Research workbench
Influenza strain PH1N1 2009 polymerase subunit pa endonuclease in complex with diketo compound 3
Analyse Influenza strain PH1N1 2009 polymerase subunit pa endonuclease in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AWG
- Type
- protein
- Length
- 750 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase pa
- UniProt
- C3W5S0
- Ligands
- CI3, MN, SO4
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase pa | protein | 187 | 51% helix, 17% strand | C3W5S0 |
| B | Polymerase pa | protein | 191 | 51% helix, 16% strand | C3W5S0 |
| C | Polymerase pa | protein | 196 | 48% helix, 16% strand | C3W5S0 |
| D | Polymerase pa | protein | 176 | 55% helix, 13% strand | C3W5S0 |
Ligands and binding sites
- CI3 · (2Z)-4-[(3S)-1-benzyl-3-(4-chlorobenzyl)piperidin-3-yl]-2-hydroxy-4-oxobut-2-enoic acid · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 14 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.81 | 0.82 | 77 | SO4, CI3, MN |
| 2 | 414 | 0.63 | 0.77 | 42 | empty |
| 3 | 349 | 0.62 | 0.78 | 41 | empty |
| 4 | 450 | 0.61 | 0.76 | 50 | SO4, CI3, MN |
| 5 | 281 | 0.58 | 0.78 | 30 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1454 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 553 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 314 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 300 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4AWG · Influenza strain pH1N1 2009 polymerase subunit PA endonuclease in complex with diketo… · 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 C3W5S0
- Elsewhere: RCSB PDB 4AWG · PDBe 4AWG · UniProt C3W5S0
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