Research workbench
Base pairing mechanism of N2,3-ethenoguanine with dttp by human polymerase iota
Analyse Base pairing mechanism of N2,3-ethenoguanine with dttp by human polymerase iota in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FS1
- Type
- protein + DNA
- Length
- 399 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA 5'-D(*TP*CP*TP*(EFG) P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3'; DNA…
- EC
- 2.7.7.7
- UniProt
- Q9UNA4
- Ligands
- TTP, MG, NA
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA 5'-D(*TP*CP*TP*(EFG) P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3' | dna | 7 | — | — |
| C | DNA 5'-D(*TP*CP*TP*(EFG) P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3' | dna | 9 | — | — |
| A | DNA polymerase iota (EC 2.7.7.7) | protein | 383 | 43% helix, 21% strand | Q9UNA4 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · chains B, C, A
- MG · Magnesium ion · metal · 3 copies · chains A, B
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.74 | 0.79 | 58 | empty |
| 2 | 493 | 0.68 | 0.79 | 38 | empty |
| 3 | 411 | 0.65 | 0.79 | 34 | MG, TTP |
| 4 | 100 | 0.60 | 0.86 | 17 | empty |
| 5 | 90 | 0.35 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–A · 878 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–A · 537 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–C · 330 Ų buried · 30 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4FS1 · Base pairing mechanism of N2,3-ethenoguanine with dTTP by human polymerase iota · the same entry in another collection · chain B against B, 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 4FS1 · PDBe 4FS1 · UniProt Q9UNA4
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