Research workbench
Structure of influenza D virus polymerase bound to vrna promoter in mode B conformation (class B2)
Analyse Structure of influenza D virus polymerase bound to vrna promoter in mode B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KUT
- Type
- protein + RNA
- Length
- 1,706 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 5 distinct chains · 38% helix, 12% 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 | 33% helix, 11% strand | K9LHF3 |
| R | 3'-vrna | rna | 12 | — | — |
| V | 5'-vrna | rna | 15 | — | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.81 | 0.84 | 97 | empty |
| 2 | 440 | 0.78 | 0.87 | 49 | empty |
| 3 | 563 | 0.76 | 0.83 | 48 | empty |
| 4 | 793 | 0.76 | 0.80 | 70 | empty |
| 5 | 726 | 0.71 | 0.78 | 75 | empty |
Interfaces
9 interfaces between chains.
- A–B · 8639 Ų buried · 79 hydrogen bonds · protein-protein
- B–C · 6181 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1851 Ų buried · 12 hydrogen bonds · protein-protein
- A–V · 1046 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–R · 725 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 6KUT · Structure of influenza D virus polymerase bound to vRNA promoter in Mode B conformation… · 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 6KUT · PDBe 6KUT · UniProt K9LHJ4 · UniProt K9LH03 · UniProt K9LHF3
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