MolNFT v1 · #78658 · protein

Crystal structure of the GDP-bound RAB1A S25N mutant in complex with the coiled-coil domain of lida from legionella pneumophila

3SFV · RAS-related protein rab-1A: “Crystal structure of the GDP-bound RAB1A S25N mutant in complex with the coiled-coil domain of lida from…”. X-ray diffraction, 1 ligand (GDP), 7 pockets (best druggability 0.82). MolNFT v1 #78658 on…

PDB: 3SFV
Type: protein
Length: 521 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-1A; Lida protein, substrate of the DOT/ICM system
UniProt: P62820, A5IFX1
Ligands: GDP
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 53% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-related protein rab-1A	protein	179	34% helix, 24% strand	P62820
B	Lida protein, substrate of the DOT/ICM system	protein	342	63% helix, 16% strand	A5IFX1

Ligands and binding sites

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

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	966	0.82	0.83	92	GDP
2	1061	0.75	0.78	92	empty
3	148	0.50	0.78	22	empty
4	156	0.50	0.78	22	empty
5	112	0.40	0.76	19	empty

Interfaces

1 interface between chains.

A–B · 2195 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

3SFV · Crystal structure of the GDP-bound Rab1a S25N mutant in complex with the coiled-coil… · the same entry in another collection · chain A against A, TM-score 1.00
P62820 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-1A (P62820) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P62820
Every structure of UniProt A5IFX1
Elsewhere: RCSB PDB 3SFV · PDBe 3SFV · UniProt P62820 · UniProt A5IFX1

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