Research workbench
Bat influenza a polymerase pre-termination complex with pyrophosphate using 44-mer vrna template with mutated OLIGO(U) sequence
Analyse Bat influenza a polymerase pre-termination complex with pyrophosphate using… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SZU
- Type
- protein + RNA
- Length
- 1,753 residues
- Chains
- 5
- Method
- electron microscopy
- 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
- H6QM92, H6QM91, H6QM90
- Ligands
- M4H, POP, MG
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 5 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein | protein | 705 | 42% helix, 18% strand | H6QM92 |
| B | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 745 | 46% helix, 17% strand | H6QM91 |
| C | Polymerase basic protein 2 | protein | 249 | 44% helix, 18% strand | H6QM90 |
| V | Vrna | rna | 44 | — | — |
| M | MRNA | rna | 10 | — | — |
Ligands and binding sites
- M4H · 5-oxidanyl-4-oxidanylidene-1-[(1-pyrrolo[2,3-b]pyridin-1-ylcyclopentyl)methyl]pyridine-3-carboxylic acid · ligand · chains A
- POP · Pyrophosphate 2- · ligand · chains B, M
- MG · Magnesium ion · metal · 6 copies · chains A, B, M, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.90 | 0.92 | 134 | empty |
| 2 | 1196 | 0.88 | 0.89 | 125 | empty |
| 3 | 926 | 0.87 | 0.89 | 83 | empty |
| 4 | 949 | 0.77 | 0.79 | 89 | empty |
| 5 | 75 | 0.76 | 0.99 | 23 | empty |
Interfaces
10 interfaces between chains.
- A–B · 8999 Ų buried · 146 hydrogen bonds · protein-protein
- B–C · 6102 Ų buried · 61 hydrogen bonds · protein-protein
- B–V · 3820 Ų buried · 78 hydrogen bonds · protein-nucleic
- A–V · 2340 Ų buried · 52 hydrogen bonds · protein-nucleic
- A–C · 1179 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6SZU · Bat Influenza A polymerase pre-termination complex with pyrophosphate using 44-mer 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 H6QM92
- Every structure of UniProt H6QM91
- Every structure of UniProt H6QM90
- Elsewhere: RCSB PDB 6SZU · PDBe 6SZU · UniProt H6QM92 · UniProt H6QM91 · UniProt H6QM90
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