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Neuropilin-1 B1 domain in complex with a VEGF-blocking Fab

Analyse Neuropilin-1 B1 domain in complex with a VEGF-blocking Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QQN
Type: protein
Length: 594 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neuropilin-1; Antibody heavy chain; Antibody light chain
UniProt: O14786
Pockets: 6 · best druggability 0.56

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neuropilin-1	protein	154	6% helix, 51% strand	O14786
H	Antibody heavy chain	protein	226	7% helix, 49% strand	—
L	Antibody light chain	protein	214	6% helix, 51% strand	—

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 3 copies · chains A, H, L

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

Pockets

6 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	225	0.56	0.79	36	empty
2	345	0.54	0.74	44	empty
3	106	0.44	0.78	28	EDO
4	84	0.31	0.73	18	empty
5	70	0.30	0.74	16	empty

Interfaces

3 interfaces between chains.

H–L · 1937 Å² buried · 17 hydrogen bonds · protein-protein
A–L · 285 Å² buried · 9 hydrogen bonds · protein-protein
A–H · 266 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

2QQN · Neuropilin-1 b1 Domain in Complex with a VEGF-Blocking Fab · 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 1.00

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 2QQN · PDBe 2QQN · UniProt O14786

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