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NEUROPILIN2-B1 domain in a complex with the C-terminal vegfc peptide

Analyse NEUROPILIN2-B1 domain in a complex with the C-terminal vegfc peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6TJT
Type: protein
Length: 323 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neuropilin-2; Vegfc C terminal peptide
UniProt: O60462
Ligands: SO4
Pockets: 2 · best druggability 0.36

Structure

x-ray diffraction · 3 distinct chains · 4% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neuropilin-2	protein	159	4% helix, 46% strand	O60462
B	Neuropilin-2	protein	158	4% helix, 46% strand	O60462
D, F	Vegfc C terminal peptide	protein	3	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B

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

Pockets

2 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	91	0.36	0.75	22	SO4
2	92	0.36	0.76	21	empty

Interfaces

3 interfaces between chains.

A–B · 443 Å² buried · 9 hydrogen bonds · protein-protein
B–F · 367 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 353 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6TJT · Neuropilin2-b1 domain in a complex with the C-terminal VEGFC peptide · the same entry in another collection · chain A against A, TM-score 1.00
O60462 · AlphaFold monomer V2.0 prediction for neuropilin-2 (O60462) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 O60462
Elsewhere: RCSB PDB 6TJT · PDBe 6TJT · UniProt O60462

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