MolNFT v1 · #89989 · protein
Crystal structure of avian influenza virus pan bound to compound 6
4E5L · Polymerase protein pa: “Crystal structure of avian influenza virus pan bound to compound 6”. X-ray diffraction, 3 ligands (DBH, MN, SO4), 8 pockets (best druggability 0.69). MolNFT v1 #89989 on GenesisL1: 3D structure, binding sites…
- PDB
- 4E5L
- Type
- protein
- Length
- 719 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase protein pa
- UniProt
- Q5EP34
- Ligands
- DBH, MN, SO4
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase protein pa | protein | 179 | 55% helix, 13% strand | Q5EP34 |
| B | Polymerase protein pa | protein | 178 | 54% helix, 13% strand | Q5EP34 |
| C, D | Polymerase protein pa | protein | 181 | 54% helix, 13% strand | Q5EP34 |
Ligands and binding sites
- DBH · 2,3-dihydroxy-benzoic acid · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 587 | 0.69 | 0.78 | 49 | MN, DBH |
| 2 | 550 | 0.68 | 0.78 | 45 | MN, DBH |
| 3 | 515 | 0.67 | 0.78 | 40 | MN, DBH |
| 4 | 475 | 0.65 | 0.77 | 45 | MN, SO4, DBH |
| 5 | 123 | 0.39 | 0.74 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 642 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 637 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 628 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 602 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4E5L · Crystal structure of avian influenza virus PAn bound to compound 6 · 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 Q5EP34
- Elsewhere: RCSB PDB 4E5L · PDBe 4E5L · UniProt Q5EP34
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