Research workbench
Crystal structure of influenza B polymerase initiation state with capped 15-mer RNA primer
Analyse Crystal structure of influenza B polymerase initiation state with capped 15-mer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QCX
- Type
- protein + RNA
- Length
- 2,248 residues
- Chains
- 6
- Method
- x-ray diffraction
- 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
- 8NK, POP, MG, PO4
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein (EC 3.1.-.-) | protein | 718 | 45% helix, 16% strand | Q5V8Z9 |
| B | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 747 | 47% helix, 15% strand | Q5V8Y6 |
| C | Polymerase basic protein 2 | protein | 733 | 36% helix, 21% strand | Q5V8X3 |
| M | RNA (5'-D(*(GDM))- R(P*GP*AP*AP*UP*GP*CP*UP*AP*UP*AP*AP*UP*AP*GP*C)-3') | rna | 15 | — | — |
| R | RNA (5'- R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*UP*CP*UP*GP*CP*UP*AP*UP*U)- 3') | rna | 21 | — | — |
| V | RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3') | rna | 14 | — | — |
Ligands and binding sites
- 8NK · 7-methylguanosine 5'-diphosphate · ligand · chains C, M
- POP · Pyrophosphate 2- · ligand · chains B, M
- MG · Magnesium ion · metal · chains B, M
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.90 | 0.94 | 108 | empty |
| 2 | 841 | 0.89 | 0.92 | 107 | empty |
| 3 | 580 | 0.87 | 0.93 | 98 | empty |
| 4 | 319 | 0.82 | 0.92 | 36 | 8NK |
| 5 | 567 | 0.79 | 0.85 | 68 | empty |
Interfaces
12 interfaces between chains.
- A–B · 8985 Ų buried · 143 hydrogen bonds · protein-protein
- B–C · 7531 Ų buried · 92 hydrogen bonds · protein-protein
- A–C · 2272 Ų buried · 24 hydrogen bonds · protein-protein
- B–R · 1306 Ų buried · 31 hydrogen bonds · protein-nucleic
- A–V · 1265 Ų buried · 19 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6QCX · Crystal structure of influenza B polymerase initiation state with capped 15-mer RNA primer · 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 Q5V8Z9
- Every structure of UniProt Q5V8Y6
- Every structure of UniProt Q5V8X3
- Elsewhere: RCSB PDB 6QCX · PDBe 6QCX · UniProt Q5V8Z9 · UniProt Q5V8Y6 · UniProt Q5V8X3
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