MolNFT v1 · #23078 · protein
Crystal structure of the RNA-dependent RNA polymerase from human rhinovirus 16
1TP7 · Genome polyprotein: “Crystal structure of the RNA-dependent RNA polymerase from human rhinovirus 16”. X-ray diffraction, 2 ligands (DMX, SO4), 20 pockets (best druggability 0.70). MolNFT v1 #23078 on GenesisL1: 3D structure, binding…
- PDB
- 1TP7
- Type
- protein
- Length
- 1,840 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- EC
- 2.7.7.48
- UniProt
- Q82122
- Ligands
- DMX, SO4
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Genome polyprotein (EC 2.7.7.48) | protein | 460 | 40% helix, 15% strand | Q82122 |
Ligands and binding sites
- DMX · 3-[benzyl(dimethyl)ammonio]propane-1-sulfonate · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.70 | 0.75 | 72 | empty |
| 2 | 898 | 0.69 | 0.75 | 69 | empty |
| 3 | 905 | 0.69 | 0.75 | 65 | empty |
| 4 | 830 | 0.68 | 0.75 | 72 | empty |
| 5 | 376 | 0.68 | 0.81 | 55 | empty |
Interfaces
4 interfaces between chains.
- A–D · 659 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 446 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 326 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 134 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 1TP7 · Crystal Structure of the RNA-dependent RNA Polymerase from Human Rhinovirus 16 · 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 Q82122
- Elsewhere: RCSB PDB 1TP7 · PDBe 1TP7 · UniProt Q82122
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