SMTL ID : 6q6i.1

Lysine decarboxylase A from Pseudomonas aeruginosa

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-10-mer

Ligands

10 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 12 residues within 4Å: Chain A: G.238, T.239, S.240, H.264, D.355, A.357, W.358, H.392, K.393 Chain H: S.428, T.429, S.430 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain H Hydrophobic interactions: A:H.264, A:A.357, A:W.358, A:K.393 Hydrogen bonds: A:T.239, A:T.239, A:T.239, A:S.240, H:T.429, H:T.429, H:S.430 Salt bridges: A:H.392 pi-Cation interactions: A:H.264 PLP.2: 12 residues within 4Å: Chain B: G.238, T.239, S.240, H.264, D.355, A.357, W.358, H.392, K.393 Chain G: S.428, T.429, S.430 13 PLIP interactions: 3 interactions with chain G, 10 interactions with chain B Hydrogen bonds: G:T.429, G:T.429, G:S.430, B:T.239, B:T.239, B:T.239, B:S.240 Hydrophobic interactions: B:H.264, B:A.357, B:W.358, B:K.393 Salt bridges: B:H.392 pi-Cation interactions: B:H.264 PLP.3: 12 residues within 4Å: Chain C: G.238, T.239, S.240, H.264, D.355, A.357, W.358, H.392, K.393 Chain F: S.428, T.429, S.430 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain F Hydrophobic interactions: C:H.264, C:A.357, C:W.358, C:K.393 Hydrogen bonds: C:T.239, C:T.239, C:T.239, C:S.240, F:T.429, F:T.429, F:S.430 Salt bridges: C:H.392 pi-Cation interactions: C:H.264 PLP.4: 12 residues within 4Å: Chain D: G.238, T.239, S.240, H.264, D.355, A.357, W.358, H.392, K.393 Chain J: S.428, T.429, S.430 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain J Hydrophobic interactions: D:H.264, D:A.357, D:W.358, D:K.393 Hydrogen bonds: D:T.239, D:T.239, D:T.239, D:S.240, J:T.429, J:T.429, J:S.430 Salt bridges: D:H.392 pi-Cation interactions: D:H.264 PLP.5: 12 residues within 4Å: Chain E: G.238, T.239, S.240, H.264, D.355, A.357, W.358, H.392, K.393 Chain I: S.428, T.429, S.430 13 PLIP interactions: 3 interactions with chain I, 10 interactions with chain E Hydrogen bonds: I:T.429, I:T.429, I:S.430, E:T.239, E:T.239, E:T.239, E:S.240 Hydrophobic interactions: E:H.264, E:A.357, E:W.358, E:K.393 Salt bridges: E:H.392 pi-Cation interactions: E:H.264 PLP.6: 12 residues within 4Å: Chain C: S.428, T.429, S.430 Chain F: G.238, T.239, S.240, H.264, D.355, A.357, W.358, H.392, K.393 12 PLIP interactions: 3 interactions with chain C, 9 interactions with chain F Hydrogen bonds: C:T.429, C:T.429, C:S.430, F:T.239, F:T.239, F:S.240 Hydrophobic interactions: F:H.264, F:A.357, F:W.358, F:K.393 Salt bridges: F:H.392 pi-Cation interactions: F:H.264 PLP.7: 12 residues within 4Å: Chain B: S.428, T.429, S.430 Chain G: G.238, T.239, S.240, H.264, D.355, A.357, W.358, H.392, K.393 12 PLIP interactions: 9 interactions with chain G, 3 interactions with chain B Hydrophobic interactions: G:H.264, G:A.357, G:W.358, G:K.393 Hydrogen bonds: G:T.239, G:T.239, G:S.240, B:T.429, B:T.429, B:S.430 Salt bridges: G:H.392 pi-Cation interactions: G:H.264 PLP.8: 12 residues within 4Å: Chain A: S.428, T.429, S.430 Chain H: G.238, T.239, S.240, H.264, D.355, A.357, W.358, H.392, K.393 12 PLIP interactions: 9 interactions with chain H, 3 interactions with chain A Hydrophobic interactions: H:H.264, H:A.357, H:W.358, H:K.393 Hydrogen bonds: H:T.239, H:T.239, H:S.240, A:T.429, A:T.429, A:S.430 Salt bridges: H:H.392 pi-Cation interactions: H:H.264 PLP.9: 12 residues within 4Å: Chain E: S.428, T.429, S.430 Chain I: G.238, T.239, S.240, H.264, D.355, A.357, W.358, H.392, K.393 12 PLIP interactions: 9 interactions with chain I, 3 interactions with chain E Hydrophobic interactions: I:H.264, I:A.357, I:W.358, I:K.393 Hydrogen bonds: I:T.239, I:T.239, I:S.240, E:T.429, E:T.429, E:S.430 Salt bridges: I:H.392 pi-Cation interactions: I:H.264 PLP.10: 12 residues within 4Å: Chain D: S.428, T.429, S.430 Chain J: G.238, T.239, S.240, H.264, D.355, A.357, W.358, H.392, K.393 12 PLIP interactions: 9 interactions with chain J, 3 interactions with chain D Hydrophobic interactions: J:H.264, J:A.357, J:W.358, J:K.393 Hydrogen bonds: J:T.239, J:T.239, J:S.240, D:T.429, D:T.429, D:S.430 Salt bridges: J:H.392 pi-Cation interactions: J:H.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kandiah, E. et al., Cryo-EM structure of Lysine decarboxylase A from Pseudomonas aeruginosa. To Be Published

Release Date

2019-09-25

Peptides

Biodegradative arginine decarboxylase: ABCDEFGHIJ

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

Biodegradative arginine decarboxylase