MolNFT v1 · #110404 · protein + DNA
Binary complex of human polymerase nu and DNA with the finger domain open
4XVL · DNA polymerase nu: “Binary complex of human polymerase nu and DNA with the finger domain open”. X-ray diffraction, 1 ligand (NA), 6 pockets (best druggability 0.74). MolNFT v1 #110404 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4XVL
- Type
- protein + DNA
- Length
- 660 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase nu; DNA (5'-D(*GP*AP*TP*CP*TP*GP*AP*CP*GP*CP*TP*AP*CP*G)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q7Z5Q5
- Ligands
- NA
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase nu (EC 2.7.7.7) | protein | 636 | 52% helix, 14% strand | Q7Z5Q5 |
| P | DNA (5'-D(*GP*AP*TP*CP*TP*GP*AP*CP*GP*CP*TP*AP*CP*G)-3') | dna | 14 | — | — |
| T | DNA (5'-D(*TP*CP*GP*TP*AP*GP*CP*GP*TP*CP*A)-3') | dna | 10 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.74 | 0.77 | 69 | empty |
| 2 | 181 | 0.66 | 0.86 | 29 | empty |
| 3 | 290 | 0.59 | 0.78 | 44 | empty |
| 4 | 213 | 0.53 | 0.77 | 25 | empty |
| 5 | 56 | 0.53 | 0.88 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–T · 888 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–P · 725 Ų buried · 10 hydrogen bonds · protein-nucleic
- P–T · 485 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Compared structures
- 4XVL · Binary complex of human polymerase nu and DNA with the finger domain open · the same entry in another collection · chain A against A, TM-score 1.00
- Q7Z5Q5 · AlphaFold monomer V2.0 prediction for DNA polymerase nu (Q7Z5Q5) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q7Z5Q5
- Elsewhere: RCSB PDB 4XVL · PDBe 4XVL · UniProt Q7Z5Q5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.