MolNFT v1 · #164710 · protein
Mopeia virus exonuclease domain complexed soak with alendronate
6T6L · Nucleoprotein: “Mopeia virus exonuclease domain complexed soak with alendronate”. X-ray diffraction, 2 ligands (MN, ZN), 6 pockets (best druggability 0.74). MolNFT v1 #164710 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6T6L
- Type
- protein
- Length
- 617 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein
- EC
- 3.1.13.-
- UniProt
- Q5S581
- Ligands
- MN, ZN
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nucleoprotein (EC 3.1.13.-) | protein | 206 | 37% helix, 19% strand | Q5S581 |
| C | Nucleoprotein (EC 3.1.13.-) | protein | 205 | 34% helix, 21% strand | Q5S581 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.74 | 0.77 | 113 | empty |
| 2 | 281 | 0.55 | 0.76 | 36 | empty |
| 3 | 170 | 0.45 | 0.75 | 23 | empty |
| 4 | 177 | 0.44 | 0.74 | 29 | MN |
| 5 | 82 | 0.37 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 542 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 402 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 340 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6T6L · Mopeia Virus Exonuclease domain complexed soak with Alendronate · 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 Q5S581
- Elsewhere: RCSB PDB 6T6L · PDBe 6T6L · UniProt Q5S581
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