MolNFT v1 · #105258 · protein + DNA
Mouse tdt, F405A mutant, in complex with a dsb substrate, C-C base pair
4QZD · DNA nucleotidylexotransferase: “Mouse tdt, F405A mutant, in complex with a dsb substrate, C-C base pair”. X-ray diffraction, 3 ligands (DCT, MG, NA), 3 pockets (best druggability 0.71). MolNFT v1 #105258 on GenesisL1: 3D structure…
- PDB
- 4QZD
- Type
- protein + DNA
- Length
- 364 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA nucleotidylexotransferase; 5'-D(*AP*AP*AP*AP*AP*C)-3'; 5'-D(*TP*TP*TP*TP*TP*GP*C)-3'
- EC
- 2.7.7.31
- UniProt
- P09838
- Ligands
- DCT, MG, NA
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA nucleotidylexotransferase (EC 2.7.7.31) | protein | 348 | 51% helix, 15% strand | P09838 |
| D | 5'-D(*AP*AP*AP*AP*AP*C)-3' | dna | 5 | — | — |
| T | 5'-D(*TP*TP*TP*TP*TP*GP*C)-3' | dna | 7 | — | — |
| U | 5'-D(*AP*AP*AP*AP*AP*C)-3' | dna | 4 | — | — |
Ligands and binding sites
- DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · chains A, T
- MG · Magnesium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A, U
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 | 1071 | 0.71 | 0.75 | 81 | MG, DCT |
| 2 | 111 | 0.61 | 0.87 | 20 | empty |
| 3 | 71 | 0.36 | 0.77 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–T · 380 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 361 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–U · 274 Ų buried · 5 hydrogen bonds · protein-nucleic
- D–T · 205 Ų buried · 16 hydrogen bonds · nucleic-nucleic
Compared structures
- 4QZD · Mouse Tdt, F405A mutant, in complex with a DSB substrate, C-C base pair · 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
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
- Elsewhere: RCSB PDB 4QZD · PDBe 4QZD · UniProt P09838
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