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Human spermidine synthase

Analyse Human spermidine synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2O06
Type: protein
Length: 586 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spermidine synthase
EC: 2.5.1.16
UniProt: P19623
Ligands: MTA, PUT, MG
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spermidine synthase (EC 2.5.1.16)	protein	297	32% helix, 31% strand	P19623
B	Spermidine synthase (EC 2.5.1.16)	protein	289	33% helix, 31% strand	P19623

Ligands and binding sites

MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 2 copies · chains A, B
PUT · 1,4-diaminobutane · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 3 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	193	0.78	0.93	42	MTA, PUT
2	144	0.77	0.94	31	MTA
3	50	0.72	0.99	22	empty
4	57	0.71	0.98	22	empty
5	86	0.47	0.82	16	empty

Interfaces

1 interface between chains.

A–B · 1739 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

2O06 · Human spermidine synthase · the same entry in another collection · chain A against A, TM-score 1.00
P19623 · AlphaFold monomer V2.0 prediction for spermidine synthase (P19623) · a predicted model of the same protein · chain B 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 P19623
Elsewhere: RCSB PDB 2O06 · PDBe 2O06 · UniProt P19623

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