SMTL ID : 4zay.1

Structure of UbiX E49Q in complex with a covalent adduct between dimethylallyl monophosphate and reduced FMN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 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)

4LS.1: 21 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, Q.49, S.104, T.105, T.107, R.139, E.140 Chain E: W.84, A.89, S.90, C.116, R.122 Ligands: PO4.6 32 PLIP interactions: 7 interactions with chain E, 22 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: E:W.84, E:A.89, C:V.45, A:Y.169, A:Y.169, A:W.200 Hydrogen bonds: E:C.116, E:R.122, C:G.13, C:S.15, C:S.39, 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:C.116, E:N.117, C:K.40, C:A.41, C:G.106, C:G.106, C:N.118, C:N.118, C:E.121, C:E.121, C:E.121, C:R.139 4LS.7: 21 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, Q.49, S.104, T.105, T.107, R.139, E.140 Chain G: W.84, A.89, S.90, C.116, R.122 Ligands: PO4.12 32 PLIP interactions: 7 interactions with chain G, 22 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: G:W.84, G:A.89, D:V.45, B:Y.169, B:Y.169, B:W.200 Hydrogen bonds: G:C.116, G:R.122, D:G.13, D:S.15, D:S.39, 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:C.116, G:N.117, D:K.40, D:A.41, D:G.106, D:G.106, D:N.118, D:N.118, D:E.121, D:E.121, D:E.121, D:R.139 4LS.13: 21 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 C: Y.169, W.200 Chain H: W.84, A.89, S.90, C.116, R.122 Ligands: PO4.18 29 PLIP interactions: 7 interactions with chain H, 19 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: H:W.84, H:A.89, A:V.45, C:Y.169, C:Y.169, C:W.200 Hydrogen bonds: H:C.116, H:R.122, A:G.13, A:S.15, A:S.39, 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:C.116, H:N.117, A:K.40, A:A.41, A:G.106, A:G.106, A:N.118, A:N.118, A:R.139 4LS.19: 21 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 D: Y.169, W.200 Chain F: W.84, A.89, S.90, C.116, R.122 Ligands: PO4.24 29 PLIP interactions: 19 interactions with chain B, 3 interactions with chain D, 7 interactions with chain F Hydrophobic interactions: B:V.45, D:Y.169, D:Y.169, D:W.200, F:W.84, F:A.89 Hydrogen bonds: B:G.13, B:S.15, B:S.39, 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:C.116, F:R.122 Water bridges: B:K.40, B:A.41, B:G.106, B:G.106, B:N.118, B:N.118, B:R.139, F:C.116, F:C.116, F:N.117 4LS.25: 21 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, Q.49, S.104, T.105, T.107, R.139, E.140 Chain I: W.84, A.89, S.90, C.116, R.122 Ligands: PO4.30 32 PLIP interactions: 22 interactions with chain G, 7 interactions with chain I, 3 interactions with chain E Hydrophobic interactions: G:V.45, I:W.84, I:A.89, E:Y.169, E:Y.169, E:W.200 Hydrogen bonds: G:G.13, G:S.15, G:S.39, G:S.39, G:S.39, G:S.104, G:T.105, G:T.107, G:T.107, G:R.139, G:R.139, I:C.116, I:R.122 Water bridges: G:K.40, G:A.41, G:G.106, G:G.106, G:N.118, G:N.118, G:E.121, G:E.121, G:E.121, G:R.139, I:C.116, I:C.116, I:N.117 4LS.31: 21 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, Q.49, S.104, T.105, T.107, R.139, E.140 Chain K: W.84, A.89, S.90, C.116, R.122 Ligands: PO4.36 29 PLIP interactions: 7 interactions with chain K, 19 interactions with chain H, 3 interactions with chain F Hydrophobic interactions: K:W.84, K:A.89, H:V.45, F:Y.169, F:Y.169, F:W.200 Hydrogen bonds: K:C.116, K:R.122, H:G.13, H:S.15, H:S.39, H:S.39, H:S.39, H:S.104, H:T.105, H:T.107, H:R.139, H:R.139, H:E.140 Water bridges: K:C.116, K:C.116, K:N.117, H:K.40, H:A.41, H:G.106, H:G.106, H:N.118, H:N.118, H:R.139 4LS.37: 21 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 G: Y.169, W.200 Chain L: W.84, A.89, S.90, C.116, R.122 Ligands: PO4.42 32 PLIP interactions: 7 interactions with chain L, 22 interactions with chain E, 3 interactions with chain G Hydrophobic interactions: L:W.84, L:A.89, E:V.45, G:Y.169, G:Y.169, G:W.200 Hydrogen bonds: L:C.116, L:R.122, E:G.13, E:S.15, E:S.39, 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:C.116, L:N.117, E:K.40, E:A.41, E:G.106, E:G.106, E:N.118, E:N.118, E:E.121, E:E.121, E:E.121, E:R.139 4LS.43: 21 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 H: Y.169, W.200 Chain J: W.84, A.89, S.90, C.116, R.122 Ligands: PO4.48 29 PLIP interactions: 19 interactions with chain F, 3 interactions with chain H, 7 interactions with chain J Hydrophobic interactions: F:V.45, H:Y.169, H:Y.169, H:W.200, J:W.84, J:A.89 Hydrogen bonds: F:G.13, F:S.15, F:S.39, 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:C.116, J:R.122 Water bridges: F:K.40, F:A.41, F:G.106, F:G.106, F:N.118, F:N.118, F:R.139, J:C.116, J:C.116, J:N.117 4LS.49: 21 residues within 4Å: Chain A: W.84, A.89, S.90, 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, Q.49, S.104, T.105, T.107, R.139, E.140 Ligands: PO4.54 31 PLIP interactions: 21 interactions with chain K, 3 interactions with chain I, 7 interactions with chain A Hydrophobic interactions: K:V.45, I:Y.169, I:Y.169, I:W.200, A:W.84, A:A.89 Hydrogen bonds: K:G.13, K:S.15, K:S.39, K:S.39, K:S.39, K:S.104, K:T.105, K:T.107, K:R.139, K:R.139, A:C.116, A:R.122 Water bridges: K:K.40, K:A.41, K:G.106, K:G.106, K:N.118, K:N.118, K:E.121, K:E.121, K:E.121, K:R.139, A:C.116, A:C.116, A:N.117 4LS.55: 21 residues within 4Å: Chain C: W.84, A.89, S.90, 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, Q.49, S.104, T.105, T.107, R.139, E.140 Ligands: PO4.60 30 PLIP interactions: 7 interactions with chain C, 3 interactions with chain J, 20 interactions with chain L Hydrophobic interactions: C:W.84, C:A.89, J:Y.169, J:Y.169, J:W.200, L:V.45 Hydrogen bonds: C:C.116, C:R.122, L:G.13, L:S.15, L:S.39, 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:C.116, C:N.117, L:K.40, L:A.41, L:G.106, L:G.106, L:N.118, L:N.118, L:R.139 4LS.61: 21 residues within 4Å: Chain D: W.84, A.89, S.90, 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 Chain K: Y.169, W.200 Ligands: PO4.66 30 PLIP interactions: 20 interactions with chain I, 7 interactions with chain D, 3 interactions with chain K Hydrophobic interactions: I:V.45, D:W.84, D:A.89, K:Y.169, K:Y.169, K:W.200 Hydrogen bonds: I:G.13, I:S.15, I:S.39, 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:C.116, D:R.122 Water bridges: I:K.40, I:A.41, I:G.106, I:G.106, I:N.118, I:N.118, I:R.139, D:C.116, D:C.116, D:N.117 4LS.67: 21 residues within 4Å: Chain B: W.84, A.89, S.90, 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 Chain L: Y.169, W.200 Ligands: PO4.72 31 PLIP interactions: 21 interactions with chain J, 7 interactions with chain B, 3 interactions with chain L Hydrophobic interactions: J:V.45, B:W.84, B:A.89, L:Y.169, L:Y.169, L:W.200 Hydrogen bonds: J:G.13, J:S.15, J:S.39, J:S.39, J:S.39, J:S.104, J:T.105, J:T.107, J:R.139, J:R.139, B:C.116, B:R.122 Water bridges: J:K.40, J:A.41, J:G.106, J:G.106, J:N.118, J:N.118, J:E.121, J:E.121, J:E.121, J:R.139, B:C.116, B:C.116, B:N.117

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

SCN.2: 6 residues within 4Å: Chain A: P.4, P.95, N.96, A.97, R.132, P.133 Ligand excluded by PLIP SCN.3: 5 residues within 4Å: Chain A: H.170, P.172, D.177, D.180, F.181 Ligand excluded by PLIP SCN.4: 4 residues within 4Å: Chain A: Y.169, H.170, P.198, W.200 Ligand excluded by PLIP SCN.8: 6 residues within 4Å: Chain B: P.4, P.95, N.96, A.97, R.132, P.133 Ligand excluded by PLIP SCN.9: 5 residues within 4Å: Chain B: H.170, P.172, D.177, D.180, F.181 Ligand excluded by PLIP SCN.10: 4 residues within 4Å: Chain B: Y.169, H.170, P.198, W.200 Ligand excluded by PLIP SCN.14: 6 residues within 4Å: Chain C: P.4, P.95, N.96, A.97, R.132, P.133 Ligand excluded by PLIP SCN.15: 5 residues within 4Å: Chain C: H.170, P.172, D.177, D.180, F.181 Ligand excluded by PLIP SCN.16: 4 residues within 4Å: Chain C: Y.169, H.170, P.198, W.200 Ligand excluded by PLIP SCN.20: 6 residues within 4Å: Chain D: P.4, P.95, N.96, A.97, R.132, P.133 Ligand excluded by PLIP SCN.21: 5 residues within 4Å: Chain D: H.170, P.172, D.177, D.180, F.181 Ligand excluded by PLIP SCN.22: 4 residues within 4Å: Chain D: Y.169, H.170, P.198, W.200 Ligand excluded by PLIP SCN.26: 6 residues within 4Å: Chain E: P.4, P.95, N.96, A.97, R.132, P.133 Ligand excluded by PLIP SCN.27: 5 residues within 4Å: Chain E: H.170, P.172, D.177, D.180, F.181 Ligand excluded by PLIP SCN.28: 4 residues within 4Å: Chain E: Y.169, H.170, P.198, W.200 Ligand excluded by PLIP SCN.32: 6 residues within 4Å: Chain F: P.4, P.95, N.96, A.97, R.132, P.133 Ligand excluded by PLIP SCN.33: 5 residues within 4Å: Chain F: H.170, P.172, D.177, D.180, F.181 Ligand excluded by PLIP SCN.34: 4 residues within 4Å: Chain F: Y.169, H.170, P.198, W.200 Ligand excluded by PLIP SCN.38: 6 residues within 4Å: Chain G: P.4, P.95, N.96, A.97, R.132, P.133 Ligand excluded by PLIP SCN.39: 5 residues within 4Å: Chain G: H.170, P.172, D.177, D.180, F.181 Ligand excluded by PLIP SCN.40: 4 residues within 4Å: Chain G: Y.169, H.170, P.198, W.200 Ligand excluded by PLIP SCN.44: 6 residues within 4Å: Chain H: P.4, P.95, N.96, A.97, R.132, P.133 Ligand excluded by PLIP SCN.45: 5 residues within 4Å: Chain H: H.170, P.172, D.177, D.180, F.181 Ligand excluded by PLIP SCN.46: 4 residues within 4Å: Chain H: Y.169, H.170, P.198, W.200 Ligand excluded by PLIP SCN.50: 6 residues within 4Å: Chain I: P.4, P.95, N.96, A.97, R.132, P.133 Ligand excluded by PLIP SCN.51: 5 residues within 4Å: Chain I: H.170, P.172, D.177, D.180, F.181 Ligand excluded by PLIP SCN.52: 4 residues within 4Å: Chain I: Y.169, H.170, P.198, W.200 Ligand excluded by PLIP SCN.56: 6 residues within 4Å: Chain J: P.4, P.95, N.96, A.97, R.132, P.133 Ligand excluded by PLIP SCN.57: 5 residues within 4Å: Chain J: H.170, P.172, D.177, D.180, F.181 Ligand excluded by PLIP SCN.58: 4 residues within 4Å: Chain J: Y.169, H.170, P.198, W.200 Ligand excluded by PLIP SCN.62: 6 residues within 4Å: Chain K: P.4, P.95, N.96, A.97, R.132, P.133 Ligand excluded by PLIP SCN.63: 5 residues within 4Å: Chain K: H.170, P.172, D.177, D.180, F.181 Ligand excluded by PLIP SCN.64: 4 residues within 4Å: Chain K: Y.169, H.170, P.198, W.200 Ligand excluded by PLIP SCN.68: 6 residues within 4Å: Chain L: P.4, P.95, N.96, A.97, R.132, P.133 Ligand excluded by PLIP SCN.69: 5 residues within 4Å: Chain L: H.170, P.172, D.177, D.180, F.181 Ligand excluded by PLIP SCN.70: 4 residues within 4Å: Chain L: Y.169, H.170, P.198, W.200 Ligand excluded by PLIP

12 x K: POTASSIUM ION(Non-covalent)

K.5: 1 residues within 4Å: Chain A: Q.81 No protein-ligand interaction detected (PLIP) K.11: 1 residues within 4Å: Chain B: Q.81 No protein-ligand interaction detected (PLIP) K.17: 1 residues within 4Å: Chain C: Q.81 No protein-ligand interaction detected (PLIP) K.23: 1 residues within 4Å: Chain D: Q.81 No protein-ligand interaction detected (PLIP) K.29: 1 residues within 4Å: Chain E: Q.81 No protein-ligand interaction detected (PLIP) K.35: 1 residues within 4Å: Chain F: Q.81 No protein-ligand interaction detected (PLIP) K.41: 1 residues within 4Å: Chain G: Q.81 No protein-ligand interaction detected (PLIP) K.47: 1 residues within 4Å: Chain H: Q.81 No protein-ligand interaction detected (PLIP) K.53: 1 residues within 4Å: Chain I: Q.81 No protein-ligand interaction detected (PLIP) K.59: 1 residues within 4Å: Chain J: Q.81 No protein-ligand interaction detected (PLIP) K.65: 1 residues within 4Å: Chain K: Q.81 No protein-ligand interaction detected (PLIP) K.71: 1 residues within 4Å: Chain L: Q.81 No protein-ligand interaction detected (PLIP)

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

PO4.6: 9 residues within 4Å: Chain A: Y.169, R.185 Chain C: R.139, E.140 Chain E: S.90, G.91, R.122, K.129 Ligands: 4LS.1 10 PLIP interactions: 2 interactions with chain A, 3 interactions with chain E, 5 interactions with chain C Hydrogen bonds: A:Y.169, E:G.91, C:E.140, C:E.140 Salt bridges: A:R.185, E:R.122, E:K.129, C:R.139 Water bridges: C:R.139, C:A.141 PO4.12: 9 residues within 4Å: Chain B: Y.169, R.185 Chain D: R.139, E.140 Chain G: S.90, G.91, R.122, K.129 Ligands: 4LS.7 10 PLIP interactions: 5 interactions with chain D, 3 interactions with chain G, 2 interactions with chain B Hydrogen bonds: D:E.140, D:E.140, G:G.91, B:Y.169 Water bridges: D:R.139, D:A.141 Salt bridges: D:R.139, G:R.122, G:K.129, B:R.185 PO4.18: 9 residues within 4Å: Chain A: R.139, E.140 Chain C: Y.169, R.185 Chain H: S.90, G.91, R.122, K.129 Ligands: 4LS.13 9 PLIP interactions: 3 interactions with chain H, 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: H:G.91, A:E.140, A:E.140 Salt bridges: H:R.122, H:K.129, A:R.139, C:R.185 Water bridges: A:R.139, A:R.139 PO4.24: 9 residues within 4Å: Chain B: R.139, E.140 Chain D: Y.169, R.185 Chain F: S.90, G.91, R.122, K.129 Ligands: 4LS.19 9 PLIP interactions: 3 interactions with chain F, 5 interactions with chain B, 1 interactions with chain D Hydrogen bonds: F:G.91, 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:R.139 PO4.30: 9 residues within 4Å: Chain E: Y.169, R.185 Chain G: R.139, E.140 Chain I: S.90, G.91, R.122, K.129 Ligands: 4LS.25 10 PLIP interactions: 5 interactions with chain G, 3 interactions with chain I, 2 interactions with chain E Hydrogen bonds: G:E.140, G:E.140, I:G.91, E:Y.169 Water bridges: G:R.139, G:R.139 Salt bridges: G:R.139, I:R.122, I:K.129, E:R.185 PO4.36: 9 residues within 4Å: Chain F: Y.169, R.185 Chain H: R.139, E.140 Chain K: S.90, G.91, R.122, K.129 Ligands: 4LS.31 9 PLIP interactions: 5 interactions with chain H, 3 interactions with chain K, 1 interactions with chain F Hydrogen bonds: H:E.140, H:E.140, K:G.91 Water bridges: H:R.139, H:A.141 Salt bridges: H:R.139, K:R.122, K:K.129, F:R.185 PO4.42: 9 residues within 4Å: Chain E: R.139, E.140 Chain G: Y.169, R.185 Chain L: S.90, G.91, R.122, K.129 Ligands: 4LS.37 10 PLIP interactions: 2 interactions with chain G, 3 interactions with chain L, 5 interactions with chain E Hydrogen bonds: G:Y.169, L:G.91, 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:R.139 PO4.48: 9 residues within 4Å: Chain F: R.139, E.140 Chain H: Y.169, R.185 Chain J: S.90, G.91, R.122, K.129 Ligands: 4LS.43 9 PLIP interactions: 5 interactions with chain F, 3 interactions with chain J, 1 interactions with chain H Hydrogen bonds: F:E.140, F:E.140, J:G.91 Water bridges: F:R.139, F:A.141 Salt bridges: F:R.139, J:R.122, J:K.129, H:R.185 PO4.54: 9 residues within 4Å: Chain A: S.90, G.91, R.122, K.129 Chain I: Y.169, R.185 Chain K: R.139, E.140 Ligands: 4LS.49 10 PLIP interactions: 3 interactions with chain A, 2 interactions with chain I, 5 interactions with chain K Hydrogen bonds: A:G.91, 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:R.139, K:A.141 PO4.60: 9 residues within 4Å: Chain C: S.90, G.91, R.122, K.129 Chain J: Y.169, R.185 Chain L: R.139, E.140 Ligands: 4LS.55 9 PLIP interactions: 3 interactions with chain C, 1 interactions with chain J, 5 interactions with chain L Hydrogen bonds: C:G.91, L:E.140, L:E.140 Salt bridges: C:R.122, C:K.129, J:R.185, L:R.139 Water bridges: L:R.139, L:R.139 PO4.66: 9 residues within 4Å: Chain D: S.90, G.91, R.122, K.129 Chain I: R.139, E.140 Chain K: Y.169, R.185 Ligands: 4LS.61 9 PLIP interactions: 3 interactions with chain D, 1 interactions with chain K, 5 interactions with chain I Hydrogen bonds: D:G.91, I:E.140, I:E.140 Salt bridges: D:R.122, D:K.129, K:R.185, I:R.139 Water bridges: I:R.139, I:R.139 PO4.72: 9 residues within 4Å: Chain B: S.90, G.91, R.122, K.129 Chain J: R.139, E.140 Chain L: Y.169, R.185 Ligands: 4LS.67 10 PLIP interactions: 5 interactions with chain J, 2 interactions with chain L, 3 interactions with chain B Hydrogen bonds: J:E.140, J:E.140, L:Y.169, B:G.91 Water bridges: J:R.139, J:A.141 Salt bridges: J:R.139, L:R.185, B:R.122, B:K.129

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

Related Entries With Identical Sequence