MolNFT v1 · #138034 · protein + DNA
Structure of mutant taq polymerase incorporating unnatural base pairs Z:P
5W6K · DNA polymerase I, thermostable: “Structure of mutant taq polymerase incorporating unnatural base pairs Z:P”. X-ray diffraction, 2 ligands (A5J, MG), 8 pockets (best druggability 0.71). MolNFT v1 #138034 on GenesisL1: 3D structure…
- PDB
- 5W6K
- Type
- protein + DNA
- Length
- 547 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*GP*CP*(DOC))-3')…
- EC
- 2.7.7.7
- UniProt
- P19821
- Ligands
- A5J, MG
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I, thermostable (EC 2.7.7.7) | protein | 522 | 51% helix, 13% strand | P19821 |
| B | DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3') | dna | 12 | — | — |
| C | DNA (5'-D(P*(1WA)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3') | dna | 13 | — | — |
Ligands and binding sites
- A5J · (1R)-1-[6-amino-5-(dihydroxyamino)-2-hydroxypyridin-3-yl]-1,4-anhydro-2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-erythro-pentitol · ligand · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, B
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 | 226 | 0.71 | 0.87 | 29 | empty |
| 2 | 408 | 0.70 | 0.82 | 45 | A5J, MG |
| 3 | 313 | 0.61 | 0.79 | 35 | empty |
| 4 | 601 | 0.61 | 0.73 | 37 | empty |
| 5 | 146 | 0.44 | 0.75 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1027 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 844 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–C · 559 Ų buried · 57 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5W6K · Structure of mutant Taq Polymerase incorporating unnatural base pairs Z:P · 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 5W6K · PDBe 5W6K · UniProt P19821
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