Research workbench
Crystal structure of full-length NS5 from dengue virus type 3
Analyse Crystal structure of full-length NS5 from dengue virus type 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CCV
- Type
- protein
- Length
- 6,716 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase NS5
- EC
- 2.1.1.56, 2.1.1.57, 2.7.7.48
- UniProt
- P27915
- Ligands
- SAH, ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 43% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase NS5 (EC 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 849 | 44% helix, 12% strand | P27915 |
| B | RNA-directed RNA polymerase NS5 (EC 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 851 | 43% helix, 12% strand | P27915 |
| C | RNA-directed RNA polymerase NS5 (EC 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 852 | 43% helix, 12% strand | P27915 |
| D | RNA-directed RNA polymerase NS5 (EC 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 848 | 44% helix, 12% strand | P27915 |
| E | RNA-directed RNA polymerase NS5 (EC 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 852 | 43% helix, 12% strand | P27915 |
| F | RNA-directed RNA polymerase NS5 (EC 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 850 | 45% helix, 12% strand | P27915 |
| G | RNA-directed RNA polymerase NS5 (EC 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 847 | 45% helix, 12% strand | P27915 |
| H | RNA-directed RNA polymerase NS5 (EC 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 767 | 41% helix, 12% strand | P27915 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ZN · Zinc ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.87 | 0.88 | 131 | empty |
| 2 | 837 | 0.81 | 0.84 | 98 | empty |
| 3 | 1113 | 0.81 | 0.83 | 129 | empty |
| 4 | 809 | 0.81 | 0.84 | 108 | empty |
| 5 | 182 | 0.81 | 0.95 | 28 | empty |
Interfaces
14 interfaces between chains.
- A–F · 1773 Ų buried · 26 hydrogen bonds · protein-protein
- D–G · 1648 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1247 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1147 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1117 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5CCV · Crystal structure of full-length NS5 from dengue virus type 3 · 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 P27915
- Elsewhere: RCSB PDB 5CCV · PDBe 5CCV · UniProt P27915
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