Research workbench
Crystal structure of IsdG from Bacillus cereus in complex with heme
Analyse Crystal structure of IsdG from Bacillus cereus in complex with heme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8AVI
- Type
- protein
- Length
- 212 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Bacillus cereus ATCC 14579
- Molecule
- Heme-degrading monooxygenase
- EC
- 1.14.99.48
- UniProt
- Q812Q3
- Ligands
- HEM
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · resolution 2 · 1 distinct chain · 24% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Heme-degrading monooxygenase (EC 1.14.99.48) | protein | 106 | 24% helix, 42% strand | Q812Q3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- PGO · S-1,2-propanediol · additive · chains A
- BU1 · 1,4-butanediol · additive · chains A, B
- PDO · 1,3-propandiol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.66 | 0.80 | 37 | HEM |
| 2 | 267 | 0.64 | 0.81 | 37 | empty |
| 3 | 379 | 0.64 | 0.78 | 35 | HEM |
| 4 | 121 | 0.47 | 0.79 | 24 | BU1, PDO |
Interfaces
1 interface between chains.
- A–B · 1704 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- Q812Q3 · AlphaFold monomer V2.0 prediction for heme-degrading monooxygenase (Q812Q3) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q812Q3
- Elsewhere: RCSB PDB 8AVI · PDBe 8AVI · UniProt Q812Q3
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