Research workbench

RAC1-GDP-zinc complex

Analyse RAC1-GDP-zinc complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2P2L
Type: protein
Length: 533 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-related C3 botulinum toxin substrate 1
UniProt: P63000
Ligands: GDP, ZN
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-related C3 botulinum toxin substrate 1	protein	176	38% helix, 21% strand	P63000
B	RAS-related C3 botulinum toxin substrate 1	protein	178	38% helix, 23% strand	P63000
C	RAS-related C3 botulinum toxin substrate 1	protein	179	36% helix, 25% strand	P63000

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
ZN · Zinc ion · metal · 8 copies · chains A, B, C

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	967	0.78	0.80	75	ZN, GDP
2	342	0.58	0.76	38	empty
3	264	0.58	0.78	42	ZN, GDP
4	233	0.56	0.78	30	ZN, GDP

Interfaces

3 interfaces between chains.

B–C · 498 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 481 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 471 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

2P2L · Rac1-GDP-Zinc Complex · the same entry in another collection · chain A against A, TM-score 1.00
P63000 · AlphaFold monomer V2.0 prediction for RAS-related C3 botulinum toxin substrate 1 (P63000) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 2P2L · PDBe 2P2L · UniProt P63000

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