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High resolution septin 9 GTPase domain in complex with GDP

Analyse High resolution septin 9 GTPase domain in complex with GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CYO
Type: protein
Length: 524 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Septin-9
UniProt: Q9UHD8
Ligands: GDP, MG
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Septin-9	protein	272	41% helix, 21% strand	Q9UHD8
B	Septin-9	protein	252	43% helix, 17% strand	Q9UHD8

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

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	163	0.76	0.93	33	empty
2	346	0.75	0.86	50	GDP, MG
3	261	0.73	0.88	42	GDP, MG
4	150	0.61	0.85	23	empty
5	69	0.38	0.78	12	empty

Interfaces

1 interface between chains.

A–B · 1510 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

5CYO · High resolution Septin 9 GTPase domain in complex with GDP · the same entry in another collection · chain A against A, TM-score 1.00
Q9UHD8 · AlphaFold monomer V2.0 prediction for septin-9 (Q9UHD8) · 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 Q9UHD8
Elsewhere: RCSB PDB 5CYO · PDBe 5CYO · UniProt Q9UHD8

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