MolNFT v1 · #57868 · protein

Mouse plexin A2 extracellular domain

3AL9 · Plexin-A2: “Mouse plexin A2 extracellular domain”. X-ray diffraction, 1 ligand (NAG), 10 pockets (best druggability 0.84). MolNFT v1 #57868 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3AL9
Type: protein
Length: 1,032 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plexin-A2
UniProt: P70207
Ligands: NAG
Pockets: 10 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Plexin-A2	protein	516	11% helix, 40% strand	P70207

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B

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

Pockets

10 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	897	0.84	0.86	90	empty
2	898	0.76	0.79	74	empty
3	597	0.72	0.79	43	EDO
4	319	0.61	0.78	36	empty
5	102	0.45	0.79	21	empty

Interfaces

1 interface between chains.

A–B · 908 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

3AL9 · Mouse Plexin A2 extracellular domain · 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 0.99

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 3AL9 · PDBe 3AL9 · UniProt P70207

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