Research workbench
Co-crystal structure of dengue virus serotype 2 RNA dependent RNA polymerase with compound 27
Analyse Co-crystal structure of dengue virus serotype 2 RNA dependent RNA polymerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K5M
- Type
- protein
- Length
- 563 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA dependent RNA polymerase
- UniProt
- B5LNH6
- Ligands
- 68T, ZN
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA dependent RNA polymerase | protein | 563 | 48% helix, 10% strand | B5LNH6 |
Ligands and binding sites
- 68T · 5-[5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl]-2,4-dimethoxy-N-[(3-methoxyphenyl)sulfonyl]benzamide · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.73 | 0.76 | 81 | 68T |
| 2 | 67 | 0.49 | 0.84 | 16 | empty |
| 3 | 98 | 0.42 | 0.78 | 23 | empty |
| 4 | 72 | 0.35 | 0.76 | 12 | empty |
| 5 | 60 | 0.32 | 0.76 | 15 | empty |
Compared structures
- 5K5M · Co-Crystal Structure of Dengue Virus Serotype 2 RNA Dependent RNA Polymerase with… · 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 B5LNH6
- Elsewhere: RCSB PDB 5K5M · PDBe 5K5M · UniProt B5LNH6
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