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Ternary complex of human DNA polymerase theta C-terminal domain binding ddgtp opposite dcmp
Analyse Ternary complex of human DNA polymerase theta C-terminal domain binding ddgtp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X0Q
- Type
- protein + DNA
- Length
- 1,294 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase theta; DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*G)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- O75417
- Ligands
- DG3, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase theta (EC 2.7.7.7) | protein | 625 | 50% helix, 12% strand | O75417 |
| E, G | DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*G)-3') | dna | 13 | — | — |
| F, H | DNA (5'-D(P*CP*TP*GP*TP*CP*AP*TP*TP*G)-3') | dna | 9 | — | — |
Ligands and binding sites
- DG3 · 2'-3'-dideoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, E, F, B, G, H
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.82 | 0.83 | 87 | empty |
| 2 | 1014 | 0.82 | 0.83 | 81 | empty |
| 3 | 850 | 0.80 | 0.83 | 81 | GOL, MG, DG3 |
| 4 | 472 | 0.75 | 0.84 | 39 | MG, DG3 |
| 5 | 451 | 0.69 | 0.80 | 52 | GOL |
Interfaces
10 interfaces between chains.
- B–G · 956 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–E · 944 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–F · 652 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–H · 648 Ų buried · 15 hydrogen bonds · protein-nucleic
- E–F · 460 Ų buried · 34 hydrogen bonds · nucleic-nucleic
Compared structures
- 4X0Q · Ternary complex of human DNA polymerase theta C-terminal domain binding ddGTP opposite… · the same entry in another collection · chain H against H, TM-score 1.00
- O75417 · AlphaFold monomer V2.0 prediction for DNA polymerase theta (O75417) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 4X0Q · PDBe 4X0Q · UniProt O75417
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