MolNFT v1 · #148053 · protein + RNA
Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter and cap analogue M7GTP
6EVK · Polymerase acidic protein: “Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter and cap analogue M7GTP”. X-ray diffraction, 3 ligands (MGP, ZN, PO4), 20 pockets (best druggability 0.84). MolNFT v1 #148053…
- PDB
- 6EVK
- Type
- protein + RNA
- Length
- 2,202 residues
- Chains
- 5
- 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
- H6QM92, H6QM91, H6QM90
- Ligands
- MGP, ZN, PO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein | protein | 699 | 44% helix, 19% strand | H6QM92 |
| B | RNA-directed RNA polymerase catalytic subunit (EC 2.7.7.48) | protein | 748 | 46% helix, 17% strand | H6QM91 |
| C | Polymerase basic protein 2 | protein | 727 | 37% helix, 23% strand | H6QM90 |
| R | RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*U)-3') | rna | 12 | — | — |
| V | RNA (5'- R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*GP*GP*G)-3') | rna | 16 | — | — |
Ligands and binding sites
- MGP · 7-methyl-guanosine-5'-triphosphate · ligand · chains C
- ZN · Zinc ion · metal · chains A, B
- PO4 · Phosphate ion · ion · 12 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 958 | 0.84 | 0.85 | 73 | PO4 |
| 2 | 847 | 0.84 | 0.86 | 89 | empty |
| 3 | 584 | 0.82 | 0.88 | 69 | empty |
| 4 | 726 | 0.80 | 0.84 | 52 | PO4 |
| 5 | 1136 | 0.79 | 0.81 | 121 | empty |
Interfaces
9 interfaces between chains.
- A–B · 9188 Ų buried · 144 hydrogen bonds · protein-protein
- B–C · 7527 Ų buried · 88 hydrogen bonds · protein-protein
- A–C · 1591 Ų buried · 16 hydrogen bonds · protein-protein
- A–V · 1315 Ų buried · 30 hydrogen bonds · protein-nucleic
- B–V · 821 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 6EVK · Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter and cap… · 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 6EVK · PDBe 6EVK · UniProt H6QM92 · UniProt H6QM91 · UniProt H6QM90
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