SMTL ID : 2vyc.2 (1 other biounit)

Crystal Structure of Acid Induced Arginine Decarboxylase from E. coli

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-10-mer

Ligands

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

PLP.1: 16 residues within 4Å: Chain A: G.229, T.230, S.231, N.234, H.255, S.257, T.319, D.347, A.349, W.350, S.383, H.385, K.386 Chain F: T.420, T.421, S.422 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain F Hydrophobic interactions: A:T.319, A:K.386 Hydrogen bonds: A:T.230, A:S.231, A:N.234, A:S.383, F:T.421, F:T.421, F:S.422 Salt bridges: A:H.385, A:K.386 pi-Stacking: A:H.255 PLP.2: 16 residues within 4Å: Chain B: G.229, T.230, S.231, N.234, H.255, S.257, T.319, D.347, A.349, W.350, S.383, H.385, K.386 Chain J: T.420, T.421, S.422 14 PLIP interactions: 3 interactions with chain J, 11 interactions with chain B Hydrogen bonds: J:T.420, J:T.421, J:S.422, B:V.228, B:T.230, B:S.231, B:N.234, B:S.383 Hydrophobic interactions: B:T.319, B:K.386 Water bridges: B:H.255 Salt bridges: B:H.385, B:K.386 pi-Stacking: B:H.255 PLP.3: 16 residues within 4Å: Chain C: G.229, T.230, S.231, N.234, H.255, S.257, T.319, D.347, A.349, W.350, S.383, H.385, K.386 Chain I: T.420, T.421, S.422 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain I Hydrophobic interactions: C:T.319, C:K.386 Hydrogen bonds: C:V.228, C:T.230, C:S.231, C:N.234, C:S.383, C:K.386, I:T.420, I:T.421, I:S.422 Salt bridges: C:H.385, C:K.386 pi-Stacking: C:H.255 PLP.4: 16 residues within 4Å: Chain D: G.229, T.230, S.231, N.234, H.255, S.257, T.319, D.347, A.349, W.350, S.383, H.385, K.386 Chain H: T.420, T.421, S.422 14 PLIP interactions: 10 interactions with chain D, 4 interactions with chain H Hydrophobic interactions: D:T.319, D:K.386 Hydrogen bonds: D:T.230, D:S.231, D:N.234, D:S.383, D:K.386, H:T.420, H:T.421, H:S.422, H:S.422 Salt bridges: D:H.385, D:K.386 pi-Stacking: D:H.255 PLP.5: 16 residues within 4Å: Chain E: G.229, T.230, S.231, N.234, H.255, S.257, T.319, D.347, A.349, W.350, S.383, H.385, K.386 Chain G: T.420, T.421, S.422 13 PLIP interactions: 9 interactions with chain E, 4 interactions with chain G Hydrophobic interactions: E:T.319, E:K.386 Hydrogen bonds: E:T.230, E:S.231, E:N.234, E:S.383, G:T.420, G:T.421, G:T.421, G:S.422 Salt bridges: E:H.385, E:K.386 pi-Stacking: E:H.255 PLP.6: 16 residues within 4Å: Chain A: T.420, T.421, S.422 Chain F: G.229, T.230, S.231, N.234, H.255, S.257, T.319, D.347, A.349, W.350, S.383, H.385, K.386 12 PLIP interactions: 9 interactions with chain F, 3 interactions with chain A Hydrophobic interactions: F:T.319, F:K.386 Hydrogen bonds: F:T.230, F:S.231, F:N.234, F:S.383, A:T.421, A:T.421, A:S.422 Salt bridges: F:H.385, F:K.386 pi-Stacking: F:H.255 PLP.7: 16 residues within 4Å: Chain E: T.420, T.421, S.422 Chain G: G.229, T.230, S.231, N.234, H.255, S.257, T.319, D.347, A.349, W.350, S.383, H.385, K.386 14 PLIP interactions: 11 interactions with chain G, 3 interactions with chain E Hydrophobic interactions: G:T.319, G:K.386 Hydrogen bonds: G:V.228, G:T.230, G:S.231, G:N.234, G:S.383, E:T.420, E:T.421, E:S.422 Water bridges: G:H.255 Salt bridges: G:H.385, G:K.386 pi-Stacking: G:H.255 PLP.8: 16 residues within 4Å: Chain D: T.420, T.421, S.422 Chain H: G.229, T.230, S.231, N.234, H.255, S.257, T.319, D.347, A.349, W.350, S.383, H.385, K.386 14 PLIP interactions: 11 interactions with chain H, 3 interactions with chain D Hydrophobic interactions: H:T.319, H:K.386 Hydrogen bonds: H:V.228, H:T.230, H:S.231, H:N.234, H:S.383, H:K.386, D:T.420, D:T.421, D:S.422 Salt bridges: H:H.385, H:K.386 pi-Stacking: H:H.255 PLP.9: 16 residues within 4Å: Chain C: T.420, T.421, S.422 Chain I: G.229, T.230, S.231, N.234, H.255, S.257, T.319, D.347, A.349, W.350, S.383, H.385, K.386 14 PLIP interactions: 10 interactions with chain I, 4 interactions with chain C Hydrophobic interactions: I:T.319, I:K.386 Hydrogen bonds: I:T.230, I:S.231, I:N.234, I:S.383, I:K.386, C:T.420, C:T.421, C:S.422, C:S.422 Salt bridges: I:H.385, I:K.386 pi-Stacking: I:H.255 PLP.10: 16 residues within 4Å: Chain B: T.420, T.421, S.422 Chain J: G.229, T.230, S.231, N.234, H.255, S.257, T.319, D.347, A.349, W.350, S.383, H.385, K.386 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain J Hydrogen bonds: B:T.420, B:T.421, B:T.421, B:S.422, J:T.230, J:S.231, J:N.234, J:S.383 Hydrophobic interactions: J:T.319, J:K.386 Salt bridges: J:H.385, J:K.386 pi-Stacking: J:H.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andrell, J. et al., Crystal Structure of the Acid Induced Arginine Decarboxylase from Escherichia Coli: Reversible Decamer Assembly Controls Enzyme Activity. Biochemistry (2009)

Release Date

2009-03-31

Peptides

BIODEGRADATIVE ARGININE DECARBOXYLASE: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
H

D
I

E
J

F
F

G
G

H
H

I
I

J
J

BIODEGRADATIVE ARGININE DECARBOXYLASE

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