MolNFT v1 · #78947 · protein

Crystal structure of human septin 3 GTPase domain

3SOP · Neuronal-specific septin-3: “Crystal structure of human septin 3 GTPase domain”. X-ray diffraction, 2 ligands (GDP, MG), 3 pockets (best druggability 0.73). MolNFT v1 #78947 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3SOP
Type: protein
Length: 500 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neuronal-specific septin-3
EC: 3.6.5.-
UniProt: Q9UH03
Ligands: GDP, MG
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neuronal-specific septin-3 (EC 3.6.5.-)	protein	248	42% helix, 18% strand	Q9UH03
B	Neuronal-specific septin-3 (EC 3.6.5.-)	protein	252	39% helix, 16% strand	Q9UH03

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	570	0.73	0.81	83	MG, GDP
2	287	0.65	0.81	45	MG, GDP
3	355	0.63	0.78	46	empty

Interfaces

1 interface between chains.

A–B · 1076 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3SOP · Crystal Structure Of Human Septin 3 GTPase Domain · the same entry in another collection · chain A against A, TM-score 1.00
Q9UH03 · AlphaFold monomer V2.0 prediction for neuronal-specific septin-3 (Q9UH03) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9UH03
Elsewhere: RCSB PDB 3SOP · PDBe 3SOP · UniProt Q9UH03

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