SMTL ID : 4rhe.1

Crystal structure of UbiX, an aromatic acid decarboxylase from the Colwellia psychrerythraea 34H

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-12-mer

Ligands

12 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 17 residues within 4Å: Chain A: T.17, G.18, A.19, S.20, S.44, A.46, V.50, S.109, T.110, T.112, R.144, E.145 Chain D: Y.174, Y.207 Chain E: W.89, S.121, R.127 20 PLIP interactions: 13 interactions with chain A, 4 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: A:V.50, D:Y.174, D:Y.207, D:Y.207, E:W.89 Hydrogen bonds: A:G.18, A:G.18, A:S.20, A:S.44, A:S.44, A:S.109, A:S.109, A:T.110, A:T.112, A:T.112, A:R.144, A:R.144, E:R.127 pi-Stacking: D:Y.207 Water bridges: E:S.121 FMN.4: 17 residues within 4Å: Chain B: T.17, G.18, A.19, S.20, S.44, A.46, V.50, S.109, T.110, T.112, R.144, E.145 Chain H: Y.207 Chain J: W.89, S.121, D.122, R.127 20 PLIP interactions: 13 interactions with chain B, 3 interactions with chain H, 4 interactions with chain J Hydrophobic interactions: B:V.50, H:Y.207, H:Y.207, J:W.89 Hydrogen bonds: B:G.18, B:G.18, B:S.20, B:S.44, B:S.44, B:S.109, B:T.110, B:T.112, B:R.144, B:R.144, J:D.122, J:R.127 Water bridges: B:S.45, B:G.111, J:S.121 pi-Stacking: H:Y.207 FMN.7: 17 residues within 4Å: Chain B: W.89, S.121, D.122, R.127 Chain C: T.17, G.18, A.19, S.20, S.44, A.46, V.50, S.109, T.110, T.112, R.144, E.145 Chain E: Y.207 22 PLIP interactions: 14 interactions with chain C, 5 interactions with chain B, 3 interactions with chain E Hydrophobic interactions: C:V.50, B:W.89, E:Y.207, E:Y.207 Hydrogen bonds: C:G.18, C:G.18, C:S.20, C:S.44, C:S.44, C:S.109, C:S.109, C:T.110, C:T.112, C:R.144, C:R.144, B:R.127 Water bridges: C:S.45, C:G.111, B:S.121, B:S.121, B:S.121 pi-Stacking: E:Y.207 FMN.9: 16 residues within 4Å: Chain A: Y.207 Chain D: T.17, G.18, A.19, S.20, S.44, A.46, V.50, S.109, T.110, T.112, R.144, E.145 Chain I: W.89, S.121, R.127 22 PLIP interactions: 13 interactions with chain D, 6 interactions with chain I, 3 interactions with chain A Hydrophobic interactions: D:V.50, I:W.89, A:Y.207, A:Y.207 Hydrogen bonds: D:G.18, D:G.18, D:S.20, D:S.44, D:S.44, D:S.109, D:T.110, D:T.112, D:R.144, D:R.144, D:E.145, I:R.127 Water bridges: D:G.111, I:S.121, I:D.122, I:D.122, I:D.122 pi-Stacking: A:Y.207 FMN.10: 18 residues within 4Å: Chain C: Y.174, Y.207 Chain E: T.17, G.18, A.19, S.20, S.44, A.46, V.50, S.109, T.110, T.112, R.144, E.145 Chain F: W.89, S.121, D.122, R.127 23 PLIP interactions: 4 interactions with chain C, 15 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: C:Y.174, C:Y.207, C:Y.207, E:V.50, F:W.89 pi-Stacking: C:Y.207 Hydrogen bonds: E:G.18, E:G.18, E:S.20, E:S.44, E:S.44, E:S.109, E:S.109, E:T.110, E:T.112, E:T.112, E:R.144, E:R.144, E:E.145, F:R.127 Water bridges: E:G.111, F:S.121, F:S.121 FMN.12: 17 residues within 4Å: Chain A: W.89, S.121, D.122, R.127 Chain F: T.17, G.18, A.19, S.20, S.44, A.46, V.50, S.109, T.110, T.112, R.144, E.145 Chain L: Y.207 22 PLIP interactions: 7 interactions with chain A, 12 interactions with chain F, 3 interactions with chain L Hydrophobic interactions: A:W.89, F:V.50, L:Y.207, L:Y.207 Hydrogen bonds: A:R.127, F:G.18, F:G.18, F:S.20, F:S.44, F:S.109, F:S.109, F:T.110, F:T.112, F:R.144, F:R.144 Water bridges: A:S.121, A:S.121, A:S.121, A:D.122, A:R.127, F:G.111 pi-Stacking: L:Y.207 FMN.13: 17 residues within 4Å: Chain G: T.17, G.18, A.19, S.20, S.44, A.46, V.50, S.109, T.110, T.112, R.144, E.145 Chain J: Y.174, Y.207 Chain K: W.89, S.121, R.127 20 PLIP interactions: 13 interactions with chain G, 4 interactions with chain J, 3 interactions with chain K Hydrophobic interactions: G:V.50, J:Y.174, J:Y.207, J:Y.207, K:W.89 Hydrogen bonds: G:G.18, G:G.18, G:S.20, G:S.44, G:S.44, G:S.109, G:S.109, G:T.110, G:T.112, G:R.144, G:R.144, G:E.145, K:R.127 pi-Stacking: J:Y.207 Water bridges: K:S.121 FMN.16: 17 residues within 4Å: Chain B: Y.207 Chain D: W.89, S.121, D.122, R.127 Chain H: T.17, G.18, A.19, S.20, S.44, A.46, V.50, S.109, T.110, T.112, R.144, E.145 22 PLIP interactions: 15 interactions with chain H, 4 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: H:V.50, D:W.89, B:Y.207, B:Y.207 Hydrogen bonds: H:G.18, H:G.18, H:S.20, H:S.44, H:S.44, H:S.109, H:T.110, H:T.112, H:T.112, H:R.144, H:R.144, H:E.145, D:D.122, D:R.127 Water bridges: H:S.45, H:G.111, D:S.121 pi-Stacking: B:Y.207 FMN.19: 17 residues within 4Å: Chain H: W.89, S.121, D.122, R.127 Chain I: T.17, G.18, A.19, S.20, S.44, A.46, V.50, S.109, T.110, T.112, R.144, E.145 Chain K: Y.207 24 PLIP interactions: 16 interactions with chain I, 5 interactions with chain H, 3 interactions with chain K Hydrophobic interactions: I:V.50, H:W.89, K:Y.207, K:Y.207 Hydrogen bonds: I:G.18, I:G.18, I:S.20, I:S.44, I:S.44, I:S.109, I:S.109, I:T.110, I:T.112, I:T.112, I:R.144, I:R.144, I:E.145, H:R.127 Water bridges: I:S.45, I:G.111, H:S.121, H:S.121, H:S.121 pi-Stacking: K:Y.207 FMN.21: 16 residues within 4Å: Chain C: W.89, S.121, R.127 Chain G: Y.207 Chain J: T.17, G.18, A.19, S.20, S.44, A.46, V.50, S.109, T.110, T.112, R.144, E.145 22 PLIP interactions: 15 interactions with chain J, 4 interactions with chain C, 3 interactions with chain G Hydrophobic interactions: J:V.50, C:W.89, G:Y.207, G:Y.207 Hydrogen bonds: J:G.18, J:G.18, J:S.20, J:S.44, J:S.44, J:S.109, J:T.110, J:T.112, J:T.112, J:R.144, J:R.144, C:R.127 Water bridges: J:S.109, J:G.111, J:G.111, C:S.121, C:D.122 pi-Stacking: G:Y.207 FMN.22: 18 residues within 4Å: Chain I: Y.174, Y.207 Chain K: T.17, G.18, A.19, S.20, S.44, A.46, V.50, S.109, T.110, T.112, R.144, E.145 Chain L: W.89, S.121, D.122, R.127 22 PLIP interactions: 13 interactions with chain K, 5 interactions with chain L, 4 interactions with chain I Hydrophobic interactions: K:V.50, L:W.89, I:Y.174, I:Y.207, I:Y.207 Hydrogen bonds: K:G.18, K:G.18, K:S.20, K:S.44, K:S.44, K:S.109, K:S.109, K:T.110, K:T.112, K:R.144, K:R.144, L:R.127 Water bridges: K:G.111, L:S.121, L:S.121, L:D.122 pi-Stacking: I:Y.207 FMN.24: 17 residues within 4Å: Chain F: Y.207 Chain G: W.89, S.121, D.122, R.127 Chain L: T.17, G.18, A.19, S.20, S.44, A.46, V.50, S.109, T.110, T.112, R.144, E.145 25 PLIP interactions: 14 interactions with chain L, 8 interactions with chain G, 3 interactions with chain F Hydrophobic interactions: L:V.50, G:W.89, F:Y.207, F:Y.207 Hydrogen bonds: L:G.18, L:G.18, L:S.20, L:S.44, L:S.109, L:S.109, L:T.110, L:T.112, L:T.112, L:R.144, L:R.144, L:E.145, G:R.127 Water bridges: L:G.111, G:S.121, G:S.121, G:S.121, G:D.122, G:D.122, G:R.127 pi-Stacking: F:Y.207

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 12 residues within 4Å: Chain A: Y.174, F.186, R.190, Y.207 Chain D: R.144, E.145 Chain I: S.95, G.96, S.97, R.127, K.134, E.135 11 PLIP interactions: 4 interactions with chain I, 4 interactions with chain A, 3 interactions with chain D Hydrogen bonds: I:G.96, I:S.97, A:Y.174, A:Y.207, A:Y.207 Salt bridges: I:R.127, I:K.134, A:R.190, D:R.144 Water bridges: D:R.144, D:T.146 SO4.3: 11 residues within 4Å: Chain A: S.95, G.96, S.97, R.127, K.134 Chain F: R.144, E.145 Chain L: Y.174, F.186, R.190, Y.207 9 PLIP interactions: 4 interactions with chain A, 3 interactions with chain F, 2 interactions with chain L Hydrogen bonds: A:G.96, A:S.97, L:Y.174 Salt bridges: A:R.127, A:K.134, F:R.144, L:R.190 Water bridges: F:R.144, F:T.146 SO4.5: 12 residues within 4Å: Chain B: R.144, E.145 Chain H: Y.174, F.186, R.190, Y.207 Chain J: S.95, G.96, S.97, R.127, K.134, E.135 8 PLIP interactions: 4 interactions with chain J, 1 interactions with chain H, 3 interactions with chain B Hydrogen bonds: J:G.96, J:S.97 Salt bridges: J:R.127, J:K.134, H:R.190, B:R.144 Water bridges: B:R.144, B:T.146 SO4.6: 11 residues within 4Å: Chain B: S.95, G.96, R.127, K.134, E.135 Chain C: R.144, E.145 Chain E: Y.174, F.186, R.190, Y.207 11 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B, 3 interactions with chain E Water bridges: C:R.144, C:T.146 Salt bridges: C:R.144, B:R.127, B:K.134, E:R.190 Hydrogen bonds: B:S.95, B:G.96, B:S.97, E:Y.207, E:Y.207 SO4.8: 12 residues within 4Å: Chain C: Y.174, F.186, R.190, Y.207 Chain E: R.144, E.145 Chain F: S.95, G.96, S.97, R.127, K.134, E.135 11 PLIP interactions: 3 interactions with chain C, 6 interactions with chain F, 2 interactions with chain E Hydrogen bonds: C:Y.207, F:S.95, F:G.96, F:S.97, F:E.135 Water bridges: C:R.190, E:R.144 Salt bridges: C:R.190, F:R.127, F:K.134, E:R.144 SO4.11: 12 residues within 4Å: Chain A: R.144, E.145 Chain D: Y.174, F.186, R.190, Y.207 Chain E: S.95, G.96, S.97, R.127, K.134, E.135 11 PLIP interactions: 5 interactions with chain E, 2 interactions with chain D, 4 interactions with chain A Hydrogen bonds: E:G.96, E:S.97, E:E.135, D:Y.174, A:E.145 Salt bridges: E:R.127, E:K.134, D:R.190, A:R.144 Water bridges: A:R.144, A:T.146 SO4.14: 12 residues within 4Å: Chain C: S.95, G.96, S.97, R.127, K.134, E.135 Chain G: Y.174, F.186, R.190, Y.207 Chain J: R.144, E.145 10 PLIP interactions: 5 interactions with chain C, 2 interactions with chain G, 3 interactions with chain J Hydrogen bonds: C:G.96, C:S.97, C:E.135, G:Y.207 Salt bridges: C:R.127, C:K.134, G:R.190, J:R.144 Water bridges: J:E.145, J:T.146 SO4.15: 11 residues within 4Å: Chain F: Y.174, F.186, R.190, Y.207 Chain G: S.95, G.96, S.97, R.127, K.134 Chain L: R.144, E.145 9 PLIP interactions: 4 interactions with chain G, 2 interactions with chain F, 3 interactions with chain L Hydrogen bonds: G:G.96, G:S.97, F:Y.207 Salt bridges: G:R.127, G:K.134, F:R.190, L:R.144 Water bridges: L:R.144, L:T.146 SO4.17: 12 residues within 4Å: Chain B: Y.174, F.186, R.190, Y.207 Chain D: S.95, G.96, S.97, R.127, K.134, E.135 Chain H: R.144, E.145 11 PLIP interactions: 3 interactions with chain H, 5 interactions with chain D, 3 interactions with chain B Water bridges: H:R.144, H:T.146 Salt bridges: H:R.144, D:R.127, D:K.134, B:R.190 Hydrogen bonds: D:G.96, D:S.97, D:E.135, B:Y.174, B:Y.207 SO4.18: 11 residues within 4Å: Chain H: S.95, G.96, R.127, K.134, E.135 Chain I: R.144, E.145 Chain K: Y.174, F.186, R.190, Y.207 12 PLIP interactions: 3 interactions with chain I, 6 interactions with chain H, 3 interactions with chain K Water bridges: I:R.144, I:T.146 Salt bridges: I:R.144, H:R.127, H:K.134, K:R.190 Hydrogen bonds: H:S.95, H:G.96, H:S.97, H:E.135, K:Y.174, K:Y.207 SO4.20: 12 residues within 4Å: Chain I: Y.174, F.186, R.190, Y.207 Chain K: R.144, E.145 Chain L: S.95, G.96, S.97, R.127, K.134, E.135 10 PLIP interactions: 5 interactions with chain L, 3 interactions with chain K, 2 interactions with chain I Hydrogen bonds: L:S.95, L:G.96, L:S.97, I:Y.174 Salt bridges: L:R.127, L:K.134, K:R.144, I:R.190 Water bridges: K:R.144, K:E.145 SO4.23: 12 residues within 4Å: Chain G: R.144, E.145 Chain J: Y.174, F.186, R.190, Y.207 Chain K: S.95, G.96, S.97, R.127, K.134, E.135 12 PLIP interactions: 4 interactions with chain G, 4 interactions with chain K, 4 interactions with chain J Hydrogen bonds: G:E.145, K:G.96, K:S.97, J:Y.174, J:Y.174, J:Y.207 Water bridges: G:R.144, G:T.146 Salt bridges: G:R.144, K:R.127, K:K.134, J:R.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Do, H. et al., Crystal structure of UbiX, an aromatic acid decarboxylase from the psychrophilic bacterium Colwellia psychrerythraea that undergoes FMN-induced conformational changes. Sci Rep (2015)

Release Date

2015-02-18

Peptides

3-octaprenyl-4-hydroxybenzoate carboxy-lyase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

3-octaprenyl-4-hydroxybenzoate carboxy-lyase