MolNFT v1 · #65743 · protein + RNA
Crystal structure of 2'-amino-2'-deoxy-cytidine-5'-triphosphate bound to norovirus gii RNA polymerase
3H5X · RNA dependent RNA polymerase: “Crystal structure of 2'-amino-2'-deoxy-cytidine-5'-triphosphate bound to norovirus gii RNA polymerase”. X-ray diffraction, 2 ligands (CSG, MN), 3 pockets (best druggability 0.79). MolNFT v1 #65743 on…
- PDB
- 3H5X
- Type
- protein + RNA
- Length
- 486 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA dependent RNA polymerase; 5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3'…
- EC
- 2.7.7.48
- UniProt
- Q70ET3
- Ligands
- CSG, MN
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA dependent RNA polymerase (EC 2.7.7.48) | protein | 470 | 43% helix, 18% strand | Q70ET3 |
| P | 5'-R(*UP*GP*CP*CP*CP*GP*GP*G)-3' | rna | 7 | — | — |
| T | 5'-R(P*UP*GP*CP*CP*CP*GP*GP*GP*C)-3' | rna | 9 | — | — |
Ligands and binding sites
- CSG · 2'-amino-2'-deoxycytidine 5'-(tetrahydrogen triphosphate) · ligand · chains A, P, T
- MN · Manganese (II) ion · metal · 4 copies · chains A, P
- GOL · Glycerol · additive · 4 copies · chains A, P, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.79 | 0.81 | 87 | MN, CSG, GOL |
| 2 | 468 | 0.78 | 0.86 | 61 | empty |
| 3 | 64 | 0.29 | 0.74 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1012 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–P · 638 Ų buried · 14 hydrogen bonds · protein-nucleic
- P–T · 374 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Compared structures
- 3H5X · Crystal Structure of 2'-amino-2'-deoxy-cytidine-5'-triphosphate bound to Norovirus GII… · 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 Q70ET3
- Elsewhere: RCSB PDB 3H5X · PDBe 3H5X · UniProt Q70ET3
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