Research workbench
Binary complex of human polymerase nu and DNA with the finger domain closed and thumb domain rotated out
Analyse Binary complex of human polymerase nu and DNA with the finger domain closed and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XVM
- Type
- protein + DNA
- Length
- 649 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase nu; DNA (5'-D(*CP*TP*AP*GP*CP*GP*TP*CP*A)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q7Z5Q5
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase nu (EC 2.7.7.7) | protein | 627 | 51% helix, 13% strand | Q7Z5Q5 |
| T | DNA (5'-D(*CP*TP*AP*GP*CP*GP*TP*CP*A)-3') | dna | 9 | — | — |
| P | DNA (5'-D(*GP*AP*TP*CP*TP*GP*AP*CP*GP*CP*TP*AP*G)-3') | dna | 13 | — | — |
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 | 180 | 0.69 | 0.88 | 24 | empty |
| 2 | 546 | 0.68 | 0.78 | 51 | empty |
| 3 | 102 | 0.55 | 0.83 | 21 | empty |
| 4 | 137 | 0.53 | 0.81 | 26 | empty |
| 5 | 85 | 0.51 | 0.83 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1010 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–P · 569 Ų buried · 9 hydrogen bonds · protein-nucleic
- T–P · 426 Ų buried · 38 hydrogen bonds · nucleic-nucleic
Compared structures
- 4XVM · Binary complex of human polymerase nu and DNA with the finger domain closed and thumb… · 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 0.91
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 4XVM · PDBe 4XVM · UniProt Q7Z5Q5
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