MolNFT v2 · #22391 · protein + DNA
Structure of the catalytic core of DNA polymerase Iota in complex with DNA and dTTP
1T3N · Template DNA strand: “Structure of the catalytic core of DNA polymerase Iota in complex with DNA and dTTP”. X-ray diffraction at 2.3, 2 ligands (TTP, MG), 13 pockets (best druggability 0.83). MolNFT v2 #22391 on GenesisL1: 3D…
- 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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