MolNFT v1 · #104536 · protein
Physical basis for NRP2 ligand binding
4QDQ · Neuropilin-2: “Physical basis for NRP2 ligand binding”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.71). MolNFT v1 #104536 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4QDQ
- Type
- protein
- Length
- 632 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuropilin-2
- UniProt
- O60462
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neuropilin-2 | protein | 316 | 5% helix, 46% strand | O60462 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.71 | 0.80 | 74 | empty |
| 2 | 221 | 0.54 | 0.78 | 36 | empty |
| 3 | 117 | 0.47 | 0.79 | 20 | empty |
| 4 | 154 | 0.46 | 0.77 | 32 | empty |
| 5 | 155 | 0.46 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 815 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 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 4QDQ · PDBe 4QDQ · UniProt O60462
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