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Human atlastin-1 (residues 1-439) bound to GDP-MG2+ exhibits an ordered amino terminus

Analyse Human atlastin-1 (residues 1-439) bound to GDP-MG2+ exhibits an ordered amino… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XJN
Type: protein
Length: 417 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Atlastin-1
EC: 3.6.5.-
UniProt: Q8WXF7
Ligands: GDP, MG
Pockets: 3 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Atlastin-1 (EC 3.6.5.-)	protein	417	47% helix, 19% strand	Q8WXF7

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

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	231	0.52	0.76	34	GDP
2	77	0.42	0.79	15	empty
3	54	0.33	0.77	14	empty

Compared structures

6XJN · Human atlastin-1 (residues 1-439) bound to GDP-Mg2+ exhibits an ordered amino terminus · the same entry in another collection · chain A against A, TM-score 1.00
Q8WXF7 · AlphaFold monomer V2.0 prediction for atlastin-1 (Q8WXF7) · a predicted model of the same protein · chain A against A, TM-score 0.69

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 Q8WXF7
Elsewhere: RCSB PDB 6XJN · PDBe 6XJN · UniProt Q8WXF7

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