Research workbench
Human norovirus polymerase bound to compound 6 (suramin derivative)
Analyse Human norovirus polymerase bound to compound 6 (suramin derivative) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NRT
- Type
- protein
- Length
- 500 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hnv-rdrp
- UniProt
- A0ZNP5
- Ligands
- 2NG
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hnv-rdrp | protein | 500 | 42% helix, 17% strand | A0ZNP5 |
Ligands and binding sites
- 2NG · 4-({4-methyl-3-[(3-nitrobenzoyl)amino]benzoyl}amino)naphthalene-1,5-disulfonic acid · ligand · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.69 | 0.77 | 68 | 2NG |
| 2 | 246 | 0.53 | 0.76 | 38 | empty |
| 3 | 58 | 0.35 | 0.78 | 15 | empty |
| 4 | 52 | 0.31 | 0.77 | 16 | empty |
Compared structures
- 4NRT · Human Norovirus polymerase bound to Compound 6 (suramin derivative) · 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 A0ZNP5
- Elsewhere: RCSB PDB 4NRT · PDBe 4NRT · UniProt A0ZNP5
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