MolNFT v1 · #116746 · protein
Human NRP2 B1 domain in complex with the peptide corresponding to the C-terminus of VEGF-a
5DN2 · Neuropilin-2: “Human NRP2 B1 domain in complex with the peptide corresponding to the C-terminus of VEGF-a”. X-ray diffraction, 3 pockets (best druggability 0.66). MolNFT v1 #116746 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DN2
- Type
- protein
- Length
- 640 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuropilin-2; Vascular endothelial growth factor a
- UniProt
- O60462, P15692
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neuropilin-2 | protein | 156 | 4% helix, 49% strand | O60462 |
| F, G | Vascular endothelial growth factor a | protein | 4 | 0% helix, 0% strand | P15692 |
| E | Vascular endothelial growth factor a | protein | 8 | 0% helix, 0% strand | P15692 |
Ligands and binding sites
- DIO · 1,4-diethylene dioxide · additive · 2 copies · chains B, D
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.66 | 0.76 | 62 | empty |
| 2 | 183 | 0.58 | 0.82 | 23 | empty |
| 3 | 283 | 0.56 | 0.77 | 40 | empty |
Interfaces
9 interfaces between chains.
- A–B · 456 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 367 Ų buried · 9 hydrogen bonds · protein-protein
- A–G · 353 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 344 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 262 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5DN2 · Human NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-A · the same entry in another collection · chain E against E, TM-score 1.00
- O60462 · AlphaFold monomer V2.0 prediction for neuropilin-2 (O60462) · a predicted model of the same protein · chain A 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 O60462
- Every structure of UniProt P15692
- Elsewhere: RCSB PDB 5DN2 · PDBe 5DN2 · UniProt O60462 · UniProt P15692
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