Research workbench
Binary complex of mouse tdt with ssdna in absence of divalent transition metal ion
Analyse Binary complex of mouse tdt with ssdna in absence of divalent transition metal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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