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Structures of the yeast dynamin-like GTPase SEY1P in complex with GDP

Analyse Structures of the yeast dynamin-like GTPase SEY1P 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: 5CA8
Type: protein
Length: 636 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein SEY1
EC: 3.6.5.5
UniProt: Q9C0L9
Ligands: GDP, MG
Pockets: 2 · best druggability 0.41

Structure

x-ray diffraction · 1 distinct chain · 58% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein SEY1 (EC 3.6.5.5)	protein	636	58% helix, 10% strand	Q9C0L9

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	121	0.41	0.75	27	MG, GDP
2	105	0.40	0.76	24	empty

Compared structures

5CA8 · Structures of the yeast dynamin-like GTPase Sey1p in complex with GDP · the same entry in another collection · chain A against A, TM-score 1.00
Q9C0L9 · AlphaFold monomer V2.0 prediction for protein SEY1 (Q9C0L9) · a predicted model of the same protein · chain A against A, TM-score 0.61

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 Q9C0L9
Elsewhere: RCSB PDB 5CA8 · PDBe 5CA8 · UniProt Q9C0L9

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