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Cocrystal structure of bacillus fragment DNA polymerase I with duplex DNA (open form)
Analyse Cocrystal structure of bacillus fragment DNA polymerase I with duplex DNA (open… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EYZ
- Type
- protein + DNA
- Length
- 603 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I; 5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DGP*DC)-3'…
- EC
- 2.7.7.7
- Ligands
- GLC, FRU, SO4
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 54% helix, 13% strand | — |
| B | 5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DGP*DC)-3' | dna | 10 | — | — |
| C | 5'-D(*DAP*DTP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DGP*DA)- 3' | dna | 13 | — | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains A
- FRU · beta-D-fructofuranose · sugar · 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
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 | 160 | 0.70 | 0.89 | 23 | empty |
| 2 | 397 | 0.68 | 0.81 | 46 | GLC, FRU |
| 3 | 739 | 0.66 | 0.75 | 62 | SO4 |
| 4 | 171 | 0.48 | 0.76 | 20 | empty |
| 5 | 136 | 0.46 | 0.77 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1191 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–B · 788 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–C · 475 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Compared structures
- 3EYZ · Cocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA (open form) · 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 3EYZ · PDBe 3EYZ
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