MolNFT v1 · #91151 · protein
Crystal structure of M. smegmatis DPRE1 in complex with FAD and covalently bound BTZ043
4F4Q: “Crystal structure of M. smegmatis DPRE1 in complex with FAD and covalently bound BTZ043”. X-ray diffraction, 2 ligands (0SK, FAD), 3 pockets (best druggability 0.79). MolNFT v1 #91151 on GenesisL1: 3D structure, binding sites and…
- 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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