MolNFT v1 · #81989 · protein

Structure of apo-glycogenin truncated at residue 270

3V8Y · Glycogenin-1: “Structure of apo-glycogenin truncated at residue 270”. X-ray diffraction, 1 ligand (CL), 3 pockets (best druggability 0.52). MolNFT v1 #81989 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3V8Y
Type: protein
Length: 259 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycogenin-1
EC: 2.4.1.186
UniProt: P13280
Ligands: CL
Pockets: 3 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycogenin-1 (EC 2.4.1.186)	protein	259	44% helix, 18% strand	P13280

Ligands and binding sites

CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	86	0.52	0.84	17	empty
2	189	0.48	0.76	25	empty
3	56	0.34	0.77	14	empty

Compared structures

3V8Y · Structure of apo-glycogenin truncated at residue 270 · the same entry in another collection · chain A against A, TM-score 1.00
P13280 · AlphaFold monomer V2.0 prediction for glycogenin-1 (P13280) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P13280
Elsewhere: RCSB PDB 3V8Y · PDBe 3V8Y · UniProt P13280

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