MolNFT v1 · #84062 · protein

RAS-related protein RAP1B with GDP

3X1W · RAS-related protein rap-1B: “RAS-related protein RAP1B with GDP”. X-ray diffraction, 3 ligands (GDP, MG, CD), 1 pocket (best druggability 0.48). MolNFT v1 #84062 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3X1W
Type: protein
Length: 167 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related protein rap-1B
UniProt: Q62636
Ligands: GDP, MG, CD
Pockets: 1 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-related protein rap-1B	protein	167	38% helix, 26% strand	Q62636

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A
CD · Cadmium ion · metal · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	138	0.48	0.78	29	GDP, MG

Compared structures

3X1W · Ras-related protein Rap1B with GDP · 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 3X1W · PDBe 3X1W · UniProt Q62636

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