrophobic interactions: D:W.200, B:V.45, F:W.84 Hydrogen bonds: B:G.13, B:G.13, B:S.15, B:S.39, B:S.104, B:T.105, B:T.107, B:T.107, B:R.139, B:R.139, F:R.122, F:R.122 Water bridges: B:K.40, B:A.41, B:G.106, B:T.107, B:N.118, B:E.121, B:R.139 4LU.17: 19 residues within 4Å: Chain E: Y.169, W.200 Chain G: T.12, G.13, A.14, S.15, S.39, A.41, V.45, E.49, S.104, T.105, T.107, R.139, E.140 Chain I: W.84, C.116, R.122 Ligands: PO4.20 23 PLIP interactions: 19 interactions with chain G, 3 interactions with chain I, 1 interactions with chain E Hydrophobic interactions: G:V.45, I:W.84, E:W.200 Hydrogen bonds: G:G.13, G:G.13, G:S.15, G:S.39, G:S.104, G:T.105, G:T.107, G:T.107, G:R.139, G:R.139, I:R.122, I:R.122 Water bridges: G:K.40, G:A.41, G:G.106, G:N.118, G:E.121, G:E.121, G:E.121, G:R.139 4LU.21: 19 residues within 4Å: Chain F: Y.169, W.200 Chain H: T.12, G.13, A.14, S.15, S.39, A.41, V.45, E.49, S.104, T.105, T.107, R.139, E.140 Chain K: W.84, C.116, R.122 Ligands: PO4.24 22 PLIP interactions: 18 interactions with chain H, 3 interactions with chain K, 1 interactions with chain F Hydrophobic interactions: H:V.45, K:W.84, F:W.200 Hydrogen bonds: H:G.13, H:G.13, H:S.15, H:S.39, H:S.104, H:T.105, H:T.107, H:R.139, H:R.139, H:E.140, K:R.122, K:R.122 Water bridges: H:K.40, H:A.41, H:G.106, H:T.107, H:N.118, H:E.121, H:R.139 4LU.25: 19 residues within 4Å: Chain E: T.12, G.13, A.14, S.15, S.39, A.41, V.45, E.49, S.104, T.105, T.107, R.139, E.140 Chain G: Y.169, W.200 Chain L: W.84, C.116, R.122 Ligands: PO4.28 23 PLIP interactions: 3 interactions with chain L, 19 interactions with chain E, 1 interactions with chain G Hydrophobic interactions: L:W.84, E:V.45, G:W.200 Hydrogen bonds: L:R.122, L:R.122, E:G.13, E:G.13, E:S.15, E:S.39, E:S.104, E:T.105, E:T.107, E:T.107, E:R.139, E:R.139 Water bridges: E:K.40, E:A.41, E:G.106, E:N.118, E:E.121, E:E.121, E:E.121, E:R.139 4LU.29: 19 residues within 4Å: Chain F: T.12, G.13, A.14, S.15, S.39, A.41, V.45, E.49, S.104, T.105, T.107, R.139, E.140 Chain H: Y.169, W.200 Chain J: W.84, C.116, R.122 Ligands: PO4.32 22 PLIP interactions: 18 interactions with chain F, 1 interactions with chain H, 3 interactions with chain J Hydrophobic interactions: F:V.45, H:W.200, J:W.84 Hydrogen bonds: F:G.13, F:G.13, F:S.15, F:S.39, F:S.104, F:T.105, F:T.107, F:R.139, F:R.139, F:E.140, J:R.122, J:R.122 Water bridges: F:K.40, F:A.41, F:G.106, F:T.107, F:N.118, F:E.121, F:R.139 4LU.33: 19 residues within 4Å: Chain A: W.84, C.116, R.122 Chain I: Y.169, W.200 Chain K: T.12, G.13, A.14, S.15, S.39, A.41, V.45, E.49, S.104, T.105, T.107, R.139, E.140 Ligands: PO4.36 22 PLIP interactions: 18 interactions with chain K, 1 interactions with chain I, 3 interactions with chain A Hydrophobic interactions: K:V.45, I:W.200, A:W.84 Hydrogen bonds: K:G.13, K:G.13, K:S.15, K:S.39, K:S.104, K:T.105, K:T.107, K:R.139, K:R.139, A:R.122, A:R.122 Water bridges: K:K.40, K:A.41, K:G.106, K:N.118, K:E.121, K:E.121, K:E.121, K:R.139 4LU.37: 19 residues within 4Å: Chain C: W.84, C.116, R.122 Chain J: Y.169, W.200 Chain L: T.12, G.13, A.14, S.15, S.39, A.41, V.45, E.49, S.104, T.105, T.107, R.139, E.140 Ligands: PO4.40 23 PLIP interactions: 19 interactions with chain L, 3 interactions with chain C, 1 interactions with chain J Hydrophobic interactions: L:V.45, C:W.84, J:W.200 Hydrogen bonds: L:G.13, L:G.13, L:S.15, 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, C:R.122 Water bridges: L:K.40, L:A.41, L:G.106, L:T.107, L:N.118, L:E.121, L:R.139 4LU.41: 19 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, E.49, S.104, T.105, T.107, R.139, E.140 Chain K: Y.169, W.200 Ligands: PO4.44 23 PLIP interactions: 19 interactions with chain I, 3 interactions with chain D, 1 interactions with chain K Hydrophobic interactions: I:V.45, D:W.84, K:W.200 Hydrogen bonds: I:G.13, I:G.13, I:S.15, 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, D:R.122 Water bridges: I:K.40, I:A.41, I:G.106, I:T.107, I:N.118, I:E.121, I:R.139 4LU.45: 19 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, E.49, S.104, T.105, T.107, R.139, E.140 Chain L: Y.169, W.200 Ligands: PO4.48 22 PLIP interactions: 18 interactions with chain J, 1 interactions with chain L, 3 interactions with chain B Hydrophobic interactions: J:V.45, L:W.200, B:W.84 Hydrogen bonds: J:G.13, J:G.13, J:S.15, J:S.39, J:S.104, J:T.105, J:T.107, J:R.139, J:R.139, B:R.122, B:R.122 Water bridges: J:K.40, J:A.41, J:G.106, J:N.118, J:E.121, J:E.121, J:E.121, J:R.139

12 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 No protein-ligand interaction detected (PLIP) SCN.6: 5 residues within 4Å: Chain B: P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.10: 5 residues within 4Å: Chain C: P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.14: 5 residues within 4Å: Chain D: P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.18: 5 residues within 4Å: Chain E: P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.22: 5 residues within 4Å: Chain F: P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.26: 5 residues within 4Å: Chain G: P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.30: 5 residues within 4Å: Chain H: P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.34: 5 residues within 4Å: Chain I: P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.38: 5 residues within 4Å: Chain J: P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.42: 5 residues within 4Å: Chain K: P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP) SCN.46: 5 residues within 4Å: Chain L: P.95, N.96, A.97, R.132, P.133 No protein-ligand interaction detected (PLIP)

24 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: S.39, K.40, Q.81, N.118 Ligand excluded by PLIP PO4.4: 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: 4LU.1 Ligand excluded by PLIP PO4.7: 4 residues within 4Å: Chain B: S.39, K.40, Q.81, N.118 Ligand excluded by PLIP PO4.8: 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: 4LU.5 Ligand excluded by PLIP PO4.11: 4 residues within 4Å: Chain C: S.39, K.40, Q.81, N.118 Ligand excluded by PLIP PO4.12: 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: 4LU.9 Ligand excluded by PLIP PO4.15: 4 residues within 4Å: Chain D: S.39, K.40, Q.81, N.118 Ligand excluded by PLIP PO4.16: 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: 4LU.13 Ligand excluded by PLIP PO4.19: 4 residues within 4Å: Chain E: S.39, K.40, Q.81, N.118 Ligand excluded by PLIP PO4.20: 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: 4LU.17 Ligand excluded by PLIP PO4.23: 4 residues within 4Å: Chain F: S.39, K.40, Q.81, N.118 Ligand excluded by PLIP PO4.24: 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: 4LU.21 Ligand excluded by PLIP PO4.27: 4 residues within 4Å: Chain G: S.39, K.40, Q.81, N.118 Ligand excluded by PLIP PO4.28: 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: 4LU.25 Ligand excluded by PLIP PO4.31: 4 residues within 4Å: Chain H: S.39, K.40, Q.81, N.118 Ligand excluded by PLIP PO4.32: 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: 4LU.29 Ligand excluded by PLIP PO4.35: 4 residues within 4Å: Chain I: S.39, K.40, Q.81, N.118 Ligand excluded by PLIP PO4.36: 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: 4LU.33 Ligand excluded by PLIP PO4.39: 4 residues within 4Å: Chain J: S.39, K.40, Q.81, N.118 Ligand excluded by PLIP PO4.40: 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: 4LU.37 Ligand excluded by PLIP PO4.43: 4 residues within 4Å: Chain K: S.39, K.40, Q.81, N.118 Ligand excluded by PLIP PO4.44: 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: 4LU.41 Ligand excluded by PLIP PO4.47: 4 residues within 4Å: Chain L: S.39, K.40, Q.81, N.118 Ligand excluded by PLIP PO4.48: 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: 4LU.45 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

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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