Research workbench
The crystal structure of the 2009/H1N1/CALIFORNIA pa endonuclease wild type bound to DNA oligomers tg and agca (from cleaved gtgagcagtg)
Analyse The crystal structure of the 2009/H1N1/CALIFORNIA pa endonuclease wild type… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WS3
- Type
- protein + DNA
- Length
- 184 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein pa-X,POLYMERASE acidic protein; DNA (5'-D(P*TP*G)-3')
- UniProt
- A0A4P2TE19, C6H0Y9
- Ligands
- MN, SO4
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein pa-X,POLYMERASE acidic protein | protein | 179 | 53% helix, 13% strand | A0A4P2TE19, C6H0Y9 |
| F | DNA (5'-D(P*TP*G)-3') | dna | 2 | — | — |
| E | DNA (5'-D(P*TP*G)-3') | dna | 3 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains A, E
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · 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 | 189 | 0.73 | 0.90 | 24 | empty |
| 2 | 74 | 0.42 | 0.80 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–E · 467 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–F · 294 Ų buried · 4 hydrogen bonds · protein-nucleic
- F–E · 50 Ų buried · 1 hydrogen bond · nucleic-nucleic
Compared structures
- 6WS3 · The crystal structure of the 2009/H1N1/California PA endonuclease wild type bound to DNA… · 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 C6H0Y9
- Elsewhere: RCSB PDB 6WS3 · PDBe 6WS3 · UniProt A0A4P2TE19 · UniProt C6H0Y9
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