MolNFT v1 · #94074 · protein

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

4HLQ · TBC1 domain family member 20: “Crystal structure of human RAB1B bound to GDP and BEF3 in complex with the gap domain of TBC1D20 from homo…”. X-ray diffraction, 4 ligands (GDP, BEF, MG), 20 pockets (best druggability 0.79). MolNFT v1…

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

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q96BZ9
Every structure of UniProt Q9H0U4
Elsewhere: RCSB PDB 4HLQ · PDBe 4HLQ · UniProt Q96BZ9 · UniProt Q9H0U4

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