Research workbench
TdT chimera (Loop1 of pol mu) - Ternary complex with 1-nt gapped DNA substrate
Analyse TdT chimera (Loop1 of pol mu) - Ternary complex with 1-nt gapped DNA substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GO5
- Type
- protein + DNA
- Length
- 724 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.35
- Source
- Mus musculus; SYNTHETIC CONSTRUCT
- Molecule
- DNA nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA…
- EC
- 2.7.7.31, 2.7.7.7
- UniProt
- P09838, Q9JIW4
- Ligands
- XC5, NA, MG
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.35 · 5 distinct chains · 50% helix, 15% 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 | 343 | 49% helix, 15% strand | P09838, Q9JIW4 |
| B | DNA nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA nucleotidylexotransferase (EC 2.7.7.31, 2.7.7.7) | protein | 335 | 51% helix, 16% strand | P09838, Q9JIW4 |
| H, N | DNA (5'-D(*CP*GP*CP*TP*GP*GP*CP*AP*AP*AP*CP*A)-3') | dna | 12 | — | — |
| F, L | DNA (5'-D(*TP*GP*TP*TP*TP*G)-3') | dna | 6 | — | — |
| G, M | DNA (5'-D(*AP*CP*AP*GP*CP*G)-3') | dna | 5 | — | — |
Ligands and binding sites
- XC5 · 2'-deoxy-5'-O-[(S)-hydroxy{[(s)-hydroxy(phosphonooxy) phosphoryl]methyl}phosphoryl]cytidine · ligand · 2 copies · chains A, H, F, B, L, N
- NA · Sodium ion · metal · 2 copies · chains A, F, B, L
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.81 | 0.83 | 105 | MG, XC5 |
| 2 | 1057 | 0.72 | 0.76 | 71 | MG, XC5 |
| 3 | 97 | 0.61 | 0.88 | 26 | empty |
| 4 | 128 | 0.51 | 0.81 | 22 | empty |
| 5 | 89 | 0.49 | 0.83 | 14 | empty |
Interfaces
13 interfaces between chains.
- B–N · 681 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–H · 660 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–L · 383 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–F · 381 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–M · 380 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 6GO5 · Tdt chimera (LOOP1 of pol mu) - ternary complex with 1-nt gapped DNA substrate · the same entry in another collection · chain N against N, TM-score 1.00
- P09838 · AlphaFold monomer V2.0 prediction for DNA nucleotidylexotransferase (P09838) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q9JIW4 · AlphaFold monomer V2.0 prediction for DNA-directed DNA/RNA polymerase mu (Q9JIW4) · a predicted model of the same protein · chain B 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 6GO5 · PDBe 6GO5 · UniProt P09838 · UniProt Q9JIW4
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