Research workbench
Crystal structure of fragment DNA polymerase I from bacillus stearothermophilus F710Y 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
- 3HP6
- Type
- protein + DNA
- Length
- 1,202 residues
- Chains
- 6
- 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*(DDG))-3'…
- EC
- 2.7.7.7
- Ligands
- D3T, GLC, FRU, MG, SO4
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA polymerase I, large fragment (EC 2.7.7.7) | protein | 580 | 55% helix, 13% strand | — |
| B, E | 5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DDG))-3' | dna | 9 | — | — |
| C, F | 5'-D(*AP*CP*GP*CP*CP*GP*TP*GP*AP*TP*CP*G)-3' | dna | 12 | — | — |
Ligands and binding sites
- D3T · 2',3'-dideoxy-thymidine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D, E, F
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, D
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.73 | 0.80 | 57 | empty |
| 2 | 836 | 0.73 | 0.78 | 60 | MG, D3T |
| 3 | 811 | 0.73 | 0.78 | 75 | MG, D3T |
| 4 | 506 | 0.70 | 0.80 | 50 | empty |
| 5 | 230 | 0.70 | 0.87 | 31 | empty |
Interfaces
7 interfaces between chains.
- A–C · 1230 Ų buried · 28 hydrogen bonds · protein-nucleic
- D–F · 1176 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–B · 821 Ų buried · 19 hydrogen bonds · protein-nucleic
- D–E · 817 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–D · 680 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (artifact, nucleotide modification).
Compared structures
- 3HP6 · Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus F710Y… · 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 3HP6 · PDBe 3HP6
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