Research workbench
Crystal structure of fragment DNA polymerase I from bacillus stearothermophilus Y714S mutant bound to G:T mismatch
Analyse Crystal structure of fragment DNA polymerase I from bacillus stearothermophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HPO
- Type
- protein + DNA
- Length
- 599 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I, large fragment; 5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DOC))-3'…
- EC
- 2.7.7.7
- Ligands
- TTP, GLC, FRU, MG, SO4
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I, large fragment (EC 2.7.7.7) | protein | 580 | 56% helix, 13% strand | — |
| B | 5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DOC))-3' | dna | 9 | — | — |
| C | 5'-D(P*GP*GP*CP*GP*TP*GP*AP*TP*CP*G)-3' | dna | 10 | — | — |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · chains A, B, C
- GLC · alpha-D-glucopyranose · sugar · chains A
- FRU · beta-D-fructofuranose · sugar · chains A
- MG · Magnesium ion · metal
- SO4 · Sulfate ion · ion · chains A
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 | 994 | 0.73 | 0.77 | 83 | MG, TTP |
| 2 | 267 | 0.71 | 0.86 | 28 | empty |
| 3 | 353 | 0.70 | 0.83 | 46 | GLC, FRU |
| 4 | 62 | 0.50 | 0.86 | 18 | empty |
| 5 | 149 | 0.48 | 0.78 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 993 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–B · 769 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–C · 426 Ų buried · 36 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (artifact, nucleotide modification).
Compared structures
- 3HPO · Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus Y714S… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3HPO · PDBe 3HPO
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