Research workbench
QDE-1 in complex with 12nt DNA template, ATP and 3'-dGTP
Analyse QDE-1 in complex with 12nt DNA template, ATP and 3'-dGTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Y7T
- Type
- protein + DNA + RNA
- Length
- 1,880 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Neurospora crassa; SYNTHETIC CONSTRUCT
- Molecule
- RNA-dependent RNA polymerase; DNA (5'-D(*GP*AP*G*AP*GP*AP*CP*CP*TP*TP*TP*T)-3'); RNA…
- EC
- 2.7.7.48
- UniProt
- Q9Y7G6
- Ligands
- GTP, ATP, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.5 · 4 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-dependent RNA polymerase (EC 2.7.7.48) | protein | 937 | 41% helix, 18% strand | Q9Y7G6 |
| B | RNA-dependent RNA polymerase (EC 2.7.7.48) | protein | 930 | 42% helix, 16% strand | Q9Y7G6 |
| C | DNA (5'-D(*GP*AP*G*AP*GP*AP*CP*CP*TP*TP*TP*T)-3') | dna | 9 | — | — |
| D | RNA (5'-R(P*AP*AP*AP*G)-3') | rna | 4 | — | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A, C, D
- ATP · Adenosine-5'-triphosphate · ligand · chains B
- MG · Magnesium ion · metal · 5 copies · chains A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.82 | 0.83 | 109 | GTP, MG |
| 2 | 93 | 0.77 | 0.97 | 19 | empty |
| 3 | 1182 | 0.75 | 0.78 | 107 | empty |
| 4 | 113 | 0.71 | 0.92 | 21 | empty |
| 5 | 71 | 0.71 | 0.96 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 6121 Ų buried · 64 hydrogen bonds · protein-protein
- A–C · 841 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–D · 463 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–D · 228 Ų buried · 11 hydrogen bonds · nucleic-nucleic
- B–C · 104 Ų buried · 1 hydrogen bond · protein-nucleic
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 Q9Y7G6
- Elsewhere: RCSB PDB 7Y7T · PDBe 7Y7T · UniProt Q9Y7G6
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