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Human RAB8A phosphorylated at SER111 in complex with gppnp

Analyse Human RAB8A phosphorylated at SER111 in complex with gppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6STG
Type: protein
Length: 341 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rab-8A
UniProt: P61006
Ligands: GNP, MG
Pockets: 2 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-related protein rab-8A	protein	172	38% helix, 27% strand	P61006
B	RAS-related protein rab-8A	protein	169	39% helix, 27% strand	P61006

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	146	0.55	0.81	29	GNP, MG
2	120	0.46	0.78	28	GNP, MG

Interfaces

1 interface between chains.

A–B · 1118 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

6STG · Human Rab8a phosphorylated at Ser111 in complex with GPPNP · the same entry in another collection · chain A against A, 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 6STG · PDBe 6STG · UniProt P61006

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