MolNFT v1 · #183272 · protein + RNA
1918 H1N1 viral influenza polymerase heterotrimer with NB8204
7NK6 · Polymerase acidic protein: “1918 H1N1 viral influenza polymerase heterotrimer with NB8204”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #183272 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7NK6
- Type
- protein + RNA
- Length
- 1,816 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
- Q3HM39, Q3HM40, Q3HM41
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 6 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein (EC 3.1.-.-) | protein | 716 | 42% helix, 16% strand | Q3HM39 |
| B | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 735 | 47% helix, 15% strand | Q3HM40 |
| C | Polymerase basic protein 2,POLYMERASE basic protein 2 | protein | 249 | 43% helix, 17% strand | Q3HM41 |
| E | RNA (5'-R(P*GP*GP*CP*CP*UP*GP*CP*U)-3') | rna | 8 | — | — |
| D | RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*CP*C)- 3') | rna | 15 | — | — |
| F | NB8204 | protein | 93 | 3% helix, 49% strand | — |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.84 | 0.85 | 108 | empty |
| 2 | 778 | 0.81 | 0.85 | 69 | empty |
| 3 | 504 | 0.80 | 0.87 | 50 | empty |
| 4 | 745 | 0.79 | 0.83 | 96 | empty |
| 5 | 462 | 0.76 | 0.84 | 60 | empty |
Interfaces
10 interfaces between chains.
- A–B · 8952 Ų buried · 106 hydrogen bonds · protein-protein
- B–C · 6782 Ų buried · 53 hydrogen bonds · protein-protein
- A–D · 1402 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–C · 1314 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 623 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7NK6 · 1918 H1N1 Viral influenza polymerase heterotrimer with Nb8204 · the same entry in another collection · chain E against E, 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 Q3HM39
- Every structure of UniProt Q3HM40
- Every structure of UniProt Q3HM41
- Elsewhere: RCSB PDB 7NK6 · PDBe 7NK6 · UniProt Q3HM39 · UniProt Q3HM40 · UniProt Q3HM41
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