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Crystal Structure of Human DNA Polymerase Eta Inserting dTMPNPP Opposite O6-Methyl-2'-deoxyguanosine
Analyse Crystal Structure of Human DNA Polymerase Eta Inserting dTMPNPP Opposite… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L1J
- Type
- protein + DNA
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.94
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase eta; DNA (5'-D(*CP*AP*TP*(6OG)P*AP*TP*GP*AP*CP*GP*CP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- 1FZ, MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · resolution 1.94 · 3 distinct chains · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 430 | 44% helix, 22% strand | Q9Y253 |
| T | DNA (5'-D(*CP*AP*TP*(6OG)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
- 1FZ · 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine · ligand · chains A, T, P
- MG · Magnesium ion · metal · 2 copies · chains A, P
- 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.80 | 0.82 | 62 | MG, 1FZ |
| 2 | 672 | 0.74 | 0.80 | 53 | empty |
| 3 | 224 | 0.67 | 0.84 | 23 | empty |
| 4 | 136 | 0.56 | 0.83 | 25 | empty |
| 5 | 101 | 0.38 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1082 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–P · 624 Ų buried · 13 hydrogen bonds · protein-nucleic
- T–P · 378 Ų buried · 29 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5L1J · Crystal structure of human DNA polymerase eta inserting dtmpnpp opposite… · 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 5L1J · PDBe 5L1J · UniProt Q9Y253
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