Research workbench
Binary complex of human polymerase nu and DNA with the finger domain open
Analyse Binary complex of human polymerase nu and DNA with the finger domain open in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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