MolNFT v1 · #116847 · protein + DNA
Crystal structure of human DNA polymerase eta inserting dgmpnpp opposite O4-ethylthymidine
5DQH: “Crystal structure of human DNA polymerase eta inserting dgmpnpp opposite O4-ethylthymidine”. X-ray diffraction, 2 ligands (XG4, MG), 4 pockets (best druggability 0.81). MolNFT v1 #116847 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DQH
- Type
- protein + DNA
- Length
- 449 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; DNA (5'-D(*CP*AP*TP*(5EJ)P*AP*TP*GP*AP*CP*GP*CP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- XG4, MG
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 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*(5EJ)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
- XG4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine · 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
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.81 | 0.82 | 85 | XG4, MG |
| 2 | 552 | 0.72 | 0.80 | 50 | empty |
| 3 | 225 | 0.68 | 0.85 | 26 | empty |
| 4 | 99 | 0.39 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1063 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–P · 615 Ų buried · 16 hydrogen bonds · protein-nucleic
- T–P · 395 Ų buried · 31 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5DQH · Crystal Structure of Human DNA Polymerase Eta Inserting dGMPNPP Opposite O4-Ethylthymidine · 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 5DQH · PDBe 5DQH · UniProt Q9Y253
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.