Research workbench
K263A mutant of polx from thermus thermophilus HB8 complexed with ca- dgtp
Analyse K263A mutant of polx from thermus thermophilus HB8 complexed with ca- dgtp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B0X
- Type
- protein
- Length
- 575 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase beta family (X family)
- EC
- 2.7.7.7
- UniProt
- Q5SJ64
- Ligands
- DGT, CA, ZN, CL
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase beta family (X family) (EC 2.7.7.7) | protein | 575 | 48% helix, 15% strand | Q5SJ64 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains A
- CA · Calcium ion · metal · 4 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 753 | 0.67 | 0.75 | 69 | DGT |
| 2 | 60 | 0.51 | 0.86 | 15 | empty |
| 3 | 110 | 0.38 | 0.74 | 20 | empty |
| 4 | 54 | 0.30 | 0.76 | 16 | empty |
| 5 | 51 | 0.28 | 0.75 | 17 | empty |
Compared structures
- 3B0X · K263A mutant of PolX from Thermus thermophilus HB8 complexed with Ca-dGTP · 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 Q5SJ64
- Elsewhere: RCSB PDB 3B0X · PDBe 3B0X · UniProt Q5SJ64
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