MolNFT v1 · #106687 · protein
Crystal structure of old yellow enzyme from candida macedoniensis AKU4588 complexed with P-hydroxybenzaldehyde
4TMC: “Crystal structure of old yellow enzyme from candida macedoniensis AKU4588 complexed with P-hydroxybenzaldehyde”. X-ray diffraction, 2 ligands (FMN, HBA), 15 pockets (best druggability 0.81). MolNFT v1 #106687 on GenesisL1: 3D…
- PDB
- 4TMC
- Type
- protein
- Length
- 1,592 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Old yellow enzyme
- UniProt
- Q6I7B7
- Ligands
- FMN, HBA
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Old yellow enzyme | protein | 399 | 38% helix, 14% strand | Q6I7B7 |
| B | Old yellow enzyme | protein | 398 | 38% helix, 14% strand | Q6I7B7 |
| D | Old yellow enzyme | protein | 396 | 39% helix, 14% strand | Q6I7B7 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- HBA · P-hydroxybenzaldehyde · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.81 | 0.90 | 48 | FMN, HBA |
| 2 | 374 | 0.80 | 0.89 | 50 | FMN, HBA |
| 3 | 369 | 0.79 | 0.88 | 61 | FMN, HBA |
| 4 | 338 | 0.79 | 0.89 | 48 | FMN, HBA |
| 5 | 404 | 0.64 | 0.78 | 47 | empty |
Interfaces
3 interfaces between chains.
- A–C · 959 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 919 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 215 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4TMC · CRYSTAL STRUCTURE of OLD YELLOW ENZYME from CANDIDA MACEDONIENSIS AKU4588 COMPLEXED with… · 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 Q6I7B7
- Elsewhere: RCSB PDB 4TMC · PDBe 4TMC · UniProt Q6I7B7
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