MolNFT v1 · #86070 · protein
Influenza strain PH1N1 2009 polymerase subunit pa endonuclease in complex with diketo compound 2
4AVG · Polymerase pa: “Influenza strain PH1N1 2009 polymerase subunit pa endonuclease in complex with diketo compound 2”. X-ray diffraction, 2 ligands (SL6, MN), 11 pockets (best druggability 0.82). MolNFT v1 #86070 on GenesisL1: 3D…
- PDB
- 4AVG
- Type
- protein
- Length
- 780 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase pa
- UniProt
- C3W5S0
- Ligands
- SL6, MN
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase pa | protein | 194 | 49% helix, 16% strand | C3W5S0 |
| B | Polymerase pa | protein | 194 | 48% helix, 16% strand | C3W5S0 |
| C | Polymerase pa | protein | 195 | 49% helix, 16% strand | C3W5S0 |
| D | Polymerase pa | protein | 197 | 46% helix, 17% strand | C3W5S0 |
Ligands and binding sites
- SL6 · (Z)-4-[4-[(4-chlorophenyl)methyl]-1-(cyclohexylmethyl)piperidin-4-yl]-2-oxidanyl-4-oxidanylidene-but-2-enoic acid · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.82 | 0.86 | 86 | empty |
| 2 | 624 | 0.68 | 0.77 | 55 | SL6, MN |
| 3 | 517 | 0.66 | 0.77 | 42 | SL6, MN |
| 4 | 504 | 0.65 | 0.76 | 47 | SL6, MN |
| 5 | 425 | 0.63 | 0.77 | 46 | SL6, MN |
Interfaces
6 interfaces between chains.
- A–B · 1249 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 562 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 475 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 459 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 307 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4AVG · 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 4AVG · PDBe 4AVG · UniProt C3W5S0
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