Research workbench
Crystal structure of fragment DNA polymerase I from bacillus stearothermophilus with self complementary 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
- 4DWI
- Type
- protein + DNA
- Length
- 600 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA (5'-D(*AP*CP*TP*GP*GP*AP*TP*CP*CP*A)-3')
- EC
- 2.7.7.7
- UniProt
- D9N168
- Ligands
- 9MG, CA, SO4
- Pockets
- 8 · best druggability 0.72
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 (5'-D(*AP*CP*TP*GP*GP*AP*TP*CP*CP*A)-3') | dna | 10 | — | — |
| C | DNA (5'-D(*AP*CP*TP*GP*GP*AP*TP*CP*CP*A)-3') | dna | 9 | — | — |
Ligands and binding sites
- 9MG · 9-methylguanine · ligand · chains B, C
- CA · Calcium ion · metal · chains C
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
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 | 898 | 0.72 | 0.77 | 64 | SO4 |
| 2 | 399 | 0.70 | 0.82 | 50 | GOL |
| 3 | 268 | 0.70 | 0.85 | 31 | empty |
| 4 | 126 | 0.47 | 0.79 | 26 | empty |
| 5 | 129 | 0.42 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1135 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–C · 802 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–C · 371 Ų buried · 31 hydrogen bonds · nucleic-nucleic
Compared structures
- 4DWI · Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with self… · 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 4DWI · PDBe 4DWI · UniProt D9N168
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