Research workbench
Neuropilin2-b1 domain in a complex with the C-terminal VEGFB167 peptide
Analyse Neuropilin2-b1 domain in a complex with the C-terminal VEGFB167 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TDB
- Type
- protein
- Length
- 641 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.45
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Neuropilin-2; C-terminal VEGFB167 peptide
- UniProt
- O60462
- Ligands
- ACE
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.45 · 6 distinct chains · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuropilin-2 | protein | 158 | 4% helix, 49% strand | O60462 |
| B, C | Neuropilin-2 | protein | 157 | 4% helix, 49% strand | O60462 |
| D | Neuropilin-2 | protein | 159 | 4% helix, 48% strand | O60462 |
| F | C-terminal VEGFB167 peptide | protein | 5 | 0% helix, 0% strand | — |
| J | C-terminal VEGFB167 peptide | protein | 2 | 0% helix, 0% strand | — |
| K | C-terminal VEGFB167 peptide | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains B, F
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.72 | 0.77 | 84 | empty |
| 2 | 247 | 0.64 | 0.82 | 28 | EDO |
| 3 | 85 | 0.30 | 0.73 | 17 | empty |
| 4 | 65 | 0.28 | 0.73 | 19 | empty |
| 5 | 73 | 0.27 | 0.72 | 19 | empty |
Interfaces
9 interfaces between chains.
- A–F · 333 Ų buried · 5 hydrogen bonds · protein-protein
- D–K · 307 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 279 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 275 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 275 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
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 6TDB · PDBe 6TDB · UniProt O60462
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