MolNFT v1 · #119414 · protein
Human metapneumovirus N0-P complex
5FVD · Nucleocapsid: “Human metapneumovirus N0-P complex”. X-ray diffraction, 1 ligand (CL), 8 pockets (best druggability 0.74). MolNFT v1 #119414 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FVD
- Type
- protein
- Length
- 739 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleocapsid; Phosphoprotein
- UniProt
- Q91F57, X4Y6K1
- Ligands
- CL
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleocapsid | protein | 343 | 66% helix, 4% strand | Q91F57 |
| B | Phosphoprotein | protein | 28 | 57% helix, 0% strand | X4Y6K1 |
| C | Nucleocapsid | protein | 341 | 67% helix, 4% strand | Q91F57 |
| D | Phosphoprotein | protein | 27 | 59% helix, 0% strand | X4Y6K1 |
Ligands and binding sites
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.74 | 0.82 | 53 | empty |
| 2 | 473 | 0.67 | 0.79 | 37 | empty |
| 3 | 504 | 0.66 | 0.77 | 43 | empty |
| 4 | 359 | 0.66 | 0.80 | 49 | empty |
| 5 | 50 | 0.37 | 0.80 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1099 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1061 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 415 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 118 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5FVD · Human metapneumovirus N0-P complex · the same entry in another collection · chain A against A, TM-score 1.00
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 Q91F57
- Every structure of UniProt X4Y6K1
- Elsewhere: RCSB PDB 5FVD · PDBe 5FVD · UniProt Q91F57 · UniProt X4Y6K1
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