MolNFT v1 · #84046 · protein

Crystal structure of atlastin from drosophila melanogaster

3X1D: “Crystal structure of atlastin from drosophila melanogaster”. X-ray diffraction, 2 ligands (GDP, MG), 6 pockets (best druggability 0.54). MolNFT v1 #84046 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3X1D
Type: protein
Length: 381 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Atlastin
EC: 3.6.5.-
UniProt: Q9VC57
Ligands: GDP, MG
Pockets: 6 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Atlastin (EC 3.6.5.-)	protein	381	35% helix, 12% strand	Q9VC57

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

6 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	282	0.54	0.76	28	empty
2	171	0.48	0.77	26	GDP, MG
3	132	0.46	0.77	22	empty
4	132	0.44	0.76	22	empty
5	57	0.38	0.80	11	empty

Compared structures

3X1D · Crystal Structure of Atlastin from Drosophila melanogaster · the same entry in another collection · chain A against A, TM-score 1.00
Q9VC57 · AlphaFold monomer V2.0 prediction for atlastin (Q9VC57) · a predicted model of the same protein · chain A against A, TM-score 0.70

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 Q9VC57
Elsewhere: RCSB PDB 3X1D · PDBe 3X1D · UniProt Q9VC57

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