MolNFT v1 · #161382 · protein + RNA
Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer and CTP
6QCV · Polymerase acidic protein: “Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer and CTP”. X-ray diffraction, 4 ligands (8NK, CTP, MG), 20 pockets (best druggability 0.90). MolNFT v1 #161382 on…
- PDB
- 6QCV
- Type
- protein + RNA
- Length
- 2,245 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, CTP, MG, PO4
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein (EC 3.1.-.-) | protein | 717 | 45% helix, 16% strand | Q5V8Z9 |
| B | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 746 | 46% helix, 16% 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*G)-3') | rna | 14 | — | — |
| 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
- CTP · Cytidine-5'-triphosphate · ligand · chains B, M, R
- MG · Magnesium ion · metal · chains B
- 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.90 | 0.92 | 123 | CTP, MG |
| 2 | 1083 | 0.89 | 0.90 | 119 | empty |
| 3 | 898 | 0.89 | 0.91 | 118 | empty |
| 4 | 570 | 0.87 | 0.92 | 61 | empty |
| 5 | 325 | 0.82 | 0.92 | 35 | 8NK |
Interfaces
12 interfaces between chains.
- A–B · 8929 Ų buried · 143 hydrogen bonds · protein-protein
- B–C · 7467 Ų buried · 88 hydrogen bonds · protein-protein
- A–C · 2274 Ų buried · 16 hydrogen bonds · protein-protein
- B–R · 1299 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–V · 1285 Ų buried · 25 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6QCV · Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA… · 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 6QCV · PDBe 6QCV · UniProt Q5V8Z9 · UniProt Q5V8Y6 · UniProt Q5V8X3
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