SMTL ID : 4ncz.1

Spermidine N-acetyltransferase from Vibrio cholerae in complex with 2-[n-cyclohexylamino]ethane sulfonate.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-12-mer

Ligands

12 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.1: 9 residues within 4Å: Chain A: R.28, N.29, I.30, H.125, V.126, A.127, F.152, I.154, V.161 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.152, A:V.161 Hydrogen bonds: A:N.29 Salt bridges: A:R.28 NHE.5: 8 residues within 4Å: Chain B: N.27, R.28, N.29, I.30, Q.89, H.125, I.154, V.161 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:H.125, B:I.154, B:V.161 Hydrogen bonds: B:N.29 NHE.10: 6 residues within 4Å: Chain C: R.28, N.29, I.30, A.127, F.152, I.154 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.152 Hydrogen bonds: C:R.28, C:R.28, C:N.29 Salt bridges: C:R.28 NHE.13: 9 residues within 4Å: Chain D: R.28, N.29, I.30, H.125, V.126, A.127, F.152, I.154, V.161 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.152, D:V.161 Hydrogen bonds: D:N.29 Salt bridges: D:R.28 NHE.17: 8 residues within 4Å: Chain E: N.27, R.28, N.29, I.30, Q.89, H.125, I.154, V.161 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:H.125, E:I.154, E:V.161 Hydrogen bonds: E:N.29 NHE.22: 6 residues within 4Å: Chain F: R.28, N.29, I.30, A.127, F.152, I.154 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:F.152 Hydrogen bonds: F:R.28, F:R.28, F:N.29 Salt bridges: F:R.28 NHE.25: 9 residues within 4Å: Chain G: R.28, N.29, I.30, H.125, V.126, A.127, F.152, I.154, V.161 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:F.152, G:V.161 Hydrogen bonds: G:N.29 Salt bridges: G:R.28 NHE.29: 8 residues within 4Å: Chain H: N.27, R.28, N.29, I.30, Q.89, H.125, I.154, V.161 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:H.125, H:I.154, H:V.161 Hydrogen bonds: H:N.29 NHE.34: 6 residues within 4Å: Chain I: R.28, N.29, I.30, A.127, F.152, I.154 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:F.152 Hydrogen bonds: I:R.28, I:R.28, I:N.29 Salt bridges: I:R.28 NHE.37: 9 residues within 4Å: Chain J: R.28, N.29, I.30, H.125, V.126, A.127, F.152, I.154, V.161 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:F.152, J:V.161 Hydrogen bonds: J:N.29 Salt bridges: J:R.28 NHE.41: 8 residues within 4Å: Chain K: N.27, R.28, N.29, I.30, Q.89, H.125, I.154, V.161 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:H.125, K:I.154, K:V.161 Hydrogen bonds: K:N.29 NHE.46: 6 residues within 4Å: Chain L: R.28, N.29, I.30, A.127, F.152, I.154 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:F.152 Hydrogen bonds: L:R.28, L:R.28, L:N.29 Salt bridges: L:R.28

16 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: N.80, Y.81, I.82 Chain C: Y.33, P.38 Ligand excluded by PLIP SO4.6: 7 residues within 4Å: Chain B: I.92, Q.97, G.98, K.99, G.100, F.101, A.102 Ligand excluded by PLIP SO4.7: 6 residues within 4Å: Chain B: N.80, Y.81, I.82 Chain H: Y.33, E.36, P.38 Ligand excluded by PLIP SO4.11: 6 residues within 4Å: Chain C: G.98, K.99, G.100, F.101, A.102, R.103 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain D: N.80, Y.81, I.82 Chain F: Y.33, P.38 Ligand excluded by PLIP SO4.18: 7 residues within 4Å: Chain E: I.92, Q.97, G.98, K.99, G.100, F.101, A.102 Ligand excluded by PLIP SO4.19: 6 residues within 4Å: Chain E: N.80, Y.81, I.82 Chain K: Y.33, E.36, P.38 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain F: G.98, K.99, G.100, F.101, A.102, R.103 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain G: N.80, Y.81, I.82 Chain I: Y.33, P.38 Ligand excluded by PLIP SO4.30: 7 residues within 4Å: Chain H: I.92, Q.97, G.98, K.99, G.100, F.101, A.102 Ligand excluded by PLIP SO4.31: 6 residues within 4Å: Chain B: Y.33, E.36, P.38 Chain H: N.80, Y.81, I.82 Ligand excluded by PLIP SO4.35: 6 residues within 4Å: Chain I: G.98, K.99, G.100, F.101, A.102, R.103 Ligand excluded by PLIP SO4.38: 5 residues within 4Å: Chain J: N.80, Y.81, I.82 Chain L: Y.33, P.38 Ligand excluded by PLIP SO4.42: 7 residues within 4Å: Chain K: I.92, Q.97, G.98, K.99, G.100, F.101, A.102 Ligand excluded by PLIP SO4.43: 6 residues within 4Å: Chain E: Y.33, E.36, P.38 Chain K: N.80, Y.81, I.82 Ligand excluded by PLIP SO4.47: 6 residues within 4Å: Chain L: G.98, K.99, G.100, F.101, A.102, R.103 Ligand excluded by PLIP

8 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: E.36, E.78 Chain C: E.36, E.78 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Metal complexes: C:E.36, C:E.78, A:E.36, A:E.78, A:E.78 CA.8: 5 residues within 4Å: Chain B: E.36, E.78 Chain H: E.36, E.78 Ligands: CA.32 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain H Metal complexes: B:E.36, B:E.78, H:E.36, H:E.36, H:E.78 CA.15: 4 residues within 4Å: Chain D: E.36, E.78 Chain F: E.36, E.78 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain F Metal complexes: D:E.36, D:E.78, D:E.78, F:E.36, F:E.78 CA.20: 5 residues within 4Å: Chain E: E.36, E.78 Chain K: E.36, E.78 Ligands: CA.44 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain K Metal complexes: E:E.36, E:E.78, K:E.36, K:E.36, K:E.78 CA.27: 4 residues within 4Å: Chain G: E.36, E.78 Chain I: E.36, E.78 5 PLIP interactions: 2 interactions with chain I, 3 interactions with chain G Metal complexes: I:E.36, I:E.78, G:E.36, G:E.78, G:E.78 CA.32: 5 residues within 4Å: Chain B: E.36, E.78 Chain H: E.36, E.78 Ligands: CA.8 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain H Metal complexes: B:E.36, B:E.36, B:E.78, H:E.36, H:E.78 CA.39: 4 residues within 4Å: Chain J: E.36, E.78 Chain L: E.36, E.78 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain L Metal complexes: J:E.36, J:E.78, J:E.78, L:E.36, L:E.78 CA.44: 5 residues within 4Å: Chain E: E.36, E.78 Chain K: E.36, E.78 Ligands: CA.20 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain K Metal complexes: E:E.36, E:E.36, E:E.78, K:E.36, K:E.78

12 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: F.35, D.55, N.56, E.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.55 Water bridges: A:D.55 NA.9: 4 residues within 4Å: Chain B: F.35, D.55, N.56, E.58 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.56 NA.12: 4 residues within 4Å: Chain C: F.35, D.55, N.56, E.58 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.58 Water bridges: C:N.56 NA.16: 4 residues within 4Å: Chain D: F.35, D.55, N.56, E.58 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.58 Water bridges: D:D.55 NA.21: 4 residues within 4Å: Chain E: F.35, D.55, N.56, E.58 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.55 NA.24: 4 residues within 4Å: Chain F: F.35, D.55, N.56, E.58 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.55 Water bridges: F:N.56 NA.28: 4 residues within 4Å: Chain G: F.35, D.55, N.56, E.58 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.56 Water bridges: G:D.55 NA.33: 4 residues within 4Å: Chain H: F.35, D.55, N.56, E.58 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:D.55 NA.36: 4 residues within 4Å: Chain I: F.35, D.55, N.56, E.58 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:D.55 Water bridges: I:N.56 NA.40: 4 residues within 4Å: Chain J: F.35, D.55, N.56, E.58 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:D.55 Water bridges: J:D.55 NA.45: 4 residues within 4Å: Chain K: F.35, D.55, N.56, E.58 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.56 NA.48: 4 residues within 4Å: Chain L: F.35, D.55, N.56, E.58 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:E.58 Water bridges: L:N.56

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

2013-11-06

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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