SMTL ID : 4ygo.1

Dodecameric structure of spermidine N-acetyltransferase from Vibrio cholerae in intermediate state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-12-mer

Ligands

12 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.33, E.75 Chain H: E.33, E.75 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain H Metal complexes: A:E.33, A:E.75, A:E.75, H:E.33, H:E.75 CA.2: 3 residues within 4Å: Chain A: P.35, E.41 Chain C: N.53 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:P.35, A:E.41, A:E.41, H2O.1 CA.4: 3 residues within 4Å: Chain B: N.53 Chain D: P.35, E.41 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:P.35, D:E.41, D:E.41, H2O.4 CA.5: 4 residues within 4Å: Chain C: E.33, E.75 Chain J: E.33, E.75 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain J Metal complexes: C:E.33, J:E.33, J:E.33, J:E.75, J:E.75 CA.6: 4 residues within 4Å: Chain C: E.34, P.35, E.41 Chain D: N.53 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.34, C:P.35, C:E.41, C:E.41, H2O.4 CA.7: 4 residues within 4Å: Chain E: E.33, E.75 Chain L: E.33, E.75 5 PLIP interactions: 2 interactions with chain L, 3 interactions with chain E Metal complexes: L:E.33, L:E.75, E:E.33, E:E.75, E:E.75 CA.8: 4 residues within 4Å: Chain B: E.33, E.75 Chain G: E.33, E.75 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain B Metal complexes: G:E.33, G:E.75, G:E.75, B:E.33, B:E.75 CA.9: 3 residues within 4Å: Chain G: P.35, E.41 Chain I: N.53 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:P.35, G:E.41, G:E.41, H2O.7 CA.11: 3 residues within 4Å: Chain H: N.53 Chain J: P.35, E.41 4 PLIP interactions: 3 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:P.35, J:E.41, J:E.41, H2O.10 CA.12: 4 residues within 4Å: Chain D: E.33, E.75 Chain I: E.33, E.75 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain I Metal complexes: D:E.33, D:E.33, D:E.75, D:E.75, I:E.33 CA.13: 4 residues within 4Å: Chain I: E.34, P.35, E.41 Chain J: N.53 5 PLIP interactions: 4 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:E.34, I:P.35, I:E.41, I:E.41, H2O.9 CA.14: 4 residues within 4Å: Chain F: E.33, E.75 Chain K: E.33, E.75 5 PLIP interactions: 3 interactions with chain K, 2 interactions with chain F Metal complexes: K:E.33, K:E.75, K:E.75, F:E.33, F:E.75

2 x MOH: METHANOL(Non-functional Binders)

MOH.3: 3 residues within 4Å: Chain A: I.89, Q.94, G.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.95 Water bridges: A:K.96, A:G.97 MOH.10: 3 residues within 4Å: Chain G: I.89, Q.94, G.95 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:G.95 Water bridges: G:K.96, G:G.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Filippova, E.V. et al., Substrate-Induced Allosteric Change in the Quaternary Structure of the Spermidine N-Acetyltransferase SpeG. J.Mol.Biol. (2015)

Release Date

2015-10-07

Peptides

Spermidine n1-acetyltransferase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
C

E
E

F
F

G
A

H
B

I
D

J
C

K
E

L
F

Spermidine n1-acetyltransferase

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