Research workbench
Cocrystal structure of bacillus fragment DNA polymerase I with duplex DNA , dctp, and zinc (closed form).
Analyse Cocrystal structure of bacillus fragment DNA polymerase I with duplex DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EZ5
- Type
- protein + DNA
- Length
- 1,201 residues
- Chains
- 6
- 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*DG)-3'…
- EC
- 2.7.7.7
- Ligands
- DAD, GLC, FRU, ZN, SO4
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 55% helix, 13% strand | — |
| D | DNA polymerase I (EC 2.7.7.7) | protein | 579 | 55% helix, 13% strand | — |
| B, E | 5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DG)-3' | dna | 9 | — | — |
| C, F | 5'-D(*DAP*DTP*DTP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DG)-3' | dna | 12 | — | — |
Ligands and binding sites
- DAD · 2',3'-dideoxyadenosine-5'-triphosphate · ligand · 2 copies · chains A, B, C, D, E, F
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, D
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, D
- ZN · Zinc ion · metal · 5 copies · chains A, B, D, E
- SO4 · Sulfate ion · ion · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.78 | 0.80 | 69 | ZN, DAD |
| 2 | 997 | 0.77 | 0.79 | 67 | ZN, DAD |
| 3 | 1199 | 0.77 | 0.79 | 103 | empty |
| 4 | 381 | 0.69 | 0.81 | 47 | GLC, FRU |
| 5 | 348 | 0.68 | 0.82 | 44 | GLC, FRU |
Interfaces
7 interfaces between chains.
- D–F · 1227 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–C · 1226 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 818 Ų buried · 21 hydrogen bonds · protein-nucleic
- D–E · 816 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–D · 725 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3EZ5 · Cocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA , dCTP, and… · 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 3EZ5 · PDBe 3EZ5
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