MolNFT v1 · #78100 · protein

The plexin A1 intracellular region in complex with RAC1

3RYT · Plexin-A1: “The plexin A1 intracellular region in complex with RAC1”. X-ray diffraction, 2 ligands (GNP, MG), 20 pockets (best druggability 0.80). MolNFT v1 #78100 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3RYT
Type: protein
Length: 1,237 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plexin-A1; RAS-related C3 botulinum toxin substrate 1
UniProt: P70206, P63000
Ligands: GNP, MG
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Plexin-A1	protein	532	55% helix, 7% strand	P70206
B	Plexin-A1	protein	531	56% helix, 7% strand	P70206
C	RAS-related C3 botulinum toxin substrate 1	protein	174	36% helix, 20% strand	P63000

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains C
MG · Magnesium ion · metal · chains C

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	164	0.80	0.95	29	empty
2	696	0.79	0.84	75	empty
3	99	0.78	0.98	27	empty
4	582	0.71	0.79	71	empty
5	299	0.66	0.82	35	empty

Interfaces

2 interfaces between chains.

A–B · 1029 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 575 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3RYT · The Plexin A1 intracellular region in complex with Rac1 · the same entry in another collection · chain A against A, TM-score 1.00
P70206 · AlphaFold monomer V2.0 prediction for plexin-A1 (P70206) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P70206
Every structure of UniProt P63000
Elsewhere: RCSB PDB 3RYT · PDBe 3RYT · UniProt P70206 · UniProt P63000

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