Research workbench
Old yellow enzyme from thermus scotoductus sa-01 complexed with P- hydroxy-benzaldehyde
Analyse Old yellow enzyme from thermus scotoductus sa-01 complexed with P… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HGJ
- Type
- protein
- Length
- 1,392 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chromate reductase
- EC
- 1.6.99.1
- UniProt
- B0JDW3
- Ligands
- FMN, HBA
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Chromate reductase (EC 1.6.99.1) | protein | 348 | 39% helix, 16% strand | B0JDW3 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, D, B, C
- HBA · P-hydroxybenzaldehyde · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.77 | 0.80 | 67 | empty |
| 2 | 1107 | 0.74 | 0.77 | 69 | empty |
| 3 | 587 | 0.74 | 0.81 | 50 | FMN, HBA |
| 4 | 599 | 0.73 | 0.80 | 55 | FMN, HBA |
| 5 | 477 | 0.65 | 0.77 | 52 | FMN, HBA |
Interfaces
3 interfaces between chains.
- A–D · 1257 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 394 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 393 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3HGJ · Old Yellow Enzyme from Thermus scotoductus SA-01 complexed with p-hydroxy-benzaldehyde · 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 B0JDW3
- Elsewhere: RCSB PDB 3HGJ · PDBe 3HGJ · UniProt B0JDW3
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