Research workbench
Crystallographic study of the recombinant flavin-binding domain of BAKER'S yeast flavocytochrome B2: comparison with the intact wild- type enzyme
Analyse Crystallographic study of the recombinant flavin-binding domain of BAKER'S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KBJ
- Type
- protein
- Length
- 785 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome B2
- EC
- 1.1.2.3
- UniProt
- P00175
- Ligands
- FMN
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome B2 (EC 1.1.2.3) | protein | 393 | 44% helix, 13% strand | P00175 |
| B | Cytochrome B2 (EC 1.1.2.3) | protein | 392 | 44% helix, 13% strand | P00175 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.75 | 0.89 | 37 | FMN, EDO |
| 2 | 271 | 0.72 | 0.86 | 45 | FMN, EDO |
| 3 | 145 | 0.46 | 0.77 | 24 | empty |
| 4 | 132 | 0.44 | 0.76 | 21 | empty |
| 5 | 93 | 0.43 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2773 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 1KBJ · Crystallographic Study of the Recombinant Flavin-binding Domain of Baker's Yeast… · the same entry in another collection · chain A against A, TM-score 1.00
- P00175 · AlphaFold monomer V2.0 prediction for cytochrome B2, mitochondrial (P00175) · a predicted model of the same protein · chain B 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 P00175
- Elsewhere: RCSB PDB 1KBJ · PDBe 1KBJ · UniProt P00175
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