MolNFT v1 · #94622 · protein + DNA
Ternary complex of mouse tdt with ssdna and incoming nucleotide
4I27 · DNA nucleotidylexotransferase: “Ternary complex of mouse tdt with ssdna and incoming nucleotide”. X-ray diffraction, 3 ligands (D3T, MG, NA), 3 pockets (best druggability 0.70). MolNFT v1 #94622 on GenesisL1: 3D structure, binding…
- PDB
- 4I27
- Type
- protein + DNA
- Length
- 367 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA nucleotidylexotransferase; 5'-D(*AP*AP*AP*AP*AP*T)-3'
- EC
- 2.7.7.31
- UniProt
- P09838
- Ligands
- D3T, MG, NA
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA nucleotidylexotransferase (EC 2.7.7.31) | protein | 361 | 48% helix, 14% strand | P09838 |
| C | 5'-D(*AP*AP*AP*AP*AP*T)-3' | dna | 6 | — | — |
Ligands and binding sites
- D3T · 2',3'-dideoxy-thymidine-5'-triphosphate · ligand · chains A, C
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains A, C
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 | 871 | 0.70 | 0.75 | 82 | MG, D3T |
| 2 | 76 | 0.31 | 0.74 | 18 | empty |
| 3 | 53 | 0.25 | 0.73 | 11 | empty |
Interfaces
1 interface between chains.
- A–C · 508 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4I27 · Ternary complex of mouse TdT with ssDNA and incoming nucleotide · 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 4I27 · PDBe 4I27 · UniProt P09838
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