Research workbench
Structure of influenza D virus polymerase bound to vrna promoter in mode a conformation (class A1)
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
- 6KUK
- Type
- protein + RNA
- Length
- 1,484 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 0.79
Structure
electron microscopy · 5 distinct chains · 39% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase 3 | protein | 511 | 36% helix, 14% strand | K9LHJ4 |
| B | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 701 | 42% helix, 11% strand | K9LH03 |
| C | Polymerase PB2 | protein | 249 | 38% helix, 9% strand | K9LHF3 |
| R | 3'-vrna | rna | 8 | — | — |
| V | 5'-vrna | rna | 15 | — | — |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.79 | 0.85 | 58 | empty |
| 2 | 926 | 0.78 | 0.81 | 94 | empty |
| 3 | 1079 | 0.77 | 0.79 | 96 | empty |
| 4 | 967 | 0.75 | 0.78 | 65 | empty |
| 5 | 930 | 0.75 | 0.78 | 67 | empty |
Interfaces
9 interfaces between chains.
- A–B · 7872 Ų buried · 74 hydrogen bonds · protein-protein
- B–C · 5928 Ų buried · 27 hydrogen bonds · protein-protein
- A–V · 1098 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–C · 1004 Ų buried · 2 hydrogen bonds · protein-protein
- B–V · 486 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 6KUK · Structure of influenza D virus polymerase bound to vRNA promoter in mode A 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 6KUK · PDBe 6KUK · UniProt K9LHJ4 · UniProt K9LH03 · UniProt K9LHF3
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