MolNFT v1 · #152991 · protein
The RNA-dependent RNA polymerase domain of dengue 2 NS5, bound with rk-0404678
6IZX · Genome polyprotein: “The RNA-dependent RNA polymerase domain of dengue 2 NS5, bound with rk-0404678”. X-ray diffraction, 3 ligands (B5C, CO, ZN), 7 pockets (best druggability 0.64). MolNFT v1 #152991 on GenesisL1: 3D structure…
- PDB
- 6IZX
- Type
- protein
- Length
- 581 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- UniProt
- C6L435
- Ligands
- B5C, CO, ZN
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein | protein | 581 | 47% helix, 11% strand | C6L435 |
Ligands and binding sites
- B5C · 2-oxo-2H-1,3-benzoxathiol-5-yl acetate · ligand · 2 copies · chains A
- CO · Cobalt (II) ion · metal · 9 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.64 | 0.75 | 65 | CO, B5C |
| 2 | 102 | 0.55 | 0.84 | 17 | B5C |
| 3 | 207 | 0.53 | 0.77 | 29 | empty |
| 4 | 129 | 0.47 | 0.78 | 21 | empty |
| 5 | 57 | 0.34 | 0.77 | 14 | empty |
Compared structures
- 6IZX · The RNA-dependent RNA polymerase domain of dengue 2 NS5, bound with RK-0404678 · 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 C6L435
- Elsewhere: RCSB PDB 6IZX · PDBe 6IZX · UniProt C6L435
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