Research workbench
Purine 2'-deoxyribosyl complex with arabinoside: ribosylated intermediate (araa)
Analyse Purine 2'-deoxyribosyl complex with arabinoside: ribosylated intermediate (araa) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S2D
- Type
- protein
- Length
- 499 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside 2-deoxyribosyltransferase
- EC
- 2.4.2.6
- UniProt
- Q8RLY5
- Ligands
- ADE, V3M
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside 2-deoxyribosyltransferase (EC 2.4.2.6) | protein | 165 | 33% helix, 19% strand | Q8RLY5 |
| B, C | Nucleoside 2-deoxyribosyltransferase (EC 2.4.2.6) | protein | 167 | 35% helix, 18% strand | Q8RLY5 |
Ligands and binding sites
- ADE · Adenine · ligand · 3 copies · chains A, B, C
- V3M · 2-deoxy-2-fluoro-alpha-D-arabinofuranose · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.75 | 0.90 | 29 | empty |
| 2 | 61 | 0.69 | 0.96 | 17 | empty |
| 3 | 205 | 0.51 | 0.77 | 30 | ADE, V3M |
| 4 | 161 | 0.50 | 0.78 | 31 | ADE, V3M |
| 5 | 104 | 0.48 | 0.80 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 986 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 927 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 905 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 1S2D · Purine 2'-Deoxyribosyl complex with arabinoside: Ribosylated Intermediate (AraA) · 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 1S2D · PDBe 1S2D · UniProt Q8RLY5
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