MolNFT v1 · #111378 · protein + DNA
Mutant human DNA polymerase eta Q38A/R61A inserting dctp opposite an 8-oxoguanine lesion
4YP3: “Mutant human DNA polymerase eta Q38A/R61A inserting dctp opposite an 8-oxoguanine lesion”. X-ray diffraction, 2 ligands (DCP, CA), 5 pockets (best druggability 0.78). MolNFT v1 #111378 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4YP3
- Type
- protein + DNA
- Length
- 442 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; DNA (5'-D(*TP*(8OG)P*AP*TP*GP*AP*CP*GP*CP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- DCP, CA
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase eta (EC 2.7.7.7) | protein | 424 | 45% helix, 21% strand | Q9Y253 |
| T | DNA (5'-D(*TP*(8OG)P*AP*TP*GP*AP*CP*GP*CP*T)-3') | dna | 10 | — | — |
| P | DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3') | dna | 8 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains A, T, P
- CA · Calcium ion · metal · 2 copies · chains A, P
- GOL · Glycerol · additive · 2 copies · chains A, T, P
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 | 1068 | 0.78 | 0.80 | 79 | DCP, CA, GOL |
| 2 | 495 | 0.70 | 0.80 | 36 | empty |
| 3 | 222 | 0.67 | 0.85 | 26 | empty |
| 4 | 57 | 0.41 | 0.81 | 14 | empty |
| 5 | 89 | 0.36 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–T · 836 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–P · 463 Ų buried · 12 hydrogen bonds · protein-nucleic
- T–P · 373 Ų buried · 25 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4YP3 · Mutant Human DNA Polymerase Eta Q38A/R61A Inserting dCTP Opposite an 8-Oxoguanine Lesion · 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 4YP3 · PDBe 4YP3 · UniProt Q9Y253
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