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The structural basis for RNA specificity and CA2 inhibition of an RNA- dependent RNA polymerase PHI6P2 CA2+ inhibition complex
Analyse The structural basis for RNA specificity and CA2 inhibition of an RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UVN
- Type
- protein + RNA
- Length
- 2,004 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase; 5'-R(*UP*UP*UP*UP*CP*CP)-3'
- EC
- 2.7.7.48
- UniProt
- P11124
- Ligands
- GTP, CA, MN
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 664 | 45% helix, 13% strand | P11124 |
| B, D, F | 5'-R(*UP*UP*UP*UP*CP*CP)-3' | rna | 4 | — | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 6 copies · chains A, C, E
- MN · Manganese (II) ion · metal · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1068 | 0.85 | 0.86 | 102 | GTP, CA |
| 2 | 1049 | 0.85 | 0.86 | 102 | GTP, CA |
| 3 | 1095 | 0.85 | 0.86 | 99 | GTP, CA |
| 4 | 1124 | 0.81 | 0.82 | 88 | empty |
| 5 | 133 | 0.76 | 0.94 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–C · 839 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 735 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 731 Ų buried · 15 hydrogen bonds · protein-nucleic
- E–F · 730 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–E · 476 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1UVN · The structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA… · 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 P11124
- Elsewhere: RCSB PDB 1UVN · PDBe 1UVN · UniProt P11124
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