Research workbench
Bst DNA polymerase I time-resolved structure, 4 hr post dATP and dCTP addition
Analyse Bst DNA polymerase I time-resolved structure, 4 hr post dATP and dCTP addition in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K5S
- Type
- protein + DNA
- Length
- 601 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.67
- Source
- Geobacillus stearothermophilus; SYNTHETIC CONSTRUCT
- Molecule
- DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- E1C9K5
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · resolution 1.67 · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | DNA (5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3') | dna | 10 | — | — |
| T | DNA (5'-D(P*AP*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*C)-3') | dna | 14 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 577 | 56% helix, 13% strand | E1C9K5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.70 | 0.76 | 74 | SO4 |
| 2 | 315 | 0.69 | 0.84 | 35 | empty |
| 3 | 346 | 0.66 | 0.81 | 44 | empty |
| 4 | 105 | 0.45 | 0.79 | 22 | empty |
| 5 | 156 | 0.42 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- T–A · 1363 Ų buried · 29 hydrogen bonds · protein-nucleic
- P–A · 856 Ų buried · 20 hydrogen bonds · protein-nucleic
- P–T · 470 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Compared structures
- 7K5S · Bst DNA polymerase I time-resolved structure, 4 hr post datp and dctp addition · 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
- Every structure of UniProt E1C9K5
- Elsewhere: RCSB PDB 7K5S · PDBe 7K5S · UniProt E1C9K5
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