Research workbench
Crystal structure of old yellow enzyme from candida macedoniensis AKU4588
Analyse Crystal structure of old yellow enzyme from candida macedoniensis AKU4588 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TMB
- Type
- protein
- Length
- 1,528 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Old yellow enzyme
- UniProt
- Q6I7B7
- Ligands
- FMN
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Old yellow enzyme | protein | 390 | 40% helix, 13% strand | Q6I7B7 |
| B | Old yellow enzyme | protein | 374 | 41% helix, 15% strand | Q6I7B7 |
| C | Old yellow enzyme | protein | 381 | 40% helix, 14% strand | Q6I7B7 |
| D | Old yellow enzyme | protein | 383 | 40% helix, 14% strand | Q6I7B7 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.74 | 0.79 | 77 | FMN |
| 2 | 731 | 0.74 | 0.79 | 76 | FMN |
| 3 | 827 | 0.74 | 0.78 | 79 | FMN |
| 4 | 427 | 0.67 | 0.79 | 50 | FMN |
| 5 | 262 | 0.63 | 0.81 | 42 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1080 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 953 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 859 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4TMB · CRYSTAL STRUCTURE of OLD YELLOW ENZYME from CANDIDA MACEDONIENSIS AKU4588 · 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 4TMB · PDBe 4TMB · UniProt Q6I7B7
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