Research workbench

Human neuronal RAB6B in three intermediate forms

Analyse Human neuronal RAB6B in three intermediate forms in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2E9S
Type: protein
Length: 468 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-6B
UniProt: Q9NRW1
Ligands: GDP, MG, NO3
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-related protein rab-6B	protein	164	40% helix, 26% strand	Q9NRW1
B	RAS-related protein rab-6B	protein	150	41% helix, 25% strand	Q9NRW1
C	RAS-related protein rab-6B	protein	154	38% helix, 26% strand	Q9NRW1

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
MG · Magnesium ion · metal · 2 copies · chains A, B
NO3 · Nitrate ion · ion · chains 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	490	0.67	0.78	44	empty
2	176	0.58	0.82	30	NO3, MG, GDP
3	109	0.39	0.75	17	empty
4	69	0.34	0.76	16	empty

Interfaces

3 interfaces between chains.

A–B · 467 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 394 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 356 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2E9S · human neuronal Rab6B in three intermediate forms · the same entry in another collection · chain A against A, TM-score 1.00
Q9NRW1 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-6B (Q9NRW1) · a predicted model of the same protein · chain A 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 Q9NRW1
Elsewhere: RCSB PDB 2E9S · PDBe 2E9S · UniProt Q9NRW1

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