Research workbench
Mopeia virus exonuclease domain partially complexed with manganese
Analyse Mopeia virus exonuclease domain partially complexed with manganese in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6T2A
- Type
- protein
- Length
- 395 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein
- EC
- 3.1.13.-
- UniProt
- Q5S581
- Ligands
- ZN, MN
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoprotein (EC 3.1.13.-) | protein | 198 | 39% helix, 16% strand | Q5S581 |
| B | Nucleoprotein (EC 3.1.13.-) | protein | 197 | 39% helix, 19% strand | Q5S581 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.55 | 0.79 | 33 | empty |
| 2 | 149 | 0.45 | 0.76 | 21 | empty |
| 3 | 131 | 0.42 | 0.76 | 22 | MN |
| 4 | 84 | 0.40 | 0.78 | 15 | empty |
| 5 | 85 | 0.39 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 353 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6T2A · Mopeia Virus Exonuclease domain partially complexed with Manganese · 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 6T2A · PDBe 6T2A · UniProt Q5S581
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