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Dodecameric structure of spermidine N-acetyltransferase from vibrio cholerae

Analyse Dodecameric structure of spermidine N-acetyltransferase from vibrio cholerae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JLY
Type: protein
Length: 1,023 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spermidine N1-acetyltransferase
UniProt: Q9KL03
Ligands: SO4
Pockets: 16 · best druggability 0.85

Structure

x-ray diffraction · 6 distinct chains · 31% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spermidine N1-acetyltransferase	protein	172	31% helix, 37% strand	Q9KL03
B	Spermidine N1-acetyltransferase	protein	171	32% helix, 38% strand	Q9KL03
C	Spermidine N1-acetyltransferase	protein	171	32% helix, 38% strand	Q9KL03
D	Spermidine N1-acetyltransferase	protein	170	32% helix, 38% strand	Q9KL03
E	Spermidine N1-acetyltransferase	protein	169	32% helix, 36% strand	Q9KL03
F	Spermidine N1-acetyltransferase	protein	170	29% helix, 38% strand	Q9KL03

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, D, E, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	848	0.85	0.87	92	empty
2	825	0.85	0.87	89	empty
3	758	0.84	0.88	77	empty
4	67	0.74	0.99	14	empty
5	64	0.73	0.98	15	empty

Interfaces

9 interfaces between chains.

A–C · 1161 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 1159 Å² buried · 27 hydrogen bonds · protein-protein
B–D · 1149 Å² buried · 23 hydrogen bonds · protein-protein
C–E · 753 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 744 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4JLY · Dodecameric structure of spermidine N-acetyltransferase from Vibrio cholerae · the same entry in another collection · chain F against F, TM-score 1.00
Q9KL03 · AlphaFold monomer V2.0 prediction for spermidine N(1)-acetyltransferase (Q9KL03) · a predicted model of the same protein · chain E against A, TM-score 0.93

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9KL03
Elsewhere: RCSB PDB 4JLY · PDBe 4JLY · UniProt Q9KL03

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