MolNFT v1 · #52103 · protein
Structure of the cap-binding domain of influenza virus polymerase subunit PB2 with bound M7GTP
2VQZ · Polymerase basic protein 2: “Structure of the cap-binding domain of influenza virus polymerase subunit PB2 with bound M7GTP”. X-ray diffraction, 1 ligand (MGT), 11 pockets (best druggability 0.66). MolNFT v1 #52103 on GenesisL1: 3D…
- PDB
- 2VQZ
- Type
- protein
- Length
- 811 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase basic protein 2
- UniProt
- P31345
- Ligands
- MGT
- Pockets
- 11 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase basic protein 2 | protein | 164 | 21% helix, 42% strand | P31345 |
| B | Polymerase basic protein 2 | protein | 162 | 22% helix, 42% strand | P31345 |
| D | Polymerase basic protein 2 | protein | 165 | 22% helix, 42% strand | P31345 |
| E | Polymerase basic protein 2 | protein | 160 | 22% helix, 42% strand | P31345 |
| F | Polymerase basic protein 2 | protein | 160 | 23% helix, 43% strand | P31345 |
Ligands and binding sites
- MGT · 7N-methyl-8-hydroguanosine-5'-triphosphate · ligand · 5 copies · chains A, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.66 | 0.77 | 38 | empty |
| 2 | 581 | 0.63 | 0.75 | 50 | empty |
| 3 | 573 | 0.62 | 0.74 | 57 | empty |
| 4 | 467 | 0.61 | 0.75 | 42 | empty |
| 5 | 163 | 0.50 | 0.77 | 20 | MGT |
Interfaces
8 interfaces between chains.
- B–E · 558 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 555 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 541 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 523 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 521 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 modified (engineered).
Compared structures
- 2VQZ · Structure of the cap-binding domain of influenza virus polymerase subunit PB2 with bound… · 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 P31345
- Elsewhere: RCSB PDB 2VQZ · PDBe 2VQZ · UniProt P31345
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