Research workbench
Crystal structure of fragment DNA polymerase I from bacillus stearothermophilus with duplex DNA, se-dgtp and calcium
Analyse Crystal structure of fragment DNA polymerase I from bacillus stearothermophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DSI
- Type
- protein + DNA
- Length
- 599 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA; Se-dgtp
- EC
- 2.7.7.7
- UniProt
- D9N168
- Ligands
- DG, CA, SO4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 581 | 56% helix, 13% strand | D9N168 |
| B | DNA | dna | 9 | — | — |
| C | Se-dgtp | dna | 9 | — | — |
Ligands and binding sites
- DG · 2'-deoxyguanosine-5'-monophosphate · ligand · chains B, C
- CA · Calcium ion · metal · chains A, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, C
- GOL · Glycerol · additive · 5 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.69 | 0.77 | 70 | SO4 |
| 2 | 347 | 0.68 | 0.82 | 40 | GOL |
| 3 | 253 | 0.68 | 0.84 | 30 | empty |
| 4 | 137 | 0.47 | 0.78 | 26 | empty |
| 5 | 138 | 0.42 | 0.74 | 18 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 878 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–C · 859 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–C · 436 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Compared structures
- 4DSI · Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with… · 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 D9N168
- Elsewhere: RCSB PDB 4DSI · PDBe 4DSI · UniProt D9N168
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