Research workbench
Klentaq DNA polymerase processing a modified primer - bearing the modification upstream at the second primer nucleotide.
Analyse Klentaq DNA polymerase processing a modified primer - bearing the modification… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FBD
- Type
- protein + DNA
- Length
- 567 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I, thermostable; DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*AP*(OH3)P*C)-3')…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- XG4, MN, MG
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 539 | 55% helix, 13% strand | P19821 |
| B | DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*AP*(OH3)P*C)-3') | dna | 12 | — | — |
| C | DNA (5'- D(P*AP*AP*AP*CP*GP*GP*TP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') | dna | 16 | — | — |
Ligands and binding sites
- XG4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine · ligand · chains A, B, C
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains B, C
- GOL · Glycerol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.73 | 0.83 | 49 | MN, XG4 |
| 2 | 876 | 0.72 | 0.77 | 47 | MG |
| 3 | 230 | 0.70 | 0.87 | 25 | empty |
| 4 | 292 | 0.61 | 0.79 | 32 | empty |
| 5 | 224 | 0.54 | 0.77 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1399 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–B · 876 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–C · 563 Ų buried · 51 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6FBD · KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream… · the same entry in another collection · chain A against A, 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 0.96
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 6FBD · PDBe 6FBD · UniProt P19821
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