Research workbench
Fujian capbinding domain in complex with NB8208
Analyse Fujian capbinding domain in complex with NB8208 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NFT
- Type
- protein
- Length
- 560 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polymerase basic protein 2; NB8208
- UniProt
- Q6E3N3
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polymerase basic protein 2 | protein | 161 | 23% helix, 42% strand | Q6E3N3 |
| C, D | NB8208 | protein | 120 | 5% helix, 53% strand | — |
| B | Polymerase basic protein 2 | protein | 159 | 23% helix, 40% strand | Q6E3N3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.70 | 0.76 | 59 | SO4 |
| 2 | 687 | 0.67 | 0.76 | 58 | SO4 |
| 3 | 90 | 0.40 | 0.77 | 18 | SO4 |
| 4 | 93 | 0.38 | 0.76 | 20 | empty |
| 5 | 94 | 0.37 | 0.75 | 17 | SO4 |
Interfaces
4 interfaces between chains.
- A–C · 595 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 592 Ų buried · 15 hydrogen bonds · protein-protein
- C–B · 427 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 409 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7NFT · Fujian capbinding domain in complex with Nb8208 · 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 Q6E3N3
- Elsewhere: RCSB PDB 7NFT · PDBe 7NFT · UniProt Q6E3N3
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