SMTL ID : 3n75.1

X-ray Crystal Structure of the Escherichia coli Inducible Lysine Decarboxylase LdcI

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-10-mer

Ligands

10 x G4P: GUANOSINE-5',3'-TETRAPHOSPHATE(Non-covalent)

G4P.1: 10 residues within 4Å: Chain A: R.97, R.206, K.417, G.418 Chain D: R.558, L.562, L.564, R.565, N.568, R.585 23 PLIP interactions: 10 interactions with chain D, 13 interactions with chain A Hydrogen bonds: D:R.558, D:R.558, D:R.565, D:N.568, D:N.568, A:R.206, A:G.418 Water bridges: D:R.585, D:R.585, A:R.206, A:R.206, A:R.206, A:R.206, A:R.206 Salt bridges: D:R.565, D:R.585, D:R.585, A:R.206, A:R.206, A:R.206, A:K.417 pi-Cation interactions: A:R.97, A:R.97 G4P.4: 10 residues within 4Å: Chain B: R.97, R.206, K.417, G.418 Chain E: R.558, L.562, L.564, R.565, N.568, R.585 18 PLIP interactions: 10 interactions with chain B, 8 interactions with chain E Hydrogen bonds: B:R.206, E:R.558, E:R.558, E:R.565, E:N.568, E:N.568 Water bridges: B:R.206, B:R.206, B:G.418 Salt bridges: B:R.206, B:R.206, B:R.206, B:K.417, E:R.565, E:R.585, E:R.585 pi-Cation interactions: B:R.97, B:R.97 G4P.7: 10 residues within 4Å: Chain A: R.558, L.562, L.564, R.565, N.568, R.585 Chain C: R.97, R.206, K.417, G.418 22 PLIP interactions: 14 interactions with chain C, 8 interactions with chain A Hydrogen bonds: C:R.206, C:G.418, A:R.558, A:R.558, A:R.565, A:N.568 Water bridges: C:R.97, C:R.206, C:R.206, C:R.206, C:R.206, C:R.206, A:Y.517 Salt bridges: C:R.206, C:R.206, C:R.206, C:K.417, A:R.565, A:R.585, A:R.585 pi-Cation interactions: C:R.97, C:R.97 G4P.10: 10 residues within 4Å: Chain B: R.558, L.562, L.564, R.565, N.568, R.585 Chain D: R.97, R.206, K.417, G.418 24 PLIP interactions: 8 interactions with chain B, 16 interactions with chain D Hydrogen bonds: B:R.558, B:R.558, B:R.565, B:N.568, B:N.568, D:R.206, D:G.418 Salt bridges: B:R.565, B:R.585, B:R.585, D:R.206, D:R.206, D:R.206, D:K.417 Water bridges: D:E.75, D:R.97, D:R.97, D:R.206, D:R.206, D:R.206, D:R.206, D:R.206 pi-Cation interactions: D:R.97, D:R.97 G4P.13: 10 residues within 4Å: Chain C: R.558, L.562, L.564, R.565, N.568, R.585 Chain E: R.97, R.206, K.417, G.418 28 PLIP interactions: 17 interactions with chain E, 11 interactions with chain C Hydrogen bonds: E:G.418, C:R.558, C:R.558, C:R.565, C:N.568 Water bridges: E:R.97, E:R.97, E:R.206, E:R.206, E:R.206, E:R.206, E:R.206, E:R.206, E:R.206, C:Y.517, C:R.565, C:R.565, C:R.565 Salt bridges: E:R.206, E:R.206, E:R.206, E:R.206, E:K.417, C:R.565, C:R.585, C:R.585 pi-Cation interactions: E:R.97, E:R.97 G4P.16: 10 residues within 4Å: Chain F: R.97, R.206, K.417, G.418 Chain I: R.558, L.562, L.564, R.565, N.568, R.585 23 PLIP interactions: 13 interactions with chain F, 10 interactions with chain I Hydrogen bonds: F:R.206, F:G.418, I:R.558, I:R.558, I:R.565, I:N.568, I:N.568 Water bridges: F:R.206, F:R.206, F:R.206, F:R.206, F:R.206, I:R.585, I:R.585 Salt bridges: F:R.206, F:R.206, F:R.206, F:K.417, I:R.565, I:R.585, I:R.585 pi-Cation interactions: F:R.97, F:R.97 G4P.19: 10 residues within 4Å: Chain G: R.97, R.206, K.417, G.418 Chain J: R.558, L.562, L.564, R.565, N.568, R.585 18 PLIP interactions: 8 interactions with chain J, 10 interactions with chain G Hydrogen bonds: J:R.558, J:R.558, J:R.565, J:N.568, J:N.568, G:R.206 Salt bridges: J:R.565, J:R.585, J:R.585, G:R.206, G:R.206, G:R.206, G:K.417 Water bridges: G:R.206, G:R.206, G:G.418 pi-Cation interactions: G:R.97, G:R.97 G4P.22: 10 residues within 4Å: Chain F: R.558, L.562, L.564, R.565, N.568, R.585 Chain H: R.97, R.206, K.417, G.418 21 PLIP interactions: 14 interactions with chain H, 7 interactions with chain F Hydrogen bonds: H:R.206, H:G.418, F:R.558, F:R.558, F:R.565, F:N.568 Water bridges: H:R.97, H:R.206, H:R.206, H:R.206, H:R.206, H:R.206 Salt bridges: H:R.206, H:R.206, H:R.206, H:K.417, F:R.565, F:R.585, F:R.585 pi-Cation interactions: H:R.97, H:R.97 G4P.25: 10 residues within 4Å: Chain G: R.558, L.562, L.564, R.565, N.568, R.585 Chain I: R.97, R.206, K.417, G.418 24 PLIP interactions: 16 interactions with chain I, 8 interactions with chain G Hydrogen bonds: I:R.206, I:G.418, G:R.558, G:R.558, G:R.565, G:N.568, G:N.568 Water bridges: I:E.75, I:R.97, I:R.97, I:R.206, I:R.206, I:R.206, I:R.206, I:R.206 Salt bridges: I:R.206, I:R.206, I:R.206, I:K.417, G:R.565, G:R.585, G:R.585 pi-Cation interactions: I:R.97, I:R.97 G4P.28: 10 residues within 4Å: Chain H: R.558, L.562, L.564, R.565, N.568, R.585 Chain J: R.97, R.206, K.417, G.418 27 PLIP interactions: 17 interactions with chain J, 10 interactions with chain H Hydrogen bonds: J:G.418, H:R.558, H:R.558, H:R.565, H:N.568 Water bridges: J:R.97, J:R.97, J:R.206, J:R.206, J:R.206, J:R.206, J:R.206, J:R.206, J:R.206, H:R.565, H:R.565, H:R.565 Salt bridges: J:R.206, J:R.206, J:R.206, J:R.206, J:K.417, H:R.565, H:R.585, H:R.585 pi-Cation interactions: J:R.97, J:R.97

10 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.2: 5 residues within 4Å: Chain A: N.8, H.9, E.16, R.20, Y.35 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.20 Water bridges: A:Y.13, A:E.17 P6G.5: 5 residues within 4Å: Chain B: N.8, H.9, E.16, R.20, Y.35 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.20 Water bridges: B:G.11 P6G.8: 5 residues within 4Å: Chain C: N.8, H.9, E.16, R.20, Y.35 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.20 P6G.11: 6 residues within 4Å: Chain D: N.8, H.9, E.16, R.20, H.23, Y.35 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.20 P6G.14: 5 residues within 4Å: Chain E: N.8, H.9, E.16, R.20, Y.35 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.20 Water bridges: E:R.20 P6G.17: 5 residues within 4Å: Chain F: N.8, H.9, E.16, R.20, Y.35 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:R.20 Water bridges: F:E.17, F:R.20 P6G.20: 5 residues within 4Å: Chain G: N.8, H.9, E.16, R.20, Y.35 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.20 Water bridges: G:G.11 P6G.23: 5 residues within 4Å: Chain H: N.8, H.9, E.16, R.20, Y.35 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:R.20 P6G.26: 6 residues within 4Å: Chain I: N.8, H.9, E.16, R.20, H.23, Y.35 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.20 P6G.29: 5 residues within 4Å: Chain J: N.8, H.9, E.16, R.20, Y.35 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:R.20 Water bridges: J:R.20

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: H.282, W.297, D.323 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.282 Water bridges: A:D.323, A:D.323 GOL.6: 3 residues within 4Å: Chain B: H.282, W.297, D.323 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.282 GOL.9: 3 residues within 4Å: Chain C: H.282, W.297, D.323 No protein-ligand interaction detected (PLIP) GOL.12: 3 residues within 4Å: Chain D: H.282, W.297, D.323 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.282 GOL.15: 3 residues within 4Å: Chain E: H.282, W.297, D.323 No protein-ligand interaction detected (PLIP) GOL.18: 3 residues within 4Å: Chain F: H.282, W.297, D.323 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:H.282 Water bridges: F:D.323 GOL.21: 3 residues within 4Å: Chain G: H.282, W.297, D.323 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:H.282 GOL.24: 3 residues within 4Å: Chain H: H.282, W.297, D.323 No protein-ligand interaction detected (PLIP) GOL.27: 3 residues within 4Å: Chain I: H.282, W.297, D.323 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:H.282 GOL.30: 3 residues within 4Å: Chain J: H.282, W.297, D.323 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kanjee, U. et al., Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. Embo J. (2011)

Release Date

2011-02-16

Peptides

Lysine decarboxylase, inducible: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

Lysine decarboxylase, inducible

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