MolNFT v1 · #165106 · protein
NEUROPILIN2-B1 domain in a complex with the C-terminal vegfc peptide
6TJT · Neuropilin-2: “NEUROPILIN2-B1 domain in a complex with the C-terminal vegfc peptide”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.36). MolNFT v1 #165106 on GenesisL1: 3D structure, binding sites and pockets in…
- 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.
| Volume (ų) | 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 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 367 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 353 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
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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