Research workbench
Structure of the catalytic core of DNA polymerase Iota in complex with DNA and dTTP
Analyse Structure of the catalytic core of DNA polymerase Iota in complex with DNA and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T3N
- Type
- protein + DNA
- Length
- 803 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Template DNA strand; Primer DNA strand; polymerase (DNA directed) iota
- UniProt
- Q9UNA4
- Ligands
- TTP, MG
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.3 · 3 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Template DNA strand | dna | 14 | — | — |
| P | Primer DNA strand | dna | 13 | — | — |
| A, B | polymerase (DNA directed) iota | protein | 388 | 41% helix, 15% strand | Q9UNA4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.83 | 0.84 | 94 | empty |
| 2 | 1050 | 0.76 | 0.79 | 69 | empty |
| 3 | 709 | 0.76 | 0.81 | 61 | empty |
| 4 | 100 | 0.66 | 0.90 | 22 | empty |
| 5 | 158 | 0.66 | 0.86 | 23 | empty |
Interfaces
6 interfaces between chains.
- T–B · 632 Ų buried · 19 hydrogen bonds · protein-nucleic
- T–A · 606 Ų buried · 24 hydrogen bonds · protein-nucleic
- P–B · 606 Ų buried · 25 hydrogen bonds · protein-nucleic
- T–P · 580 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- P–A · 404 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 1T3N · Structure of the catalytic core of DNA polymerase iota in complex with DNA and dttp · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UNA4 · AlphaFold monomer V2.0 prediction for DNA polymerase iota (Q9UNA4) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9UNA4
- Elsewhere: RCSB PDB 1T3N · PDBe 1T3N · UniProt Q9UNA4
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