MolNFT v1 · #52295 · protein + DNA
Uracil recognition in archaeal DNA polymerases captured by X-ray crystallography.
2VWJ: “Uracil recognition in archaeal DNA polymerases captured by X-ray crystallography.”. X-ray diffraction, 1 ligand (K), 12 pockets (best druggability 0.78). MolNFT v1 #52295 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2VWJ
- Type
- protein + DNA
- Length
- 783 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; 5'-D(*AP*AP*UP*GP*GP*AP*GP*AP*CP*GP…
- EC
- 2.7.7.7
- UniProt
- P56689
- Ligands
- K
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 757 | 40% helix, 22% strand | P56689 |
| B | 5'-D(*AP*AP*UP*GP*GP*AP*GP*AP*CP*GP *GP*CP*TP*TP*TP*TP*GP*CP*CP*GP*TP*GP*TP*C)-3' | dna | 26 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.78 | 0.83 | 60 | empty |
| 2 | 438 | 0.67 | 0.80 | 43 | K |
| 3 | 104 | 0.64 | 0.89 | 19 | empty |
| 4 | 344 | 0.61 | 0.78 | 28 | empty |
| 5 | 213 | 0.54 | 0.78 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1488 Ų buried · 37 hydrogen bonds · protein-nucleic
Compared structures
- 2VWJ · Uracil Recognition in Archaeal DNA Polymerases Captured by X-ray Crystallography. · the same entry in another collection · chain A against A, TM-score 1.00
- P56689 · AlphaFold monomer V2.0 prediction for DNA polymerase (P56689) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P56689
- Elsewhere: RCSB PDB 2VWJ · PDBe 2VWJ · UniProt P56689
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