MolNFT v1 · #125304 · protein

Plexin A1 full extracellular region, domains 1 to 10, to 4 ångström

5L56 · Plexin-A1: “Plexin A1 full extracellular region, domains 1 to 10, to 4 ångström”. X-ray diffraction, 3 ligands (MAN, NAG, BMA), 9 pockets (best druggability 0.80). MolNFT v1 #125304 on GenesisL1: 3D structure, binding sites and…

PDB: 5L56
Type: protein
Length: 1,171 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Plexin-A1
UniProt: P70206
Ligands: MAN, NAG, BMA
Pockets: 9 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Plexin-A1	protein	1171	7% helix, 39% strand	P70206

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 22 copies · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A
BMA · beta-D-mannopyranose · sugar · 9 copies

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

Pockets

9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	987	0.80	0.81	77	empty
2	200	0.55	0.79	21	empty
3	119	0.42	0.76	18	empty
4	115	0.38	0.75	27	empty
5	65	0.34	0.77	14	empty

Modifications

Observed in the structure: 24 disulfide, 10 glycan (disulfide, N-glycosylation).

Compared structures

5L56 · Plexin A1 full extracellular region, domains 1 to 10, to 4 angstrom · 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 0.97

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
Elsewhere: RCSB PDB 5L56 · PDBe 5L56 · UniProt P70206

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