Research workbench
Crystal structure of M. smegmatis DPRE1 in complex with FAD and covalently bound BTZ043
Analyse Crystal structure of M. smegmatis DPRE1 in complex with FAD and covalently… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F4Q
- Type
- protein
- Length
- 412 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DPRE1
- UniProt
- A0R607
- Ligands
- 0SK, FAD
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DPRE1 | protein | 412 | 31% helix, 26% strand | A0R607 |
Ligands and binding sites
- 0SK · 8-(hydroxyamino)-2-[(2S)-2-methyl-1,4-dioxa-8-azaspiro[4.5]dec-8-yl]-6-(trifluoromethyl)-4H-1,3-benzothiazin-4-one · ligand · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- GOL · Glycerol · additive · chains A
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 | 594 | 0.79 | 0.84 | 79 | 0SK, FAD |
| 2 | 74 | 0.55 | 0.87 | 21 | empty |
| 3 | 55 | 0.26 | 0.73 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4F4Q · Crystal structure of M. smegmatis DprE1 in complex with FAD and covalently bound BTZ043 · the same entry in another collection · chain A against A, TM-score 1.00
- A0R607 · AlphaFold monomer V2.0 prediction for decaprenylphosphoryl-beta-D- ribose oxidase (A0R607) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 A0R607
- Elsewhere: RCSB PDB 4F4Q · PDBe 4F4Q · UniProt A0R607
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