MolNFT v1 · #110405 · protein + DNA
Binary complex of human polymerase nu and DNA with the finger domain closed and thumb domain rotated out
4XVM · DNA polymerase nu: “Binary complex of human polymerase nu and DNA with the finger domain closed and thumb domain rotated out”. X-ray diffraction, 9 pockets (best druggability 0.69). MolNFT v1 #110405 on GenesisL1: 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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