Research workbench

RAS-related protein RAP1B(L9V) with gppnhp

Analyse RAS-related protein RAP1B(L9V) with gppnhp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3X1Y
Type: protein
Length: 166 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rap-1B
UniProt: Q62636
Ligands: GNP, MG, CD
Pockets: 2 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-related protein rap-1B	protein	166	36% helix, 25% strand	Q62636

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
MG · Magnesium ion · metal · chains A
CD · Cadmium ion · metal · chains A
GOL · Glycerol · additive · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	154	0.46	0.77	29	GNP, MG
2	56	0.32	0.76	13	empty

Compared structures

3X1Y · Ras-related protein Rap1B(L9V) with GppNHp · the same entry in another collection · chain A against A, TM-score 1.00
Q62636 · AlphaFold monomer V2.0 prediction for RAS-related protein rap-1B (Q62636) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q62636
Elsewhere: RCSB PDB 3X1Y · PDBe 3X1Y · UniProt Q62636

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