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Crystal structure of GDP-bound RAB8:GRAB

Analyse Crystal structure of GDP-bound RAB8:GRAB in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LI0
Type: protein
Length: 613 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-8A; Guanine nucleotide exchange factor for rab-3A
UniProt: P61006, Q8TBN0
Ligands: GDP
Pockets: 5 · best druggability 0.45

Structure

x-ray diffraction · 5 distinct chains · 60% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-related protein rab-8A	protein	171	39% helix, 29% strand	P61006
B	RAS-related protein rab-8A	protein	171	39% helix, 27% strand	P61006
C, D	Guanine nucleotide exchange factor for rab-3A	protein	69	97% helix, 0% strand	Q8TBN0
E	Guanine nucleotide exchange factor for rab-3A	protein	64	95% helix, 0% strand	Q8TBN0
F	Guanine nucleotide exchange factor for rab-3A	protein	69	96% helix, 0% strand	Q8TBN0

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

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	98	0.45	0.79	19	empty
2	68	0.37	0.78	17	empty
3	89	0.36	0.76	14	empty
4	74	0.36	0.77	16	empty
5	78	0.33	0.75	12	empty

Interfaces

7 interfaces between chains.

C–D · 1481 Å² buried · 4 hydrogen bonds · protein-protein
E–F · 1297 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 751 Å² buried · 3 hydrogen bonds · protein-protein
A–E · 725 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 613 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4LI0 · Crystal structure of GDP-bound Rab8:GRAB · the same entry in another collection · chain F against F, TM-score 1.00
P61006 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-8A (P61006) · a predicted model of the same protein · chain B against A, TM-score 0.92
Q8TBN0 · AlphaFold monomer V2.0 prediction for guanine nucleotide exchange factor for rab-3A… · a predicted model of the same protein · chain E against A, TM-score 0.76

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 P61006
Every structure of UniProt Q8TBN0
Elsewhere: RCSB PDB 4LI0 · PDBe 4LI0 · UniProt P61006 · UniProt Q8TBN0

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