Research workbench
Structure of influenza D virus apo polymerase
Analyse Structure of influenza D virus apo polymerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KV5
- Type
- protein
- Length
- 1,679 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.6
- Source
- Influenza D virus (D/swine/Oklahoma/1334/2011)
- Molecule
- Polymerase 3; RNA-directed RNA polymerase catalytic subunit; Polymerase PB2
- EC
- 2.7.7.48
- UniProt
- K9LHJ4, K9LH03, K9LHF3
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 4.6 · 3 distinct chains · 38% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase 3 | protein | 688 | 37% helix, 11% strand | K9LHJ4 |
| B | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 696 | 41% helix, 12% strand | K9LH03 |
| C | Polymerase PB2 | protein | 295 | 32% helix, 11% strand | K9LHF3 |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.83 | 0.84 | 131 | empty |
| 2 | 584 | 0.78 | 0.84 | 56 | empty |
| 3 | 1116 | 0.75 | 0.78 | 77 | empty |
| 4 | 969 | 0.75 | 0.78 | 70 | empty |
| 5 | 871 | 0.73 | 0.78 | 100 | empty |
Interfaces
3 interfaces between chains.
- A–B · 8641 Ų buried · 82 hydrogen bonds · protein-protein
- B–C · 6147 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1788 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6KV5 · Structure of influenza D virus apo polymerase · 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 K9LHJ4
- Every structure of UniProt K9LH03
- Every structure of UniProt K9LHF3
- Elsewhere: RCSB PDB 6KV5 · PDBe 6KV5 · UniProt K9LHJ4 · UniProt K9LH03 · UniProt K9LHF3
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