MolNFT v1 · #55379 · protein

Structure of the complex between DOCK2 and RAC1.

2YIN · Dedicator of cytokinesis protein 2: “Structure of the complex between DOCK2 and RAC1.”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #55379 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2YIN
Type: protein
Length: 1,182 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dedicator of cytokinesis protein 2; RAS-related C3 botulinum toxin substrate 1
UniProt: Q92608, P63000
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dedicator of cytokinesis protein 2	protein	411	58% helix, 15% strand	Q92608
B	Dedicator of cytokinesis protein 2	protein	410	56% helix, 15% strand	Q92608
C	RAS-related C3 botulinum toxin substrate 1	protein	180	37% helix, 23% strand	P63000
D	RAS-related C3 botulinum toxin substrate 1	protein	181	40% helix, 23% strand	P63000

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1168	0.81	0.83	98	empty
2	1167	0.80	0.82	97	empty
3	89	0.76	0.97	18	empty
4	357	0.69	0.82	40	empty
5	265	0.56	0.76	36	empty

Interfaces

6 interfaces between chains.

B–D · 1916 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 1904 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 549 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 96 Å² buried · 1 hydrogen bond · protein-protein
A–D · 63 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2YIN · STRUCTURE OF THE COMPLEX BETWEEN Dock2 AND Rac1. · the same entry in another collection · chain D against D, TM-score 1.00
Q92608 · AlphaFold monomer V2.0 prediction for dedicator of cytokinesis protein 2 (Q92608) · a predicted model of the same protein · chain B against A, TM-score 0.97
P63000 · AlphaFold monomer V2.0 prediction for RAS-related C3 botulinum toxin substrate 1 (P63000) · a predicted model of the same protein · chain C 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 Q92608
Every structure of UniProt P63000
Elsewhere: RCSB PDB 2YIN · PDBe 2YIN · UniProt Q92608 · UniProt P63000

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