MolNFT v1 · #64559 · protein + DNA
Ternary complex of DNA polymerase IOTA:DNA:DTTP with an abasic site at the templating position
3G6Y: “Ternary complex of DNA polymerase IOTA:DNA:DTTP with an abasic site at the templating position”. X-ray diffraction, 2 ligands (TTP, MG), 7 pockets (best druggability 0.73). MolNFT v1 #64559 on GenesisL1: 3D structure, binding sites…
- PDB
- 3G6Y
- Type
- protein + DNA
- Length
- 388 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase iota; Primer DNA strand; Template DNA strand
- EC
- 2.7.7.7
- UniProt
- Q9UNA4
- Ligands
- TTP, MG
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase iota (EC 2.7.7.7) | protein | 373 | 46% helix, 20% strand | Q9UNA4 |
| P | Primer DNA strand | dna | 7 | — | — |
| T | Template DNA strand | dna | 8 | — | — |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · chains A, P, T
- MG · Magnesium ion · metal · 2 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.73 | 0.79 | 52 | empty |
| 2 | 546 | 0.68 | 0.79 | 39 | empty |
| 3 | 405 | 0.67 | 0.80 | 40 | TTP, MG |
| 4 | 74 | 0.41 | 0.79 | 13 | empty |
| 5 | 122 | 0.38 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–T · 680 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–P · 492 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–T · 320 Ų buried · 24 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3G6Y · Ternary complex of DNA Polymerase iota:DNA:dTTP with an abasic site at the templating… · 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 0.99
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 Q9UNA4
- Elsewhere: RCSB PDB 3G6Y · PDBe 3G6Y · UniProt Q9UNA4
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