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Crystal structure of human RAB1B bound to GDP and BEF3 in complex with the gap domain of TBC1D20 from homo sapiens

Analyse Crystal structure of human RAB1B bound to GDP and BEF3 in complex with the gap… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HLQ
Type: protein
Length: 2,259 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TBC1 domain family member 20; RAS-related protein rab-1B
UniProt: Q96BZ9, Q9H0U4
Ligands: GDP, BEF, MG, SO4
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 5 distinct chains · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TBC1 domain family member 20	protein	280	65% helix, 0% strand	Q96BZ9
B, F	RAS-related protein rab-1B	protein	172	37% helix, 28% strand	Q9H0U4
C, E, G, I	TBC1 domain family member 20	protein	281	65% helix, 0% strand	Q96BZ9
D, H	RAS-related protein rab-1B	protein	170	35% helix, 26% strand	Q9H0U4
J	RAS-related protein rab-1B	protein	171	34% helix, 26% strand	Q9H0U4

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D, E, F, G, H, I, J
BEF · Beryllium trifluoride ion · ligand · 5 copies · chains A, B, C, D, E, F, G, H, I, J
MG · Magnesium ion · metal · 5 copies · chains B, C, D, E, F, G, H, J
SO4 · Sulfate ion · ion · 5 copies · chains A, C, E, H, I

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	996	0.79	0.81	94	MG, GDP, BEF
2	1123	0.79	0.80	109	MG, GDP, BEF
3	1047	0.73	0.76	90	empty
4	458	0.67	0.79	51	GDP, BEF
5	519	0.67	0.78	61	empty

Interfaces

13 interfaces between chains.

A–B · 1291 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1270 Å² buried · 14 hydrogen bonds · protein-protein
I–J · 1214 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 1188 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 1123 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

4HLQ · Crystal structure of human rab1b bound to GDP and BEF3 in complex with the GAP domain of… · the same entry in another collection · chain J against J, TM-score 1.00
Q96BZ9 · AlphaFold monomer V2.0 prediction for TBC1 domain family member 20 (Q96BZ9) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

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Every structure of UniProt Q96BZ9
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Elsewhere: RCSB PDB 4HLQ · PDBe 4HLQ · UniProt Q96BZ9 · UniProt Q9H0U4

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