Research workbench
Crystal structure of avian influenza a virus in complex with tmp
Analyse Crystal structure of avian influenza a virus in complex with tmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HW4
- Type
- protein
- Length
- 711 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase acidic protein
- UniProt
- Q9Q0U9
- Ligands
- TMP, MG
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein | protein | 178 | 53% helix, 13% strand | Q9Q0U9 |
| B | Polymerase acidic protein | protein | 180 | 52% helix, 13% strand | Q9Q0U9 |
| C | Polymerase acidic protein | protein | 177 | 51% helix, 13% strand | Q9Q0U9 |
| D | Polymerase acidic protein | protein | 176 | 53% helix, 14% strand | Q9Q0U9 |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · 3 copies · chains A, B, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.77 | 0.79 | 88 | MG, TMP |
| 2 | 900 | 0.71 | 0.76 | 75 | MG, TMP |
| 3 | 497 | 0.70 | 0.80 | 42 | MG |
| 4 | 587 | 0.65 | 0.75 | 47 | empty |
| 5 | 51 | 0.49 | 0.87 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 596 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 336 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 38 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3HW4 · Crystal structure of avian influenza A virus in complex with TMP · 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 Q9Q0U9
- Elsewhere: RCSB PDB 3HW4 · PDBe 3HW4 · UniProt Q9Q0U9
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