Research workbench
Crystal structure of human norovirus RNA-dependent RNA-polymerase bound to the inhibitor ppnds
Analyse Crystal structure of human norovirus RNA-dependent RNA-polymerase bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LQ3
- Type
- protein + RNA
- Length
- 497 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent RNA-polymerase; 5'-R(P*GP*G)-3'
- UniProt
- Q2N379
- Ligands
- 20V, MG
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-dependent RNA-polymerase | protein | 495 | 41% helix, 17% strand | Q2N379 |
| R | 5'-R(P*GP*G)-3' | rna | 2 | — | — |
Ligands and binding sites
- 20V · 3-[(E)-{4-formyl-5-hydroxy-6-methyl-3-[(phosphonooxy)methyl]pyridin-2-yl}diazenyl]-7-nitronaphthalene-1,5-disulfonic acid · ligand · 4 copies · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.79 | 0.83 | 80 | 20V |
| 2 | 55 | 0.35 | 0.78 | 15 | empty |
| 3 | 51 | 0.32 | 0.77 | 15 | empty |
| 4 | 62 | 0.29 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–R · 301 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 4LQ3 · Crystal structure of human norovirus RNA-dependent RNA-polymerase bound to the inhibitor… · 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 Q2N379
- Elsewhere: RCSB PDB 4LQ3 · PDBe 4LQ3 · UniProt Q2N379
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