MolNFT v1 · #167363 · protein

Crystal structure of mouse RABL3 in complex with gtpgammas

6VII · Rab-like protein 3: “Crystal structure of mouse RABL3 in complex with gtpgammas”. X-ray diffraction, 2 ligands (GSP, MG), 4 pockets (best druggability 0.71). MolNFT v1 #167363 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6VII
Type: protein
Length: 373 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rab-like protein 3
UniProt: Q9D4V7
Ligands: GSP, MG
Pockets: 4 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Rab-like protein 3	protein	190	40% helix, 24% strand	Q9D4V7
A	Rab-like protein 3	protein	183	39% helix, 23% strand	Q9D4V7

Ligands and binding sites

GSP · 5'-guanosine-diphosphate-monothiophosphate · ligand · 2 copies · chains B, A
MG · Magnesium ion · metal · 2 copies · chains B, A

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

Pockets

4 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	536	0.71	0.80	58	empty
2	110	0.43	0.78	25	MG, GSP
3	118	0.42	0.76	24	MG, GSP
4	79	0.41	0.79	20	empty

Interfaces

1 interface between chains.

B–A · 926 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6VII · Crystal structure of mouse RABL3 in complex with GTPgammaS · the same entry in another collection · chain B against B, TM-score 1.00
Q9D4V7 · AlphaFold monomer V2.0 prediction for rab-like protein 3 (Q9D4V7) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q9D4V7
Elsewhere: RCSB PDB 6VII · PDBe 6VII · UniProt Q9D4V7

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.