Research workbench
Bst DNA polymerase I FANA/DNA binary complex
Analyse Bst DNA polymerase I FANA/DNA binary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MU4
- Type
- protein + DNA
- Length
- 601 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.62
- Source
- Geobacillus stearothermophilus; SYNTHETIC CONSTRUCT
- Molecule
- DNA (5'-D(P*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3'); DNA polymerase I; Fana…
- EC
- 2.7.7.7
- UniProt
- E1C9K5
- Ligands
- MG, SO4
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · resolution 1.62 · 3 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | DNA (5'-D(P*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3') | dna | 11 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 577 | 55% helix, 13% strand | E1C9K5 |
| T | Fana (5'-D(P*(UF2)P*(A5L)P*(CFL)P*(GFL)P*(UF2)P*(GFL)P*(A5L)P*(UF2)P*(CFL)P*(GFL)P*(CFL))-3') | dna | 13 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains P, A, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 838 | 0.74 | 0.78 | 71 | MPD |
| 2 | 260 | 0.71 | 0.86 | 31 | empty |
| 3 | 381 | 0.70 | 0.82 | 45 | empty |
| 4 | 317 | 0.65 | 0.80 | 30 | MPD |
| 5 | 460 | 0.64 | 0.77 | 45 | SO4, MG |
Interfaces
3 interfaces between chains.
- P–A · 758 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–T · 731 Ų buried · 10 hydrogen bonds · protein-nucleic
- P–T · 526 Ų buried · 52 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 13 modified (nucleotide modification).
Compared structures
- 6MU4 · Bst DNA polymerase I FANA/DNA binary complex · 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 6MU4 · PDBe 6MU4 · UniProt E1C9K5
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