MolNFT v1 · #116673 · protein
N-terminal his tagged appol exonuclease mutant
5DKT · Prex DNA polymerase: “N-terminal his tagged appol exonuclease mutant”. X-ray diffraction, 2 ligands (NA, SO4), 9 pockets (best druggability 0.70). MolNFT v1 #116673 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DKT
- Type
- protein
- Length
- 577 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prex DNA polymerase
- EC
- 2.7.7.7
- UniProt
- Q8ILY1
- Ligands
- NA, SO4
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prex DNA polymerase (EC 2.7.7.7) | protein | 577 | 47% helix, 17% strand | Q8ILY1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.70 | 0.98 | 19 | empty |
| 2 | 608 | 0.69 | 0.78 | 60 | SO4, NA |
| 3 | 125 | 0.47 | 0.78 | 26 | empty |
| 4 | 113 | 0.47 | 0.79 | 21 | empty |
| 5 | 61 | 0.42 | 0.81 | 14 | empty |
Compared structures
- 5DKT · N-terminal His tagged apPOL exonuclease mutant · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8ILY1
- Elsewhere: RCSB PDB 5DKT · PDBe 5DKT · UniProt Q8ILY1
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