Research workbench
Purine 2'DEOXYRIBOSYLTRANSFERASE + 2'-deoxyadenosine
Analyse Purine 2'DEOXYRIBOSYLTRANSFERASE + 2'-deoxyadenosine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S2G
- 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
- 3D1
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 34% 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 | 35% helix, 19% strand | Q8RLY5 |
Ligands and binding sites
- 3D1 · (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.72 | 0.89 | 26 | empty |
| 2 | 70 | 0.64 | 0.92 | 17 | empty |
| 3 | 281 | 0.53 | 0.75 | 46 | 3D1 |
| 4 | 215 | 0.51 | 0.76 | 34 | 3D1 |
| 5 | 171 | 0.50 | 0.78 | 33 | 3D1 |
Interfaces
3 interfaces between chains.
- B–C · 972 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 914 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 850 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1S2G · Purine 2'deoxyribosyltransferase + 2'-deoxyadenosine · 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 1S2G · PDBe 1S2G · UniProt Q8RLY5
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