Research workbench
Purine 2'DEOXYRIBOSYLTRANSFERASE + bromopurine
Analyse Purine 2'DEOXYRIBOSYLTRANSFERASE + bromopurine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S2I
- Type
- protein
- Length
- 499 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine trans deoxyribosylase
- EC
- 2.4.2.6
- UniProt
- Q8RLY5
- Ligands
- BP1
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine trans deoxyribosylase (EC 2.4.2.6) | protein | 165 | 33% helix, 19% strand | Q8RLY5 |
| B, C | Purine trans deoxyribosylase (EC 2.4.2.6) | protein | 167 | 36% helix, 19% strand | Q8RLY5 |
Ligands and binding sites
- BP1 · 6-bromo-7H-purine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.78 | 0.90 | 39 | empty |
| 2 | 263 | 0.53 | 0.76 | 45 | BP1 |
| 3 | 183 | 0.52 | 0.78 | 30 | BP1 |
| 4 | 222 | 0.51 | 0.76 | 31 | BP1 |
| 5 | 111 | 0.46 | 0.79 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–C · 985 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 923 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 856 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1S2I · Purine 2'deoxyribosyltransferase + bromopurine · 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 Q8RLY5
- Elsewhere: RCSB PDB 1S2I · PDBe 1S2I · UniProt Q8RLY5
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