Research workbench
Crystal structure analysis of nucleoside 2- deoxyribosyltransferase complexed with 5-methyl-2'- deoxypseudouridine
Analyse Crystal structure analysis of nucleoside 2- deoxyribosyltransferase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F8Y
- Type
- protein
- Length
- 312 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside 2-deoxyribosyltransferase
- EC
- 2.4.2.6
- UniProt
- Q9R5V5
- Ligands
- 5MD
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nucleoside 2-deoxyribosyltransferase (EC 2.4.2.6) | protein | 156 | 45% helix, 15% strand | Q9R5V5 |
Ligands and binding sites
- 5MD · 2'-deoxy-1-methyl-pseudouridine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.70 | 0.94 | 24 | 5MD |
| 2 | 71 | 0.70 | 0.96 | 23 | 5MD |
Interfaces
1 interface between chains.
- A–B · 1599 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1F8Y · Crystal structure analysis of nucleoside 2-deoxyribosyltransferase complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9R5V5 · AlphaFold monomer V2.0 prediction for nucleoside deoxyribosyltransferase (Q9R5V5) · a predicted model of the same protein · chain A 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 Q9R5V5
- Elsewhere: RCSB PDB 1F8Y · PDBe 1F8Y · UniProt Q9R5V5
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