Research workbench
Crystal structure of a salicylic aldehyde base in the pre-insertion site of fragment DNA polymerase I from bacillus stearothermophilus
Analyse Crystal structure of a salicylic aldehyde base in the pre-insertion site of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XY7
- Type
- protein + DNA
- Length
- 601 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I; 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP)-3'…
- EC
- 2.7.7.7
- UniProt
- E1C9K5
- Ligands
- GLC, FRU, SO4
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 55% helix, 12% strand | E1C9K5 |
| B | 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP)-3' | dna | 10 | — | — |
| C | 5'-D(*SAYP*CP*GP*AP*GP*TP*CP*AP*GP*GP*CP)-3' | dna | 11 | — | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains A
- FRU · beta-D-fructofuranose · sugar · chains A
- SO4 · Sulfate ion · ion · 2 copies · 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 | 236 | 0.70 | 0.86 | 29 | empty |
| 2 | 406 | 0.69 | 0.81 | 43 | GLC, FRU |
| 3 | 406 | 0.61 | 0.77 | 53 | empty |
| 4 | 115 | 0.49 | 0.80 | 19 | empty |
| 5 | 70 | 0.35 | 0.77 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1027 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 825 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–C · 456 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2XY7 · Crystal structure of a salicylic aldehyde base in the pre-insertion site of fragment DNA… · 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 E1C9K5
- Elsewhere: RCSB PDB 2XY7 · PDBe 2XY7 · UniProt E1C9K5
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