MolNFT v1 · #94625 · protein + DNA
Binary complex of mouse tdt with ssdna in absence of divalent transition metal ion
4I2A · DNA nucleotidylexotransferase: “Binary complex of mouse tdt with ssdna in absence of divalent transition metal ion”. X-ray diffraction, 2 ligands (MG, NA), 3 pockets (best druggability 0.73). MolNFT v1 #94625 on GenesisL1: 3D…
- PDB
- 4I2A
- Type
- protein + DNA
- Length
- 365 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA nucleotidylexotransferase; 5'-D(*AP*AP*(BRU)P*AP*A)-3'
- EC
- 2.7.7.31
- UniProt
- P09838
- Ligands
- MG, NA
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA nucleotidylexotransferase (EC 2.7.7.31) | protein | 360 | 49% helix, 14% strand | P09838 |
| C | 5'-D(*AP*AP*(BRU)P*AP*A)-3' | dna | 5 | — | — |
Ligands and binding sites
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 | 800 | 0.73 | 0.79 | 65 | MG |
| 2 | 56 | 0.36 | 0.79 | 22 | empty |
| 3 | 88 | 0.34 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–C · 507 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4I2A · Binary complex of mouse TdT with ssDNA in absence of divalent transition metal ion · 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 1.00
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 4I2A · PDBe 4I2A · UniProt P09838
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