Research workbench
Bst DNA polymerase I pre-insertion complex structure
Analyse Bst DNA polymerase I pre-insertion complex structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DSU
- Type
- protein + DNA
- Length
- 598 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- E1C9K5
- Ligands
- DZ4, MG, SO4
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3') | dna | 10 | — | — |
| T | DNA (5'-D(P*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3') | dna | 11 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 577 | 56% helix, 14% strand | E1C9K5 |
Ligands and binding sites
- DZ4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine · ligand · chains P, A
- MG · Magnesium ion · metal · chains 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
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.77 | 0.98 | 27 | empty |
| 2 | 941 | 0.71 | 0.75 | 68 | MG, DZ4 |
| 3 | 140 | 0.70 | 0.90 | 19 | empty |
| 4 | 351 | 0.67 | 0.81 | 42 | empty |
| 5 | 230 | 0.57 | 0.78 | 25 | empty |
Interfaces
3 interfaces between chains.
- T–A · 836 Ų buried · 8 hydrogen bonds · protein-nucleic
- P–A · 802 Ų buried · 22 hydrogen bonds · protein-nucleic
- P–T · 473 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Compared structures
- 6DSU · Bst DNA polymerase I pre-insertion complex structure · 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 6DSU · PDBe 6DSU · UniProt E1C9K5
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