MolNFT v1 · #109983 · protein + DNA
Binary complex structure of klenow fragment of taq DNA polymerase I707L mutant with DNA containing ttt overhang
4XIU · Synthetic oligonucleotide primer strand: “Binary complex structure of klenow fragment of taq DNA polymerase I707L mutant with DNA containing ttt…”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.68). MolNFT v1…
- 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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