MolNFT v1 · #86075 · protein
Influenza strain PH1N1 2009 polymerase subunit pa endonuclease in complex with dtmp
4AVL · Polymerase pa: “Influenza strain PH1N1 2009 polymerase subunit pa endonuclease in complex with dtmp”. X-ray diffraction, 2 ligands (TMP, MN), 8 pockets (best druggability 0.76). MolNFT v1 #86075 on GenesisL1: 3D structure, binding…
- PDB
- 4AVL
- Type
- protein
- Length
- 759 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase pa
- UniProt
- C3W5S0
- Ligands
- TMP, MN
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase pa | protein | 180 | 53% helix, 14% strand | C3W5S0 |
| B | Polymerase pa | protein | 190 | 49% helix, 16% strand | C3W5S0 |
| C | Polymerase pa | protein | 191 | 49% helix, 16% strand | C3W5S0 |
| D | Polymerase pa | protein | 198 | 48% helix, 16% strand | C3W5S0 |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · 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
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.76 | 0.80 | 81 | empty |
| 2 | 910 | 0.73 | 0.77 | 93 | empty |
| 3 | 468 | 0.70 | 0.80 | 57 | MN, TMP |
| 4 | 441 | 0.69 | 0.80 | 53 | MN, TMP |
| 5 | 429 | 0.65 | 0.78 | 50 | MN, TMP |
Interfaces
5 interfaces between chains.
- A–D · 1266 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 536 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 429 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 382 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 301 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4AVL · Influenza strain pH1N1 2009 polymerase subunit PA endonuclease in complex with dTMP · 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 4AVL · PDBe 4AVL · UniProt C3W5S0
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