MolNFT v1 · #123331 · protein

X-ray structure of neuropilin-1 B1 domain complexed with arg-7 ligand.

5JGQ: “X-ray structure of neuropilin-1 B1 domain complexed with arg-7 ligand.”. X-ray diffraction, 1 ligand (6JY), 3 pockets (best druggability 0.41). MolNFT v1 #123331 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5JGQ
Type: protein
Length: 312 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neuropilin-1
UniProt: O14786
Ligands: 6JY
Pockets: 3 · best druggability 0.41

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neuropilin-1	protein	158	6% helix, 48% strand	O14786
B	Neuropilin-1	protein	154	6% helix, 49% strand	O14786

Ligands and binding sites

6JY · N~2~-(benzenecarbonyl)-L-arginine · ligand · chains B
DMS · Dimethyl sulfoxide · additive · chains A

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	100	0.41	0.77	19	empty
2	99	0.38	0.76	19	empty
3	90	0.34	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 382 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5JGQ · X-ray structure of neuropilin-1 b1 domain complexed with Arg-7 ligand. · 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 B 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 O14786
Elsewhere: RCSB PDB 5JGQ · PDBe 5JGQ · UniProt O14786

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