MolNFT v1 · #91935 · protein + DNA
Base pairing mechanism of N2,3-ethenoguanine with dctp by human polymerase iota
4FS2 · DNA (5'-D(*TP*CP*TP*(EFG) P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP…: “Base pairing mechanism of N2,3-ethenoguanine with dctp by human polymerase iota”. X-ray diffraction, 3 ligands (DCP, MG, NA), 4 pockets (best druggability 0.76). MolNFT…
- PDB
- 4FS2
- Type
- protein + DNA
- Length
- 398 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
- DCP, MG, NA
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 45% 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 | 8 | — | — |
| A | DNA polymerase iota (EC 2.7.7.7) | protein | 383 | 45% helix, 21% strand | Q9UNA4 |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains B, C, A
- MG · Magnesium ion · metal · 3 copies · chains A, B
- NA · Sodium ion · metal · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.76 | 0.79 | 69 | MG, DCP |
| 2 | 708 | 0.74 | 0.80 | 58 | empty |
| 3 | 80 | 0.33 | 0.74 | 13 | empty |
| 4 | 55 | 0.31 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–A · 685 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–A · 524 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 321 Ų buried · 23 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4FS2 · Base pairing mechanism of N2,3-ethenoguanine with dCTP 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 4FS2 · PDBe 4FS2 · UniProt Q9UNA4
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