Research workbench
Human DNA polymerase eta-DNA ternary complex: reaction with 1 mM Mn2+ for 180s
Analyse Human DNA polymerase eta-DNA ternary complex: reaction with 1 mM Mn2+ for 180s in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KFC
- Type
- protein + DNA
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase eta; DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- DTP, MN, CA
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.5 · 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(*CP*AP*TP*TP*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
- MN · Manganese (II) ion · metal · 2 copies · chains A, P
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.81 | 0.82 | 84 | CA, MN, DTP |
| 2 | 220 | 0.67 | 0.85 | 21 | empty |
| 3 | 281 | 0.65 | 0.82 | 27 | empty |
| 4 | 309 | 0.58 | 0.77 | 33 | empty |
| 5 | 109 | 0.39 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1028 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–P · 618 Ų buried · 16 hydrogen bonds · protein-nucleic
- T–P · 370 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Compared structures
- 5KFC · Human DNA polymerase eta-DNA ternary complex: reaction with 1 mm MN2+ for 180S · 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 5KFC · PDBe 5KFC · UniProt Q9Y253
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