MolNFT v1 · #12262 · protein
Crystallographic study of the recombinant flavin-binding domain of BAKER'S yeast flavocytochrome B2: comparison with the intact wild- type enzyme
1KBI: “Crystallographic study of the recombinant flavin-binding domain of BAKER'S yeast flavocytochrome B2…”. X-ray diffraction, 4 ligands (FMN, HEM, PYR), 14 pockets (best druggability 0.86). MolNFT v1 #12262 on GenesisL1: 3D structure…
- PDB
- 1KBI
- Type
- protein
- Length
- 909 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, HEM, PYR, PO4
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome B2 (EC 1.1.2.3) | protein | 504 | 40% helix, 14% strand | P00175 |
| B | Cytochrome B2 (EC 1.1.2.3) | protein | 405 | 45% helix, 12% strand | P00175 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- PYR · Pyruvic acid · ligand · chains B
- PO4 · Phosphate ion · ion · chains B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.86 | 0.87 | 102 | HEM, FMN |
| 2 | 402 | 0.71 | 0.83 | 57 | FMN, PYR |
| 3 | 85 | 0.50 | 0.83 | 13 | MPD |
| 4 | 68 | 0.46 | 0.83 | 14 | MPD |
| 5 | 132 | 0.46 | 0.77 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2852 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1KBI · 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 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 P00175
- Elsewhere: RCSB PDB 1KBI · PDBe 1KBI · UniProt P00175
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