MolNFT v1 · #29292 · protein
Crystal structure of oxidized yqjm from bacillus subtilis
1Z41 · Probable NADH-dependent flavin oxidoreductase yqjm: “Crystal structure of oxidized yqjm from bacillus subtilis”. X-ray diffraction, 2 ligands (FMN, SO4), 4 pockets (best druggability 0.70). MolNFT v1 #29292 on GenesisL1: 3D…
- PDB
- 1Z41
- Type
- protein
- Length
- 674 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable NADH-dependent flavin oxidoreductase yqjm
- EC
- 1.-.-.-
- UniProt
- P54550
- Ligands
- FMN, SO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable NADH-dependent flavin oxidoreductase yqjm (EC 1.-.-.-) | protein | 337 | 38% helix, 16% strand | P54550 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.70 | 0.80 | 51 | SO4, FMN |
| 2 | 413 | 0.68 | 0.80 | 46 | SO4, FMN |
| 3 | 182 | 0.50 | 0.77 | 33 | empty |
| 4 | 56 | 0.27 | 0.74 | 10 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1189 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
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 P54550
- Elsewhere: RCSB PDB 1Z41 · PDBe 1Z41 · UniProt P54550
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