Research workbench
Uracil recognition in archaeal DNA polymerases captured by X-ray crystallography. V93Q polymerase variant
Analyse Uracil recognition in archaeal DNA polymerases captured by X-ray… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VWK
- Type
- protein
- Length
- 773 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase
- EC
- 2.7.7.7
- UniProt
- P56689
- Ligands
- NA, SO4
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 773 | 40% helix, 22% strand | P56689 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.76 | 0.81 | 77 | empty |
| 2 | 341 | 0.59 | 0.76 | 54 | SO4 |
| 3 | 183 | 0.50 | 0.77 | 22 | empty |
| 4 | 181 | 0.49 | 0.76 | 23 | empty |
| 5 | 198 | 0.48 | 0.75 | 31 | SO4 |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2VWK · Uracil Recognition in Archaeal DNA Polymerases Captured by X-ray Crystallography. V93Q… · 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 0.90
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 2VWK · PDBe 2VWK · UniProt P56689
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