MolNFT v1 · #104369 · protein + DNA
Human DNA polymerase eta extending primer immediately after a phenanthriplatin adducted G
4Q8F: “Human DNA polymerase eta extending primer immediately after a phenanthriplatin adducted G”. X-ray diffraction, 2 ligands (XG4, MG), 5 pockets (best druggability 0.79). MolNFT v1 #104369 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4Q8F
- Type
- protein + DNA
- Length
- 444 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase eta; 5'-D(*CP*AP*TP*CP*GP*TP*CP*AP*CP*AP*CP*T)-3'…
- EC
- 2.7.7.7
- UniProt
- Q9Y253
- Ligands
- XG4, MG
- Pockets
- 5 · best druggability 0.79
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 | 425 | 44% helix, 22% strand | Q9Y253 |
| T | 5'-D(*CP*AP*TP*CP*GP*TP*CP*AP*CP*AP*CP*T)-3' | dna | 11 | — | — |
| P | 5'-D(*AP*GP*TP*GP*TP*GP*AP*C)-3' | dna | 8 | — | — |
Ligands and binding sites
- XG4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine · ligand · 2 copies · chains A, T, P
- MG · Magnesium ion · metal · 2 copies · chains A, P
- GOL · Glycerol · additive · 3 copies · chains A, T
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 | 1094 | 0.79 | 0.81 | 64 | MG, XG4 |
| 2 | 505 | 0.71 | 0.81 | 39 | GOL |
| 3 | 240 | 0.64 | 0.82 | 21 | empty |
| 4 | 105 | 0.39 | 0.76 | 17 | empty |
| 5 | 68 | 0.34 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–T · 946 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–P · 522 Ų buried · 12 hydrogen bonds · protein-nucleic
- T–P · 381 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4Q8F · Human DNA polymerase eta extending primer immediately after a phenanthriplatin adducted G · 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 4Q8F · PDBe 4Q8F · UniProt Q9Y253
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