MolNFT v1 · #36456 · protein
Crystal structure of nucleoside 2-deoxyribosyltransferase from trypanosoma brucei at 1.6 a resolution with BENZO[CD]INDOL-2(1H)-one bound
2F67: “Crystal structure of nucleoside 2-deoxyribosyltransferase from trypanosoma brucei at 1.6 a resolution with…”. X-ray diffraction, 2 ligands (12B, SO4), 3 pockets (best druggability 0.70). MolNFT v1 #36456 on GenesisL1: 3D structure…
- PDB
- 2F67
- 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
- 12B, SO4
- Pockets
- 3 · best druggability 0.70
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
- 12B · Benzo[cd]indol-2(1H)-one · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.70 | 0.91 | 24 | 12B, GOL |
| 2 | 137 | 0.68 | 0.89 | 26 | GOL, 12B |
| 3 | 53 | 0.44 | 0.84 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2037 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 2F67 · Crystal structure of Nucleoside 2-deoxyribosyltransferase from Trypanosoma brucei at 1.6… · the same entry in another collection · chain B against B, 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 2F67 · PDBe 2F67 · UniProt Q57VC7
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