Research workbench
Binary complex of human polymerase nu and DNA with the finger domain ajar
Analyse Binary complex of human polymerase nu and DNA with the finger domain ajar in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XVI
- Type
- protein + DNA
- Length
- 672 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase nu; DNA (5'-D(*AP*CP*TP*CP*TP*GP*AP*CP*GP*CP*TP*AP*GP*G)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q7Z5Q5
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase nu (EC 2.7.7.7) | protein | 647 | 49% helix, 15% strand | Q7Z5Q5 |
| P | DNA (5'-D(*AP*CP*TP*CP*TP*GP*AP*CP*GP*CP*TP*AP*GP*G)-3') | dna | 14 | — | — |
| T | DNA (5'-D(*CP*CP*TP*AP*GP*CP*GP*TP*CP*AP*G)-3') | dna | 11 | — | — |
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.72 | 0.95 | 16 | empty |
| 2 | 1047 | 0.72 | 0.76 | 70 | empty |
| 3 | 53 | 0.60 | 0.92 | 16 | empty |
| 4 | 291 | 0.59 | 0.78 | 36 | empty |
| 5 | 58 | 0.53 | 0.87 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–T · 787 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–P · 671 Ų buried · 16 hydrogen bonds · protein-nucleic
- P–T · 516 Ų buried · 44 hydrogen bonds · nucleic-nucleic
Compared structures
- 4XVI · Binary complex of human polymerase nu and DNA with the finger domain ajar · 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 4XVI · PDBe 4XVI · UniProt Q7Z5Q5
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