MolNFT v1 · #86104 · protein
Influenza strain PH1N1 2009 polymerase subunit pa endonuclease in complex with 2 4-dioxo-4-phenylbutanoic acid dpba
4AWF · Polymerase pa: “Influenza strain PH1N1 2009 polymerase subunit pa endonuclease in complex with 2 4-dioxo-4-phenylbutanoic…”. X-ray diffraction, 2 ligands (XI7, MN), 7 pockets (best druggability 0.76). MolNFT v1 #86104 on GenesisL1…
- PDB
- 4AWF
- Type
- protein
- Length
- 752 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase pa
- UniProt
- C3W5S0
- Ligands
- XI7, MN
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase pa | protein | 191 | 50% helix, 15% strand | C3W5S0 |
| B | Polymerase pa | protein | 190 | 51% helix, 15% strand | C3W5S0 |
| C | Polymerase pa | protein | 186 | 51% helix, 15% strand | C3W5S0 |
| D | Polymerase pa | protein | 185 | 51% helix, 15% strand | C3W5S0 |
Ligands and binding sites
- XI7 · 2-4-dioxo-4-phenylbutanoic 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
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.76 | 0.82 | 71 | empty |
| 2 | 532 | 0.74 | 0.82 | 50 | empty |
| 3 | 569 | 0.65 | 0.76 | 54 | MN, XI7 |
| 4 | 344 | 0.63 | 0.78 | 48 | MN, XI7 |
| 5 | 492 | 0.62 | 0.75 | 44 | MN, XI7 |
Interfaces
4 interfaces between chains.
- A–D · 594 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 586 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 414 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 403 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4AWF · Influenza strain pH1N1 2009 polymerase subunit PA endonuclease in complex with 2… · 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 4AWF · PDBe 4AWF · UniProt C3W5S0
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