Research workbench
The 2.6 ångströms refined structure of the escherichia COLI recombinant saccharomyces cerevisiae flavocytochrome B2-sulphite complex
Analyse The 2.6 ångströms refined structure of the escherichia COLI recombinant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LTD
- Type
- protein
- Length
- 867 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavocytochrome B2
- EC
- 1.1.2.3
- UniProt
- P00175
- Ligands
- FMN, HEM, SO3
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Flavocytochrome B2 (EC 1.1.2.3) | protein | 481 | 43% helix, 13% strand | P00175 |
| B | Flavocytochrome B2 (EC 1.1.2.3) | protein | 386 | 44% 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
- SO3 · Sulfite ion · ion · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.86 | 0.88 | 96 | SO3, FMN, HEM |
| 2 | 194 | 0.74 | 0.90 | 34 | SO3, FMN |
| 3 | 223 | 0.53 | 0.77 | 29 | empty |
| 4 | 82 | 0.49 | 0.82 | 16 | empty |
| 5 | 135 | 0.48 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2587 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 1LTD · The 2.6 ångströms refined structure of the escherichia COLI recombinant saccharomyces… · 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 0.99
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 1LTD · PDBe 1LTD · UniProt P00175
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