Research workbench
Structure of influenza a H5N1 PB2 cap-binding domain with bound cap analogue (compound 8E)
Analyse Structure of influenza a H5N1 PB2 cap-binding domain with bound cap analogue… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CB7
- Type
- protein
- Length
- 313 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase basic subunit 2
- UniProt
- Q2LG68
- Ligands
- 41G
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase basic subunit 2 | protein | 159 | 24% helix, 42% strand | Q2LG68 |
| B | Polymerase basic subunit 2 | protein | 154 | 25% helix, 44% strand | Q2LG68 |
Ligands and binding sites
- 41G · 5-[2-(2-azanyl-7-methyl-6-oxidanylidene-1H-purin-9-ium-9-yl)ethanoyl]-2-oxidanyl-benzoic acid · ligand · chains B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.62 | 0.81 | 32 | empty |
| 2 | 198 | 0.51 | 0.77 | 30 | empty |
| 3 | 117 | 0.44 | 0.77 | 20 | 41G |
| 4 | 78 | 0.37 | 0.77 | 18 | GOL |
| 5 | 57 | 0.29 | 0.74 | 23 | GOL |
Interfaces
1 interface between chains.
- A–B · 349 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4CB7 · Structure of Influenza A H5N1 PB2 cap-binding domain with bound cap analogue (compound 8e) · 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 Q2LG68
- Elsewhere: RCSB PDB 4CB7 · PDBe 4CB7 · UniProt Q2LG68
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