Research workbench
Binary complex structure of klenow fragment of taq DNA polymerase I707L mutant with DNA containing ttt overhang
Analyse Binary complex structure of klenow fragment of taq DNA polymerase I707L mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XIU
- Type
- protein + DNA
- Length
- 565 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Synthetic oligonucleotide primer strand; Synthetic oligonucleotide template strand; DNA…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- MG
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Synthetic oligonucleotide primer strand | dna | 12 | — | — |
| C | Synthetic oligonucleotide template strand | dna | 14 | — | — |
| A | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 539 | 51% helix, 12% strand | P19821 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.68 | 0.86 | 27 | empty |
| 2 | 653 | 0.63 | 0.74 | 50 | MG |
| 3 | 267 | 0.60 | 0.79 | 36 | empty |
| 4 | 237 | 0.56 | 0.78 | 25 | empty |
| 5 | 58 | 0.40 | 0.81 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1105 Ų buried · 28 hydrogen bonds · protein-nucleic
- B–A · 824 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–C · 556 Ų buried · 55 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4XIU · Binary complex structure of Klenow fragment of Taq DNA polymerase I707L mutant with DNA… · the same entry in another collection · chain B against B, TM-score 1.00
- P19821 · AlphaFold monomer V2.0 prediction for DNA polymerase I, thermostable (P19821) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P19821
- Elsewhere: RCSB PDB 4XIU · PDBe 4XIU · UniProt P19821
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