MolNFT v1 · #148602 · protein + DNA
Klentaq DNA polymerase processing a modified primer - bearing the modification upstream at the fifth primer nucleotide.
6FBG · DNA polymerase I, thermostable: “Klentaq DNA polymerase processing a modified primer - bearing the modification upstream at the fifth primer…”. X-ray diffraction, 2 ligands (XG4, MN), 8 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 6FBG
- Type
- protein + DNA
- Length
- 566 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*AP*(OH3)P*CP*GP*GP*C)-3')…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- XG4, MN
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 538 | 54% helix, 13% strand | P19821 |
| B | DNA (5'-D(*GP*AP*CP*CP*AP*CP*AP*(OH3)P*CP*GP*GP*C)-3') | dna | 12 | — | — |
| C | DNA (5'-D(*AP*AP*AP*CP*GP*CP*CP*GP*GP*TP*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
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.75 | 0.79 | 45 | empty |
| 2 | 247 | 0.72 | 0.88 | 29 | empty |
| 3 | 481 | 0.72 | 0.82 | 41 | MN, XG4 |
| 4 | 278 | 0.61 | 0.80 | 30 | EDO |
| 5 | 106 | 0.47 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1412 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–B · 893 Ų buried · 28 hydrogen bonds · protein-nucleic
- B–C · 560 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6FBG · 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 6FBG · PDBe 6FBG · UniProt P19821
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