Research workbench
Influenza B polymerase pre-initiation complex
Analyse Influenza B polymerase pre-initiation complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QCS
- Type
- protein + RNA
- Length
- 2,240 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 0.89
Structure
electron microscopy · 6 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein (EC 3.1.-.-) | protein | 715 | 42% helix, 15% strand | Q5V8Z9 |
| B | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 750 | 44% helix, 16% strand | Q5V8Y6 |
| C | Polymerase basic protein 2 | protein | 742 | 32% helix, 20% strand | Q5V8X3 |
| M | Capped RNA | rna | 4 | — | — |
| V | 5 end | rna | 14 | — | — |
| R | 3 end | rna | 15 | — | — |
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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.89 | 0.91 | 119 | empty |
| 2 | 672 | 0.85 | 0.89 | 90 | empty |
| 3 | 537 | 0.81 | 0.87 | 59 | GTG |
| 4 | 157 | 0.80 | 0.96 | 31 | empty |
| 5 | 691 | 0.77 | 0.82 | 62 | empty |
Interfaces
11 interfaces between chains.
- A–B · 8898 Ų buried · 109 hydrogen bonds · protein-protein
- B–C · 7216 Ų buried · 75 hydrogen bonds · protein-protein
- A–C · 2148 Ų buried · 15 hydrogen bonds · protein-protein
- A–V · 1261 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–R · 990 Ų buried · 21 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6QCS · Influenza B polymerase pre-initiation complex · 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 6QCS · PDBe 6QCS · UniProt Q5V8Z9 · UniProt Q5V8Y6 · UniProt Q5V8X3
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