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Crystal structure of spermidine synthase from pyrococcus horikoshii OT3, P1 form

Analyse Crystal structure of spermidine synthase from pyrococcus horikoshii OT3, P1 form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ZSU
Type: protein
Length: 1,654 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spermidine synthase
EC: 2.5.1.16
UniProt: O57950
Ligands: AG3
Pockets: 14 · best druggability 0.77

Structure

x-ray diffraction · 6 distinct chains · 33% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spermidine synthase (EC 2.5.1.16)	protein	280	33% helix, 33% strand	O57950
B	Spermidine synthase (EC 2.5.1.16)	protein	278	34% helix, 33% strand	O57950
C	Spermidine synthase (EC 2.5.1.16)	protein	273	33% helix, 33% strand	O57950
D	Spermidine synthase (EC 2.5.1.16)	protein	271	32% helix, 34% strand	O57950
E	Spermidine synthase (EC 2.5.1.16)	protein	279	35% helix, 33% strand	O57950
F	Spermidine synthase (EC 2.5.1.16)	protein	273	32% helix, 33% strand	O57950

Ligands and binding sites

AG3 · 1-{4-[(3-aminopropyl)amino]butyl}guanidine · ligand · 3 copies · chains A, C, E

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

Pockets

14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1130	0.77	0.79	109	empty
2	219	0.72	0.88	39	AG3
3	196	0.71	0.88	36	AG3
4	232	0.65	0.83	38	AG3
5	211	0.61	0.81	29	empty

Interfaces

6 interfaces between chains.

C–D · 1911 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1909 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 1899 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 500 Å² buried · 3 hydrogen bonds · protein-protein
D–E · 369 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

2ZSU · Crystal structure of spermidine synthase from Pyrococcus horikoshii OT3, P1 form · the same entry in another collection · chain F against F, TM-score 1.00
O57950 · AlphaFold monomer V2.0 prediction for polyamine aminopropyltransferase (O57950) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 O57950
Elsewhere: RCSB PDB 2ZSU · PDBe 2ZSU · UniProt O57950

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