Research workbench
Influenza strain PH1N1 2009 polymerase subunit pa endonuclease in complex with dtmp
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
- 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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