Research workbench
Influenza B polymerase elongation complex
Analyse Influenza B polymerase elongation complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QCT
- Type
- protein + RNA
- Length
- 2,224 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase acidic protein; RNA-directed RNA polymerase catalytic subunit; Polymerase…
- EC
- 3.1.-.-, 2.7.7.48
- UniProt
- Q5V8Z9, Q5V8Y6, Q5V8X3
- Ligands
- GTG, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 6 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein (EC 3.1.-.-) | protein | 722 | 43% helix, 15% strand | Q5V8Z9 |
| B | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 735 | 43% helix, 16% strand | Q5V8Y6 |
| C | Polymerase basic protein 2 | protein | 729 | 36% helix, 18% strand | Q5V8X3 |
| V | 5 end | rna | 13 | — | — |
| R | 3 end | rna | 13 | — | — |
| M | Capped RNA | rna | 12 | — | — |
Ligands and binding sites
- GTG · 7-methyl-guanosine-5'-triphosphate-5'-guanosine · ligand · chains C, M
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 694 | 0.86 | 0.91 | 96 | empty |
| 2 | 337 | 0.83 | 0.93 | 55 | empty |
| 3 | 795 | 0.82 | 0.85 | 82 | empty |
| 4 | 692 | 0.82 | 0.86 | 68 | GTG |
| 5 | 617 | 0.80 | 0.85 | 74 | empty |
Interfaces
11 interfaces between chains.
- A–B · 9131 Ų buried · 113 hydrogen bonds · protein-protein
- B–C · 6914 Ų buried · 68 hydrogen bonds · protein-protein
- A–C · 2166 Ų buried · 19 hydrogen bonds · protein-protein
- A–V · 1251 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–R · 1082 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6QCT · Influenza B polymerase elongation complex · the same entry in another collection · chain C against C, 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 Q5V8Z9
- Every structure of UniProt Q5V8Y6
- Every structure of UniProt Q5V8X3
- Elsewhere: RCSB PDB 6QCT · PDBe 6QCT · UniProt Q5V8Z9 · UniProt Q5V8Y6 · UniProt Q5V8X3
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