Research workbench
Human DNA Pol eta S113A with dA-ended primer and dATP: in crystallo reaction for 230 s
Analyse Human DNA Pol eta S113A with dA-ended primer and dATP: in crystallo reaction… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M87
- Type
- protein + DNA
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.85
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase eta; DNA (5'-D(*CP*AP*TP*TP*TP*TP*GP*AP*CP*GP*CP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- DTP, DPO, MG, CA
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.85 · 3 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 429 | 45% helix, 22% strand | Q9Y253 |
| T | DNA (5'-D(*CP*AP*TP*TP*TP*TP*GP*AP*CP*GP*CP*T)-3') | dna | 11 | — | — |
| P | DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*AP*A)-3') | dna | 9 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, T, P
- DPO · Diphosphate · ligand · chains A, P
- MG · Magnesium ion · metal · 3 copies · chains A, P
- CA · Calcium ion · metal · chains A, P
- GOL · Glycerol · additive · 3 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.76 | 0.83 | 37 | empty |
| 2 | 569 | 0.71 | 0.80 | 52 | empty |
| 3 | 218 | 0.67 | 0.85 | 21 | empty |
| 4 | 260 | 0.49 | 0.74 | 26 | DPO, MG |
| 5 | 99 | 0.44 | 0.79 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1053 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–P · 792 Ų buried · 23 hydrogen bonds · protein-nucleic
- T–P · 426 Ų buried · 36 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7M87 · Human DNA pol eta S113A with da-ended primer and datp: in crystallo reaction for 230 S · the same entry in another collection · chain A against A, TM-score 1.00
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 7M87 · PDBe 7M87 · UniProt Q9Y253
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