Research workbench
TdT chimera (Loop1 of pol mu) - binary complex with ddCTP
Analyse TdT chimera (Loop1 of pol mu) - binary complex with ddCTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GO4
- Type
- protein
- Length
- 357 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.96
- Source
- Mus musculus
- Molecule
- DNA nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA…
- EC
- 2.7.7.31, 2.7.7.7
- UniProt
- P09838, Q9JIW4
- Ligands
- DCT, NA, MG
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · resolution 1.96 · 1 distinct chain · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA nucleotidylexotransferase (EC 2.7.7.31, 2.7.7.7) | protein | 357 | 52% helix, 14% strand | P09838, Q9JIW4 |
Ligands and binding sites
- DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · chains A
- NA · Sodium ion · metal · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.65 | 0.76 | 53 | MG, DCT |
| 2 | 63 | 0.30 | 0.75 | 13 | NA |
| 3 | 58 | 0.29 | 0.74 | 13 | empty |
Compared structures
- 6GO4 · Tdt chimera (LOOP1 of pol mu) - binary complex with ddctp · the same entry in another collection · chain A against A, TM-score 1.00
- P09838 · AlphaFold monomer V2.0 prediction for DNA nucleotidylexotransferase (P09838) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9JIW4 · AlphaFold monomer V2.0 prediction for DNA-directed DNA/RNA polymerase mu (Q9JIW4) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P09838
- Every structure of UniProt Q9JIW4
- Elsewhere: RCSB PDB 6GO4 · PDBe 6GO4 · UniProt P09838 · UniProt Q9JIW4
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