Research workbench
Structure of influenza D virus polymerase bound to vRNA promoter in Mode A conformation(Class A2)
Analyse Structure of influenza D virus polymerase bound to vRNA promoter in Mode A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KUP
- Type
- protein + RNA
- Length
- 1,484 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.3
- Source
- Influenza D virus (D/swine/Oklahoma/1334/2011); SYNTHETIC CONSTRUCT
- Molecule
- Polymerase 3; RNA-directed RNA polymerase catalytic subunit; Polymerase PB2; 3'-vRNA…
- EC
- 2.7.7.48
- UniProt
- K9LHJ4, K9LH03, K9LHF3
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · resolution 4.3 · 5 distinct chains · 40% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase 3 | protein | 511 | 38% helix, 13% strand | K9LHJ4 |
| B | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 701 | 43% helix, 12% strand | K9LH03 |
| C | Polymerase PB2 | protein | 249 | 37% helix, 9% strand | K9LHF3 |
| R | 3'-vRNA | rna | 8 | — | — |
| V | 5'-vRNA | rna | 15 | — | — |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.81 | 0.82 | 110 | empty |
| 2 | 420 | 0.79 | 0.88 | 56 | empty |
| 3 | 864 | 0.76 | 0.80 | 77 | empty |
| 4 | 979 | 0.75 | 0.78 | 65 | empty |
| 5 | 485 | 0.75 | 0.83 | 45 | empty |
Interfaces
9 interfaces between chains.
- A–B · 7919 Ų buried · 81 hydrogen bonds · protein-protein
- B–C · 5922 Ų buried · 28 hydrogen bonds · protein-protein
- A–V · 1089 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–C · 970 Ų buried · 2 hydrogen bonds · protein-protein
- B–V · 486 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 6KUP · Structure of influenza D virus polymerase bound to vrna promoter in mode a… · 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 6KUP · PDBe 6KUP · UniProt K9LHJ4 · UniProt K9LH03 · UniProt K9LHF3
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