Research workbench
Crystal structure of rcl with 5'-phiosphorothioate-adenosine
Analyse Crystal structure of rcl with 5'-phiosphorothioate-adenosine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FYK
- Type
- protein
- Length
- 499 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribonucleoside 5'-monophosphate N-glycosidase
- EC
- 3.2.2.-
- UniProt
- O35820
- Ligands
- SRA, SO4
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyribonucleoside 5'-monophosphate N-glycosidase (EC 3.2.2.-) | protein | 126 | 44% helix, 17% strand | O35820 |
| B | Deoxyribonucleoside 5'-monophosphate N-glycosidase (EC 3.2.2.-) | protein | 124 | 49% helix, 18% strand | O35820 |
| C | Deoxyribonucleoside 5'-monophosphate N-glycosidase (EC 3.2.2.-) | protein | 125 | 46% helix, 18% strand | O35820 |
| D | Deoxyribonucleoside 5'-monophosphate N-glycosidase (EC 3.2.2.-) | protein | 124 | 46% helix, 18% strand | O35820 |
Ligands and binding sites
- SRA · Adenosine -5'-thio-monophosphate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.62 | 0.81 | 36 | SRA |
| 2 | 121 | 0.59 | 0.85 | 23 | SRA |
| 3 | 203 | 0.59 | 0.80 | 34 | SRA |
| 4 | 196 | 0.57 | 0.80 | 33 | SRA |
Interfaces
2 interfaces between chains.
- C–D · 1433 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1430 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4FYK · Crystal structure of rcl with 5'-phiosphorothioate-adenosine · the same entry in another collection · chain D against D, TM-score 1.00
- O35820 · AlphaFold monomer V2.0 prediction for 2'-deoxynucleoside 5'-phosphate N-hydrolase 1… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O35820
- Elsewhere: RCSB PDB 4FYK · PDBe 4FYK · UniProt O35820
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