Research workbench
Tdt chimera (LOOP1 of pol mu) - full DNA synapsis complex
Analyse Tdt chimera (LOOP1 of pol mu) - full DNA synapsis complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GO7
- Type
- protein + DNA
- Length
- 377 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 0.69
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 16% 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 | 338 | 51% helix, 16% strand | P09838, Q9JIW4 |
| F, G | DNA (5'-D(*AP*AP*AP*AP*AP*C)-3') | dna | 6 | — | — |
| E, I, J | DNA (5'-D(*TP*TP*TP*TP*TP*GP*C)-3') | dna | 7 | — | — |
| H | DNA (5'-D(*TP*TP*TP*TP*TP*GP*C)-3') | dna | 6 | — | — |
Ligands and binding sites
- DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · chains A, E, H
- NA · Sodium ion · metal · chains A, E
- 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.69 | 0.75 | 66 | NA, DCT, MG |
| 2 | 153 | 0.63 | 0.86 | 23 | empty |
| 3 | 162 | 0.43 | 0.74 | 16 | empty |
Interfaces
12 interfaces between chains.
- A–E · 451 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–F · 434 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–H · 350 Ų buried · 4 hydrogen bonds · protein-nucleic
- F–J · 320 Ų buried · 17 hydrogen bonds · nucleic-nucleic
- G–I · 314 Ų buried · 14 hydrogen bonds · nucleic-nucleic
Compared structures
- 6GO7 · TdT chimera (Loop1 of pol mu) - full DNA synapsis complex · the same entry in another collection · chain J against J, 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 0.95
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 P09838
- Every structure of UniProt Q9JIW4
- Elsewhere: RCSB PDB 6GO7 · PDBe 6GO7 · UniProt P09838 · UniProt Q9JIW4
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