Research workbench
Bst DNA polymerase I time-resolved structure, 8 min post datp addition
Analyse Bst DNA polymerase I time-resolved structure, 8 min post datp addition in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K5Q
- Type
- protein + DNA
- Length
- 600 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*G*CP*GP*AP*TP*CP*AP*CP*GP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- E1C9K5
- Ligands
- DTP, SO4
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | DNA (5'-D(P*G*CP*GP*AP*TP*CP*AP*CP*GP*T)-3') | dna | 10 | — | — |
| T | DNA (5'-D(P*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3') | dna | 13 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 577 | 56% helix, 13% strand | E1C9K5 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains P, T, A
- SO4 · Sulfate ion · ion · 3 copies · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.74 | 0.77 | 71 | SO4, DTP |
| 2 | 277 | 0.69 | 0.84 | 30 | empty |
| 3 | 405 | 0.68 | 0.80 | 47 | empty |
| 4 | 297 | 0.65 | 0.81 | 30 | empty |
| 5 | 57 | 0.57 | 0.90 | 14 | empty |
Interfaces
3 interfaces between chains.
- T–A · 955 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–A · 696 Ų buried · 19 hydrogen bonds · protein-nucleic
- P–T · 494 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7K5Q · Bst DNA polymerase I time-resolved structure, 8 min post dATP addition · the same entry in another collection · chain P against P, 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 7K5Q · PDBe 7K5Q · UniProt E1C9K5
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