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Crystal structure of fragment DNA polymerase I from bacillus stearothermophilus with 2'-mese-arabino-guanosine derivatized DNA
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
- 4O0I
- Type
- protein + DNA
- Length
- 602 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I; 5'-D(*C*(1TW)P*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
- EC
- 2.7.7.7
- UniProt
- D9N168
- Ligands
- NA, SO4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 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 | D9N168 |
| B | 5'-D(*C*(1TW)P*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3' | dna | 11 | — | — |
| C | 5'-D(*C*(1TW)P*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3' | dna | 11 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
- GOL · Glycerol · additive · chains A
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 | 186 | 0.69 | 0.88 | 23 | empty |
| 2 | 328 | 0.68 | 0.82 | 42 | GOL, NA |
| 3 | 692 | 0.68 | 0.76 | 63 | empty |
| 4 | 123 | 0.45 | 0.77 | 23 | empty |
| 5 | 87 | 0.37 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 904 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–C · 838 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 497 Ų buried · 44 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4O0I · 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 4O0I · PDBe 4O0I · UniProt D9N168
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