MolNFT v2 · #116987 · protein + DNA
Crystal Structure of Human DNA Polymerase Eta Inserting dATP Opposite O4-Methylhymidine
5DLF: “Crystal Structure of Human DNA Polymerase Eta Inserting dATP Opposite O4-Methylhymidine”. X-ray diffraction at 1.97, 2 ligands (DTP, CA), 5 pockets (best druggability 0.81). MolNFT v2 #116987 on GenesisL1: 3D structure, binding…
- PDB
- 5DLF
- Type
- protein + DNA
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.97
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase eta; DNA (5'-D(*C*AP*TP*(5DB)P*AP*TP*GP*AP*CP*GP*CP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- DTP, CA
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.97 · 3 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 430 | 43% helix, 21% strand | Q9Y253 |
| T | DNA (5'-D(*C*AP*TP*(5DB)P*AP*TP*GP*AP*CP*GP*CP*T)-3') | dna | 11 | — | — |
| P | DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3') | dna | 8 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, T, P
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.81 | 0.84 | 52 | DTP, CA |
| 2 | 453 | 0.73 | 0.83 | 39 | empty |
| 3 | 237 | 0.64 | 0.83 | 25 | empty |
| 4 | 106 | 0.39 | 0.75 | 16 | empty |
| 5 | 69 | 0.35 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–T · 960 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–P · 579 Ų buried · 12 hydrogen bonds · protein-nucleic
- T–P · 368 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5DLF · Crystal structure of human DNA polymerase eta inserting datp opposite O4-methylhymidine · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y253 · AlphaFold monomer V2.0 prediction for DNA polymerase eta (Q9Y253) · 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 Q9Y253
- Elsewhere: RCSB PDB 5DLF · PDBe 5DLF · UniProt Q9Y253
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