MolNFT v1 · #66633 · protein
The crystal structure of avian influenza virus PA_N in complex with ump
3HW3 · Polymerase acidic protein: “The crystal structure of avian influenza virus PA_N in complex with ump”. X-ray diffraction, 2 ligands (U5P, MG), 7 pockets (best druggability 0.72). MolNFT v1 #66633 on GenesisL1: 3D structure, binding…
- PDB
- 3HW3
- Type
- protein
- Length
- 710 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase acidic protein
- UniProt
- Q9Q0U9
- Ligands
- U5P, MG
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase acidic protein | protein | 177 | 53% helix, 13% strand | Q9Q0U9 |
| B | Polymerase acidic protein | protein | 180 | 52% helix, 13% strand | Q9Q0U9 |
| C | Polymerase acidic protein | protein | 177 | 53% helix, 13% strand | Q9Q0U9 |
| D | Polymerase acidic protein | protein | 176 | 53% helix, 13% strand | Q9Q0U9 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · chains A
- 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
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 | 566 | 0.72 | 0.80 | 45 | MG, U5P |
| 2 | 515 | 0.69 | 0.79 | 45 | MG |
| 3 | 556 | 0.69 | 0.78 | 42 | MG |
| 4 | 514 | 0.68 | 0.79 | 40 | MG |
| 5 | 647 | 0.66 | 0.75 | 46 | empty |
Interfaces
3 interfaces between chains.
- A–B · 608 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 339 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3HW3 · The crystal structure of avian influenza virus PA_N in complex with UMP · 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 3HW3 · PDBe 3HW3 · UniProt Q9Q0U9
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