Research workbench
A crystal structure of alphavirus nonstructural protein 4 (NSP4) reveals an intrinsically dynamic RNA-dependent RNA polymerase
Analyse A crystal structure of alphavirus nonstructural protein 4 (NSP4) reveals an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VB4
- Type
- protein
- Length
- 917 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase NSP4
- EC
- 2.7.7.48
- UniProt
- P03317
- Ligands
- MG
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase NSP4 (EC 2.7.7.48) | protein | 456 | 56% helix, 9% strand | P03317 |
| B | RNA-directed RNA polymerase NSP4 (EC 2.7.7.48) | protein | 461 | 56% helix, 10% strand | P03317 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, 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
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.80 | 0.83 | 75 | GOL |
| 2 | 330 | 0.71 | 0.84 | 40 | MG |
| 3 | 328 | 0.70 | 0.84 | 44 | MG |
| 4 | 208 | 0.66 | 0.84 | 41 | GOL |
| 5 | 83 | 0.62 | 0.90 | 16 | GOL |
Interfaces
1 interface between chains.
- A–B · 3757 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7VB4 · A crystal structure of alphavirus nonstructural protein 4 (nsP4) reveals an intrinsically… · 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 P03317
- Elsewhere: RCSB PDB 7VB4 · PDBe 7VB4 · UniProt P03317
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