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Crystal structure of the cap-binding domain of polymerase basic protein 2 from influenza virus A/BAR-headed GS/QINGHAI/15C/2005 (H5N1) with bound M7GTP
Analyse Crystal structure of the cap-binding domain of polymerase basic protein 2 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ES5
- Type
- protein
- Length
- 653 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase basic subunit 2
- UniProt
- Q4FAV8
- Ligands
- MGT, SO4
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase basic subunit 2 | protein | 165 | 22% helix, 41% strand | Q4FAV8 |
| B | Polymerase basic subunit 2 | protein | 165 | 22% helix, 42% strand | Q4FAV8 |
| C | Polymerase basic subunit 2 | protein | 163 | 22% helix, 42% strand | Q4FAV8 |
| D | Polymerase basic subunit 2 | protein | 160 | 23% helix, 37% strand | Q4FAV8 |
Ligands and binding sites
- MGT · 7N-methyl-8-hydroguanosine-5'-triphosphate · ligand · 4 copies · chains A, B, D, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.83 | 0.84 | 143 | MGT |
| 2 | 526 | 0.68 | 0.79 | 58 | empty |
| 3 | 261 | 0.55 | 0.77 | 27 | MGT |
| 4 | 97 | 0.40 | 0.76 | 19 | MGT |
| 5 | 83 | 0.37 | 0.76 | 18 | MGT |
Interfaces
6 interfaces between chains.
- A–B · 582 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 562 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 557 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 276 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 65 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ES5 · Crystal structure of the cap-binding domain of polymerase basic protein 2 from influenza… · 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 Q4FAV8
- Elsewhere: RCSB PDB 4ES5 · PDBe 4ES5 · UniProt Q4FAV8
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