MolNFT v1 · #169435 · protein + DNA + RNA
Polymerase domain of polymerase-theta
6XBU · DNA polymerase theta: “Polymerase domain of polymerase-theta”. X-ray diffraction, 1 ligand (DG3), 10 pockets (best druggability 0.62). MolNFT v1 #169435 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XBU
- Type
- protein + DNA + RNA
- Length
- 620 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase theta; DNA (5'-D(P*GP*TP*CP*AP*TP*TP*G)-3'); RNA…
- EC
- 2.7.7.7
- UniProt
- O75417
- Ligands
- DG3
- Pockets
- 10 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase theta (EC 2.7.7.7) | protein | 605 | 42% helix, 13% strand | O75417 |
| F | DNA (5'-D(P*GP*TP*CP*AP*TP*TP*G)-3') | dna | 8 | — | — |
| E | RNA (5'-R(P*CP*CP*AP*AP*UP*GP*A)-3') | rna | 7 | — | — |
Ligands and binding sites
- DG3 · 2'-3'-dideoxyguanosine-5'-triphosphate · ligand · chains A, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.62 | 0.78 | 39 | DG3 |
| 2 | 276 | 0.59 | 0.79 | 32 | empty |
| 3 | 272 | 0.56 | 0.77 | 30 | empty |
| 4 | 276 | 0.55 | 0.76 | 35 | empty |
| 5 | 137 | 0.53 | 0.81 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–E · 616 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–F · 459 Ų buried · 5 hydrogen bonds · protein-nucleic
- F–E · 331 Ų buried · 25 hydrogen bonds · nucleic-nucleic
Compared structures
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 O75417
- Elsewhere: RCSB PDB 6XBU · PDBe 6XBU · UniProt O75417
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