MolNFT v1 · #36453 · protein
Crystal structure of nucleoside 2-deoxyribosyltransferase from trypanosoma brucei at 1.6 a resolution with 1-methylquinolin-2(1H)- one bound
2F64: “Crystal structure of nucleoside 2-deoxyribosyltransferase from trypanosoma brucei at 1.6 a resolution with…”. X-ray diffraction, 2 ligands (12Q, SO4), 2 pockets (best druggability 0.72). MolNFT v1 #36453 on GenesisL1: 3D structure…
- PDB
- 2F64
- Type
- protein
- Length
- 316 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
- Q57VC7
- Ligands
- 12Q, SO4
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nucleoside 2-deoxyribosyltransferase (EC 2.4.2.6) | protein | 158 | 39% helix, 13% strand | Q57VC7 |
Ligands and binding sites
- 12Q · 1-methylquinolin-2(1H)-one · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 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 | 116 | 0.72 | 0.93 | 23 | 12Q, GOL |
| 2 | 147 | 0.70 | 0.90 | 28 | 12Q, GOL |
Interfaces
1 interface between chains.
- A–B · 2053 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 2F64 · Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.6… · 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 Q57VC7
- Elsewhere: RCSB PDB 2F64 · PDBe 2F64 · UniProt Q57VC7
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