MolNFT v1 · #137182 · protein

Human atlastin-3, GDP-bound

5VGR: “Human atlastin-3, GDP-bound”. X-ray diffraction, 1 ligand (GDP), 10 pockets (best druggability 0.61). MolNFT v1 #137182 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VGR
Type: protein
Length: 771 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Atlastin-3
EC: 3.6.5.-
UniProt: Q6DD88
Ligands: GDP
Pockets: 10 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Atlastin-3 (EC 3.6.5.-)	protein	408	47% helix, 17% strand	Q6DD88
B	Atlastin-3 (EC 3.6.5.-)	protein	363	44% helix, 19% strand	Q6DD88

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B

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

Pockets

10 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	54	0.61	0.92	18	empty
2	317	0.60	0.78	31	GDP
3	289	0.59	0.78	31	GDP
4	56	0.53	0.88	19	empty
5	119	0.48	0.80	21	empty

Interfaces

1 interface between chains.

A–B · 60 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5VGR · Human Atlastin-3, GDP-bound · the same entry in another collection · chain A against A, TM-score 1.00
Q6DD88 · AlphaFold monomer V2.0 prediction for atlastin-3 (Q6DD88) · a predicted model of the same protein · chain B against A, TM-score 0.77

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 Q6DD88
Elsewhere: RCSB PDB 5VGR · PDBe 5VGR · UniProt Q6DD88

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