MolNFT v1 · #127776 · protein

Wild type human RAC1-GDP

5N6O · RAS-related C3 botulinum toxin substrate 1: “Wild type human RAC1-GDP”. X-ray diffraction, 2 ligands (GDP, MG), 4 pockets (best druggability 0.68). MolNFT v1 #127776 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5N6O
Type: protein
Length: 352 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related C3 botulinum toxin substrate 1
UniProt: P63000
Ligands: GDP, MG
Pockets: 4 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RAS-related C3 botulinum toxin substrate 1	protein	176	39% helix, 21% strand	P63000

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

4 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	331	0.68	0.82	30	empty
2	122	0.42	0.76	30	GDP, MG
3	97	0.40	0.77	28	GDP, MG
4	91	0.39	0.77	14	empty

Interfaces

1 interface between chains.

A–B · 548 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5N6O · Wild type human Rac1-GDP · the same entry in another collection · chain A against A, TM-score 1.00

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 P63000
Elsewhere: RCSB PDB 5N6O · PDBe 5N6O · UniProt P63000

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