Research workbench
Crystal structure of fragment DNA polymerase I from bacillus stearothermophilus with duplex DNA, ppi 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
- 4DSK
- Type
- protein + DNA
- Length
- 599 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*CP*G)-3'); DNA (5'…
- EC
- 2.7.7.7
- UniProt
- D9N168
- Ligands
- POP, CA
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*CP*G)-3') | dna | 10 | — | — |
| C | DNA (5'- D(*TP*CP*AP*CP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3') | dna | 14 | — | — |
| A | DNA polymerase (EC 2.7.7.7) | protein | 575 | 56% helix, 13% strand | D9N168 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.70 | 0.77 | 65 | CA, POP |
| 2 | 333 | 0.67 | 0.81 | 43 | empty |
| 3 | 104 | 0.63 | 0.89 | 19 | empty |
| 4 | 156 | 0.48 | 0.77 | 23 | empty |
| 5 | 54 | 0.47 | 0.85 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–A · 1176 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–A · 812 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–C · 574 Ų buried · 43 hydrogen bonds · nucleic-nucleic
Compared structures
- 4DSK · Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with… · the same entry in another collection · chain B against B, 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 4DSK · PDBe 4DSK · UniProt D9N168
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