Research workbench
Influenza B polymerase bound to four heptad repeats of serine 5 phosphorylated pol II ctd
Analyse Influenza B polymerase bound to four heptad repeats of serine 5 phosphorylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M3J
- Type
- protein + RNA
- Length
- 2,216 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
- 2.7.7.48, 2.7.7.6
- UniProt
- Q5V8Z9, Q5V8Y6, Q5V8X3
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein | protein | 716 | 45% helix, 16% strand | Q5V8Z9 |
| B | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 733 | 48% helix, 16% strand | Q5V8Y6 |
| C | Polymerase basic protein 2 | protein | 730 | 38% helix, 22% strand | Q5V8X3 |
| R | RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*UP*C)-3') | rna | 14 | — | — |
| V | RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3') | rna | 14 | — | — |
| X | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 9 | 0% helix, 0% strand | — |
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 | 1103 | 0.89 | 0.90 | 134 | empty |
| 2 | 894 | 0.80 | 0.83 | 65 | empty |
| 3 | 544 | 0.79 | 0.86 | 77 | empty |
| 4 | 934 | 0.78 | 0.80 | 73 | empty |
| 5 | 945 | 0.77 | 0.79 | 77 | empty |
Interfaces
11 interfaces between chains.
- A–B · 9035 Ų buried · 125 hydrogen bonds · protein-protein
- B–C · 6832 Ų buried · 79 hydrogen bonds · protein-protein
- A–C · 2170 Ų buried · 24 hydrogen bonds · protein-protein
- A–V · 1285 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–R · 582 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 5M3J · Influenza B polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD · 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 5M3J · PDBe 5M3J · UniProt Q5V8Z9 · UniProt Q5V8Y6 · UniProt Q5V8X3
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