Research workbench
Crystal structure of a S-diastereomer analogue of the spore photoproduct in complex with fragment DNA polymerase I from bacillus stearothermophilus
Analyse Crystal structure of a S-diastereomer analogue of the spore photoproduct in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y1I
- Type
- protein + DNA
- Length
- 600 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I; 5'-D(*GP*AP*CP*CP*AP*AP*CP*CP*CP*TP)-3'…
- EC
- 2.7.7.7
- UniProt
- D7D223
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.75
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 | D7D223 |
| B | 5'-D(*GP*AP*CP*CP*AP*AP*CP*CP*CP*TP)-3' | dna | 10 | — | — |
| C | 5'-D(*AP*GP*GP*GP*PBTP*THM*GP*GP*TP*CP)-3' | dna | 10 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.75 | 0.90 | 24 | empty |
| 2 | 435 | 0.71 | 0.82 | 44 | empty |
| 3 | 271 | 0.59 | 0.78 | 37 | SO4 |
| 4 | 148 | 0.48 | 0.77 | 23 | empty |
| 5 | 109 | 0.47 | 0.79 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 812 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–B · 735 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 443 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 2Y1I · Crystal structure of a S-diastereomer analogue of the spore photoproduct in complex 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 D7D223
- Elsewhere: RCSB PDB 2Y1I · PDBe 2Y1I · UniProt D7D223
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