SMTL ID : 5ug4.1

Structure of spermidine N-acetyltransferase SpeG from Vibrio cholerae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-12-mer

Ligands

36 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.33, E.75 Chain C: E.75 Ligands: CA.11 5 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:E.75, A:E.33, A:E.33, A:E.75, H2O.3 CA.2: 4 residues within 4Å: Chain A: E.34, P.35, E.41 Chain B: N.53 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.34, A:P.35, A:E.41, H2O.5, H2O.6 CA.5: 7 residues within 4Å: Chain B: E.33, E.75 Chain H: E.33, E.75 Ligands: CA.6, CA.35, CA.36 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: B:E.33, B:E.75, H:E.33, H2O.4, H2O.22 CA.6: 6 residues within 4Å: Chain B: E.33, E.75 Chain H: E.75 Ligands: CA.5, CA.35, CA.37 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.33, B:E.75, H2O.6 CA.7: 4 residues within 4Å: Chain B: E.75 Chain H: E.33, E.75 Ligands: CA.36 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.75 CA.8: 4 residues within 4Å: Chain B: E.34, P.35, E.41 Chain I: N.53 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.34, B:P.35, B:E.41, H2O.25, H2O.26 CA.11: 6 residues within 4Å: Chain A: E.33, E.75 Chain C: E.33, E.75 Ligands: CA.1, CA.12 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:E.33, C:E.75, C:E.75, A:E.75, H2O.2 CA.12: 4 residues within 4Å: Chain A: E.75 Chain C: E.33, E.75 Ligands: CA.11 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:E.33, C:E.75, A:E.75, H2O.1, H2O.8 CA.13: 4 residues within 4Å: Chain C: E.34, P.35, E.41 Chain D: N.53 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.34, C:P.35, C:E.41, H2O.10, H2O.12 CA.16: 4 residues within 4Å: Chain D: E.33, E.75 Chain F: E.75 Ligands: CA.26 5 PLIP interactions: 1 interactions with chain F, 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: F:E.75, D:E.33, D:E.33, D:E.75, H2O.12 CA.17: 4 residues within 4Å: Chain D: E.34, P.35, E.41 Chain E: N.53 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.34, D:P.35, D:E.41, H2O.14, H2O.15 CA.20: 7 residues within 4Å: Chain E: E.33, E.75 Chain K: E.33, E.75 Ligands: CA.21, CA.50, CA.51 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: E:E.33, E:E.75, K:E.33, H2O.13, H2O.31 CA.21: 6 residues within 4Å: Chain E: E.33, E.75 Chain K: E.75 Ligands: CA.20, CA.50, CA.52 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.33, E:E.75, H2O.15 CA.22: 4 residues within 4Å: Chain E: E.75 Chain K: E.33, E.75 Ligands: CA.51 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.75 CA.23: 4 residues within 4Å: Chain E: E.34, P.35, E.41 Chain L: N.53 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.34, E:P.35, E:E.41, H2O.34, H2O.35 CA.26: 6 residues within 4Å: Chain D: E.33, E.75 Chain F: E.33, E.75 Ligands: CA.16, CA.27 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: F:E.33, F:E.75, F:E.75, D:E.75, H2O.11 CA.27: 4 residues within 4Å: Chain D: E.75 Chain F: E.33, E.75 Ligands: CA.26 5 PLIP interactions: 2 interactions with chain F, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: F:E.33, F:E.75, D:E.75, H2O.10, H2O.17 CA.28: 4 residues within 4Å: Chain A: N.53 Chain F: E.34, P.35, E.41 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.34, F:P.35, F:E.41, H2O.1, H2O.3 CA.31: 4 residues within 4Å: Chain G: E.33, E.75 Chain I: E.75 Ligands: CA.41 5 PLIP interactions: 3 interactions with chain G, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: G:E.33, G:E.33, G:E.75, I:E.75, H2O.21 CA.32: 4 residues within 4Å: Chain G: E.34, P.35, E.41 Chain H: N.53 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.34, G:P.35, G:E.41, H2O.23, H2O.24 CA.35: 7 residues within 4Å: Chain B: E.33, E.75 Chain H: E.33, E.75 Ligands: CA.5, CA.6, CA.36 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: B:E.33, B:E.75, H:E.33, H2O.4, H2O.22 CA.36: 6 residues within 4Å: Chain B: E.75 Chain H: E.33, E.75 Ligands: CA.5, CA.7, CA.35 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:E.33, H:E.75, H2O.24 CA.37: 4 residues within 4Å: Chain B: E.33, E.75 Chain H: E.75 Ligands: CA.6 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.75 CA.38: 4 residues within 4Å: Chain C: N.53 Chain H: E.34, P.35, E.41 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.34, H:P.35, H:E.41, H2O.6, H2O.7 CA.41: 6 residues within 4Å: Chain G: E.33, E.75 Chain I: E.33, E.75 Ligands: CA.31, CA.42 5 PLIP interactions: 3 interactions with chain I, 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: I:E.33, I:E.75, I:E.75, G:E.75, H2O.20 CA.42: 4 residues within 4Å: Chain G: E.75 Chain I: E.33, E.75 Ligands: CA.41 5 PLIP interactions: 2 interactions with chain I, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: I:E.33, I:E.75, G:E.75, H2O.19, H2O.26 CA.43: 4 residues within 4Å: Chain I: E.34, P.35, E.41 Chain J: N.53 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.34, I:P.35, I:E.41, H2O.28, H2O.30 CA.46: 4 residues within 4Å: Chain J: E.33, E.75 Chain L: E.75 Ligands: CA.56 5 PLIP interactions: 3 interactions with chain J, 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: J:E.33, J:E.33, J:E.75, L:E.75, H2O.30 CA.47: 4 residues within 4Å: Chain J: E.34, P.35, E.41 Chain K: N.53 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.34, J:P.35, J:E.41, H2O.32, H2O.33 CA.50: 7 residues within 4Å: Chain E: E.33, E.75 Chain K: E.33, E.75 Ligands: CA.20, CA.21, CA.51 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: E:E.33, E:E.75, K:E.33, H2O.13, H2O.31 CA.51: 6 residues within 4Å: Chain E: E.75 Chain K: E.33, E.75 Ligands: CA.20, CA.22, CA.50 3 PLIP interactions: 2 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:E.33, K:E.75, H2O.33 CA.52: 4 residues within 4Å: Chain E: E.33, E.75 Chain K: E.75 Ligands: CA.21 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:E.75 CA.53: 4 residues within 4Å: Chain F: N.53 Chain K: E.34, P.35, E.41 5 PLIP interactions: 3 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:E.34, K:P.35, K:E.41, H2O.16, H2O.16 CA.56: 6 residues within 4Å: Chain J: E.33, E.75 Chain L: E.33, E.75 Ligands: CA.46, CA.57 5 PLIP interactions: 3 interactions with chain L, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: L:E.33, L:E.75, L:E.75, J:E.75, H2O.29 CA.57: 4 residues within 4Å: Chain J: E.75 Chain L: E.33, E.75 Ligands: CA.56 5 PLIP interactions: 2 interactions with chain L, 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: L:E.33, L:E.75, J:E.75, H2O.28, H2O.35 CA.58: 4 residues within 4Å: Chain G: N.53 Chain L: E.34, P.35, E.41 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.34, L:P.35, L:E.41, H2O.19, H2O.21

12 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: N.22, N.26, E.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.22, A:E.37 ACT.9: 3 residues within 4Å: Chain B: H.122, A.124, I.151 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.124, B:I.151 Water bridges: B:A.124 ACT.14: 2 residues within 4Å: Chain C: I.151, V.158 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.151, C:V.158 ACT.18: 3 residues within 4Å: Chain D: N.22, N.26, E.37 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.22, D:E.37 ACT.24: 3 residues within 4Å: Chain E: H.122, A.124, I.151 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:A.124, E:I.151 Water bridges: E:A.124 ACT.29: 2 residues within 4Å: Chain F: I.151, V.158 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:I.151, F:V.158 ACT.33: 3 residues within 4Å: Chain G: N.22, N.26, E.37 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.22, G:E.37 ACT.39: 3 residues within 4Å: Chain H: H.122, A.124, I.151 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:A.124, H:I.151 Water bridges: H:A.124 ACT.44: 2 residues within 4Å: Chain I: I.151, V.158 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:I.151, I:V.158 ACT.48: 3 residues within 4Å: Chain J: N.22, N.26, E.37 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:N.22, J:E.37 ACT.54: 3 residues within 4Å: Chain K: H.122, A.124, I.151 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:A.124, K:I.151 Water bridges: K:A.124 ACT.59: 2 residues within 4Å: Chain L: I.151, V.158 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:I.151, L:V.158

4 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.4: 4 residues within 4Å: Chain A: H.122, V.123, A.124, N.127 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.124 Hydrogen bonds: A:A.124 MRD.19: 4 residues within 4Å: Chain D: H.122, V.123, A.124, N.127 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:A.124 Hydrogen bonds: D:A.124 MRD.34: 4 residues within 4Å: Chain G: H.122, V.123, A.124, N.127 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:A.124 Hydrogen bonds: G:A.124 MRD.49: 4 residues within 4Å: Chain J: H.122, V.123, A.124, N.127 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:A.124 Hydrogen bonds: J:A.124

4 x EOH: ETHANOL(Non-functional Binders)

EOH.10: 1 residues within 4Å: Chain B: N.53 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.53 EOH.25: 1 residues within 4Å: Chain E: N.53 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.53 EOH.40: 1 residues within 4Å: Chain H: N.53 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.53 EOH.55: 1 residues within 4Å: Chain K: N.53 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.53

4 x MOH: METHANOL(Non-functional Binders)

MOH.15: 2 residues within 4Å: Chain C: N.53, Y.78 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.53 MOH.30: 2 residues within 4Å: Chain F: N.53, Y.78 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.53 MOH.45: 2 residues within 4Å: Chain I: N.53, Y.78 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.53 MOH.60: 2 residues within 4Å: Chain L: N.53, Y.78 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:N.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Filippova, E.V. et al., Structure of spermidine N-acetyltransferase SpeG from Vibrio cholerae. To Be Published

Release Date

2017-01-25

Peptides

Spermidine N(1)-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 N(1)-acetyltransferase

Related Entries With Identical Sequence