Research workbench

Mouse neuropilin-1, extracellular domains 1-4 (A1A2B1B2)

Analyse Mouse neuropilin-1, extracellular domains 1-4 (A1A2B1B2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GZ9
Type: protein
Length: 562 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neuropilin-1
UniProt: P97333
Ligands: NAG, BMA, CA, SO4
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neuropilin-1	protein	562	4% helix, 45% strand	P97333

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
BMA · beta-D-mannopyranose · sugar
CA · Calcium ion · metal · 2 copies · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A
EDO · 1,2-ethanediol · additive · 3 copies · chains A

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

Pockets

4 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	410	0.64	0.78	59	SO4, EDO
2	124	0.44	0.77	20	EDO
3	75	0.43	0.80	16	empty
4	50	0.32	0.78	18	empty

Modifications

Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

4GZ9 · Mouse Neuropilin-1, extracellular domains 1-4 (a1a2b1b2) · the same entry in another collection · chain A against A, TM-score 1.00
P97333 · AlphaFold monomer V2.0 prediction for neuropilin-1 (P97333) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 P97333
Elsewhere: RCSB PDB 4GZ9 · PDBe 4GZ9 · UniProt P97333

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.