SMTL ID : 4r87.2 (2 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

homo-12-mer

Ligands

12 x COA: COENZYME A(Non-covalent)

COA.1: 20 residues within 4Å: Chain A: I.30, Y.33, I.90, I.91, I.92, Q.97, G.98, K.99, G.100, F.101, A.102, R.103, H.125, V.126, N.130, K.132, A.133, H.135, L.136, Y.137 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.30, A:Y.33, A:I.91 Hydrogen bonds: A:I.90, A:I.92, A:Q.97, A:G.98, A:K.99, A:G.100, A:G.100, A:A.102, A:N.130 Salt bridges: A:R.103, A:H.135 COA.3: 21 residues within 4Å: Chain B: I.30, Y.33, W.34, I.90, I.91, I.92, H.96, Q.97, G.98, K.99, G.100, F.101, A.102, R.103, H.125, V.126, N.130, K.132, H.135, L.136, Y.137 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.33 Hydrogen bonds: B:I.90, B:I.92, B:G.98, B:K.99, B:G.100, B:G.100, B:F.101, B:A.102, B:N.130 Water bridges: B:Q.97 Salt bridges: B:R.103, B:H.135 COA.4: 8 residues within 4Å: Chain C: I.92, Q.97, G.98, K.99, G.100, F.101, A.102, L.136 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.98, C:K.99, C:G.100, C:F.101, C:A.102 Water bridges: C:G.100, C:R.103 COA.6: 19 residues within 4Å: Chain D: Y.33, W.34, I.90, I.91, I.92, Q.97, G.98, K.99, G.100, F.101, A.102, R.103, H.125, V.126, N.130, K.132, H.135, L.136, Y.137 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:I.90, D:I.92, D:Q.97, D:G.98, D:G.100, D:A.102, D:N.130 Salt bridges: D:R.103, D:H.135 COA.9: 20 residues within 4Å: Chain E: I.30, Y.33, I.90, I.91, I.92, Q.97, G.98, K.99, G.100, F.101, A.102, R.103, H.125, V.126, N.130, K.132, A.133, H.135, L.136, Y.137 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:I.30, E:Y.33, E:I.91 Hydrogen bonds: E:I.90, E:I.92, E:Q.97, E:G.98, E:K.99, E:G.100, E:G.100, E:A.102, E:N.130 Salt bridges: E:R.103, E:H.135 COA.11: 21 residues within 4Å: Chain F: I.30, Y.33, W.34, I.90, I.91, I.92, H.96, Q.97, G.98, K.99, G.100, F.101, A.102, R.103, H.125, V.126, N.130, K.132, H.135, L.136, Y.137 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:Y.33 Hydrogen bonds: F:I.90, F:I.92, F:G.98, F:K.99, F:G.100, F:G.100, F:F.101, F:A.102, F:N.130 Water bridges: F:Q.97 Salt bridges: F:R.103, F:H.135 COA.12: 8 residues within 4Å: Chain G: I.92, Q.97, G.98, K.99, G.100, F.101, A.102, L.136 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:G.98, G:K.99, G:G.100, G:F.101, G:A.102 Water bridges: G:G.100, G:R.103 COA.14: 19 residues within 4Å: Chain H: Y.33, W.34, I.90, I.91, I.92, Q.97, G.98, K.99, G.100, F.101, A.102, R.103, H.125, V.126, N.130, K.132, H.135, L.136, Y.137 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:I.90, H:I.92, H:Q.97, H:G.98, H:G.100, H:A.102, H:N.130 Salt bridges: H:R.103, H:H.135 COA.17: 20 residues within 4Å: Chain I: I.30, Y.33, I.90, I.91, I.92, Q.97, G.98, K.99, G.100, F.101, A.102, R.103, H.125, V.126, N.130, K.132, A.133, H.135, L.136, Y.137 14 PLIP interactions: 14 interactions with chain I Hydrophobic interactions: I:I.30, I:Y.33, I:I.91 Hydrogen bonds: I:I.90, I:I.92, I:Q.97, I:G.98, I:K.99, I:G.100, I:G.100, I:A.102, I:N.130 Salt bridges: I:R.103, I:H.135 COA.19: 21 residues within 4Å: Chain J: I.30, Y.33, W.34, I.90, I.91, I.92, H.96, Q.97, G.98, K.99, G.100, F.101, A.102, R.103, H.125, V.126, N.130, K.132, H.135, L.136, Y.137 13 PLIP interactions: 13 interactions with chain J Hydrophobic interactions: J:Y.33 Hydrogen bonds: J:I.90, J:I.92, J:G.98, J:K.99, J:G.100, J:G.100, J:F.101, J:A.102, J:N.130 Water bridges: J:Q.97 Salt bridges: J:R.103, J:H.135 COA.20: 8 residues within 4Å: Chain K: I.92, Q.97, G.98, K.99, G.100, F.101, A.102, L.136 7 PLIP interactions: 7 interactions with chain K Hydrogen bonds: K:G.98, K:K.99, K:G.100, K:F.101, K:A.102 Water bridges: K:G.100, K:R.103 COA.22: 19 residues within 4Å: Chain L: Y.33, W.34, I.90, I.91, I.92, Q.97, G.98, K.99, G.100, F.101, A.102, R.103, H.125, V.126, N.130, K.132, H.135, L.136, Y.137 9 PLIP interactions: 9 interactions with chain L Hydrogen bonds: L:I.90, L:I.92, L:Q.97, L:G.98, L:G.100, L:A.102, L:N.130 Salt bridges: L:R.103, L:H.135

9 x SPM: SPERMINE(Non-covalent)

SPM.2: 10 residues within 4Å: Chain A: E.36, E.37, Y.39, E.40, E.44 Chain K: H.52, I.53, D.55, E.58, R.59 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.36, A:E.40, A:E.44, A:E.44 SPM.5: 12 residues within 4Å: Chain A: H.52, I.53, D.55, N.56, R.59 Chain C: N.25, M.31, E.36, E.37, Y.39, E.40, E.44 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:I.53, C:N.25, C:E.36 SPM.7: 13 residues within 4Å: Chain D: N.25, M.31, E.36, E.37, Y.39, E.40, E.44 Chain F: H.52, I.53, H.54, D.55, E.58, R.59 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain F Hydrogen bonds: D:E.40, F:I.53, F:D.55, F:R.59, F:R.59 Water bridges: D:N.25, D:N.25 SPM.10: 10 residues within 4Å: Chain C: H.52, I.53, D.55, E.58, R.59 Chain E: E.36, E.37, Y.39, E.40, E.44 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.36, E:E.40, E:E.44, E:E.44 SPM.13: 12 residues within 4Å: Chain E: H.52, I.53, D.55, N.56, R.59 Chain G: N.25, M.31, E.36, E.37, Y.39, E.40, E.44 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain G Hydrogen bonds: E:I.53, G:N.25, G:E.36 SPM.15: 13 residues within 4Å: Chain H: N.25, M.31, E.36, E.37, Y.39, E.40, E.44 Chain J: H.52, I.53, H.54, D.55, E.58, R.59 7 PLIP interactions: 4 interactions with chain J, 3 interactions with chain H Hydrogen bonds: J:I.53, J:D.55, J:R.59, J:R.59, H:E.40 Water bridges: H:N.25, H:N.25 SPM.18: 10 residues within 4Å: Chain G: H.52, I.53, D.55, E.58, R.59 Chain I: E.36, E.37, Y.39, E.40, E.44 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:E.36, I:E.40, I:E.44, I:E.44 SPM.21: 12 residues within 4Å: Chain I: H.52, I.53, D.55, N.56, R.59 Chain K: N.25, M.31, E.36, E.37, Y.39, E.40, E.44 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain I Hydrogen bonds: K:N.25, K:E.36, I:I.53 SPM.23: 13 residues within 4Å: Chain B: H.52, I.53, H.54, D.55, E.58, R.59 Chain L: N.25, M.31, E.36, E.37, Y.39, E.40, E.44 7 PLIP interactions: 3 interactions with chain L, 4 interactions with chain B Hydrogen bonds: L:E.40, B:I.53, B:D.55, B:R.59, B:R.59 Water bridges: L:N.25, L:N.25

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 2 residues within 4Å: Chain B: K.51 Chain D: H.54 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.51 PEG.16: 2 residues within 4Å: Chain F: K.51 Chain H: H.54 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:K.51 PEG.24: 2 residues within 4Å: Chain J: K.51 Chain L: H.54 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:K.51

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

2015-03-25

Peptides

Spermidine n1-acetyltransferase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

E
E

F
F

G
G

H
H

I
E

J
F

K
G

L
H

Spermidine n1-acetyltransferase

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