MolNFT v1 · #98723 · protein

Crystal structure of RAB8 in its active gppnhp-bound form

4LHW · RAS-related protein rab-8A: “Crystal structure of RAB8 in its active gppnhp-bound form”. X-ray diffraction, 2 ligands (GNP, MG), 12 pockets (best druggability 0.83). MolNFT v1 #98723 on GenesisL1: 3D structure, binding sites and…

PDB: 4LHW
Type: protein
Length: 859 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-8A
UniProt: P61006
Ligands: GNP, MG
Pockets: 12 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	RAS-related protein rab-8A	protein	171	37% helix, 29% strand	P61006
B	RAS-related protein rab-8A	protein	173	38% helix, 28% strand	P61006
D	RAS-related protein rab-8A	protein	173	37% helix, 28% strand	P61006

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 5 copies · chains A, B, C, D, E
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B

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

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	726	0.83	0.87	98	MG, GNP
2	50	0.68	0.97	18	empty
3	464	0.64	0.77	45	empty
4	154	0.62	0.84	29	MG, GNP
5	85	0.54	0.86	21	empty

Interfaces

8 interfaces between chains.

A–B · 604 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 498 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 494 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 321 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 211 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4LHW · Crystal structure of Rab8 in its active GppNHp-bound form · the same entry in another collection · chain E against E, 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 0.99

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 P61006
Elsewhere: RCSB PDB 4LHW · PDBe 4LHW · UniProt P61006

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