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Crystal structure of the B1B2 domains from human neuropilin-1

Analyse Crystal structure of the B1B2 domains from human neuropilin-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QQI
Type: protein
Length: 315 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neuropilin-1
UniProt: O14786
Pockets: 5 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neuropilin-1	protein	315	6% helix, 44% strand	O14786

Ligands and binding sites

GOL · Glycerol · additive · chains A

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

Pockets

5 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	122	0.62	0.86	28	empty
2	246	0.53	0.76	32	empty
3	75	0.34	0.76	22	empty
4	63	0.33	0.76	13	empty
5	51	0.30	0.76	13	empty

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

2QQI · Crystal Structure of the b1b2 Domains from Human Neuropilin-1 · the same entry in another collection · chain A against A, TM-score 1.00
O14786 · AlphaFold monomer V2.0 prediction for neuropilin-1 (O14786) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 O14786
Elsewhere: RCSB PDB 2QQI · PDBe 2QQI · UniProt O14786

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