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Mouse plexin A2, extracellular domains 1-4

Analyse Mouse plexin A2, extracellular domains 1-4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3OKT
Type: protein
Length: 656 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plexin-A2
UniProt: P70207
Ligands: NAG, NA, CL
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Plexin-A2	protein	656	11% helix, 39% strand	P70207

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
NA · Sodium ion · metal · chains A
CL · Chloride ion · ion · 2 copies · chains A
GOL · Glycerol · additive · 4 copies · chains A

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

Pockets

6 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	993	0.76	0.78	86	GOL
2	92	0.48	0.82	21	empty
3	52	0.47	0.86	22	empty
4	162	0.43	0.74	26	empty
5	66	0.35	0.77	21	empty

Modifications

Observed in the structure: 14 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

3OKT · Mouse Plexin A2, extracellular domains 1-4 · the same entry in another collection · chain A against A, TM-score 1.00
P70207 · AlphaFold monomer V2.0 prediction for plexin-A2 (P70207) · 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 P70207
Elsewhere: RCSB PDB 3OKT · PDBe 3OKT · UniProt P70207

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