SMTL ID : 4mhd.1

Crystal structure of spermidine N-acetyltransferase from Vibrio cholerae in complex with spermidine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-12-mer

Ligands

12 x SPD: SPERMIDINE(Non-covalent)

SPD.1: 11 residues within 4Å: Chain A: E.57, E.58, Y.60, E.61, E.65 Chain C: Y.102 Chain H: H.73, I.74, D.76, E.79, R.80 5 PLIP interactions: 1 interactions with chain H, 4 interactions with chain A Hydrogen bonds: H:I.74, A:E.57, A:E.58, A:E.65 Hydrophobic interactions: A:Y.60 SPD.2: 10 residues within 4Å: Chain B: E.57, E.58, E.61, E.65 Chain C: H.73, I.74, D.76, N.77, E.79, R.80 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:I.74, C:D.76, B:E.57, B:E.65 SPD.3: 10 residues within 4Å: Chain C: E.57, E.58, Y.60, E.61, E.65 Chain D: H.73, I.74, D.76, E.79, R.80 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:E.57, C:E.57, C:E.65, D:I.74, D:D.76 SPD.4: 11 residues within 4Å: Chain D: E.57, E.58, Y.60, E.61, E.65 Chain F: Y.102 Chain K: H.73, I.74, D.76, E.79, R.80 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain K Hydrophobic interactions: D:Y.60 Hydrogen bonds: D:E.57, D:E.58, D:E.65, K:I.74 SPD.5: 10 residues within 4Å: Chain E: E.57, E.58, E.61, E.65 Chain F: H.73, I.74, D.76, N.77, E.79, R.80 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:I.74, F:D.76, E:E.57, E:E.65 SPD.6: 10 residues within 4Å: Chain A: H.73, I.74, D.76, E.79, R.80 Chain F: E.57, E.58, Y.60, E.61, E.65 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain F Hydrogen bonds: A:I.74, A:D.76, F:E.57, F:E.57, F:E.65 SPD.7: 11 residues within 4Å: Chain B: H.73, I.74, D.76, E.79, R.80 Chain G: E.57, E.58, Y.60, E.61, E.65 Chain I: Y.102 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain G Hydrogen bonds: B:I.74, G:E.58, G:E.65 Hydrophobic interactions: G:Y.60 SPD.8: 10 residues within 4Å: Chain H: E.57, E.58, E.61, E.65 Chain I: H.73, I.74, D.76, N.77, E.79, R.80 6 PLIP interactions: 2 interactions with chain I, 4 interactions with chain H Hydrogen bonds: I:I.74, I:D.76, H:E.57, H:E.57, H:E.65 Water bridges: H:E.65 SPD.9: 10 residues within 4Å: Chain I: E.57, E.58, Y.60, E.61, E.65 Chain J: H.73, I.74, D.76, E.79, R.80 5 PLIP interactions: 2 interactions with chain J, 3 interactions with chain I Hydrogen bonds: J:I.74, J:D.76, I:E.57, I:E.65 Water bridges: I:E.65 SPD.10: 11 residues within 4Å: Chain E: H.73, I.74, D.76, E.79, R.80 Chain J: E.57, E.58, Y.60, E.61, E.65 Chain L: Y.102 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain E Hydrophobic interactions: J:Y.60 Hydrogen bonds: J:E.58, J:E.65, E:I.74 SPD.11: 10 residues within 4Å: Chain K: E.57, E.58, E.61, E.65 Chain L: H.73, I.74, D.76, N.77, E.79, R.80 6 PLIP interactions: 2 interactions with chain L, 4 interactions with chain K Hydrogen bonds: L:I.74, L:D.76, K:E.57, K:E.57, K:E.65 Water bridges: K:E.65 SPD.12: 10 residues within 4Å: Chain G: H.73, I.74, D.76, E.79, R.80 Chain L: E.57, E.58, Y.60, E.61, E.65 5 PLIP interactions: 2 interactions with chain G, 3 interactions with chain L Hydrogen bonds: G:I.74, G:D.76, L:E.57, L:E.65 Water bridges: L:E.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Filippova, E.V. et al., A Novel Polyamine Allosteric Site of SpeG from Vibrio cholerae Is Revealed by Its Dodecameric Structure. J.Mol.Biol. (2015)

Release Date

2013-09-25

Peptides

Spermidine n1-acetyltransferase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

G
A

H
B

I
C

J
A

K
B

L
C

Spermidine n1-acetyltransferase

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