MolNFT v1 · #179960 · protein + RNA
The crystal structure of the 2009/H1N1/CALIFORNIA pa endonuclease mutant E119D bound to RNA oligomer AG*CAUC (*uncleaveable bond, -uc disordered)
7KL3 · Protein pa-X: “The crystal structure of the 2009/H1N1/CALIFORNIA pa endonuclease mutant E119D bound to RNA oligomer AG*CAUC…”. X-ray diffraction, 3 ligands (A, RQA, SO4), 2 pockets (best druggability 0.64). MolNFT v1 #179960 on…
- PDB
- 7KL3
- Type
- protein + RNA
- Length
- 179 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein pa-X; RNA (5'-R(P*AP*GP*CP*A)-3')
- UniProt
- A0A4P2TE19, A0A646SQW7
- Ligands
- A, RQA, SO4
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein pa-X | protein | 177 | 54% helix, 13% strand | A0A4P2TE19, A0A646SQW7 |
| B | RNA (5'-R(P*AP*GP*CP*A)-3') | rna | 2 | — | — |
Ligands and binding sites
- A · Adenosine-5'-monophosphate · ligand · chains A
- RQA · 5'-O-sulfocytidine · ligand · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.64 | 0.90 | 20 | empty |
| 2 | 132 | 0.44 | 0.77 | 16 | RQA |
Interfaces
1 interface between chains.
- A–B · 441 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7KL3 · The crystal structure of the 2009/H1N1/California PA endonuclease mutant E119D bound to… · 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 A0A4P2TE19
- Every structure of UniProt A0A646SQW7
- Elsewhere: RCSB PDB 7KL3 · PDBe 7KL3 · UniProt A0A4P2TE19 · UniProt A0A646SQW7
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