Research workbench
Crystal structure of influenza B polymerase with bound 5' vrna
Analyse Crystal structure of influenza B polymerase with bound 5' vrna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FMZ
- Type
- protein + RNA
- Length
- 4,309 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase acidic protein; RNA-directed RNA polymerase catalytic subunit; Polymerase…
- EC
- 2.7.7.48
- UniProt
- Q5V8Z9, Q5V8Y6, Q5V8X3
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 7 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein | protein | 712 | 46% helix, 16% strand | Q5V8Z9 |
| B | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 708 | 45% helix, 15% strand | Q5V8Y6 |
| C | Polymerase basic protein 2 | protein | 714 | 37% helix, 20% strand | Q5V8X3 |
| D | Polymerase acidic protein | protein | 715 | 45% helix, 17% strand | Q5V8Z9 |
| E | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 733 | 44% helix, 15% strand | Q5V8Y6 |
| F | Polymerase basic protein 2 | protein | 703 | 37% helix, 20% strand | Q5V8X3 |
| H, V | 5'-R(*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP)-3' | rna | 12 | — | — |
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 | 1155 | 0.88 | 0.90 | 135 | empty |
| 2 | 1163 | 0.87 | 0.88 | 135 | empty |
| 3 | 130 | 0.79 | 0.97 | 31 | empty |
| 4 | 1080 | 0.78 | 0.80 | 80 | empty |
| 5 | 1170 | 0.78 | 0.80 | 105 | empty |
Interfaces
13 interfaces between chains.
- D–E · 9224 Ų buried · 139 hydrogen bonds · protein-protein
- A–B · 9059 Ų buried · 143 hydrogen bonds · protein-protein
- B–C · 6857 Ų buried · 80 hydrogen bonds · protein-protein
- E–F · 6553 Ų buried · 81 hydrogen bonds · protein-protein
- D–F · 2148 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5FMZ · Crystal structure of Influenza B polymerase with bound 5' vRNA · 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 5FMZ · PDBe 5FMZ · UniProt Q5V8Z9 · UniProt Q5V8Y6 · UniProt Q5V8X3
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