Research workbench
Crystal structure of the heme oxygenase from corynebacterium diphtheriae (hmuo) in complex with heme binding ditiothreitol (dtt)
Analyse Crystal structure of the heme oxygenase from corynebacterium diphtheriae (hmuo)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I8R
- Type
- protein
- Length
- 623 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heme oxygenase
- UniProt
- Q54AI1
- Ligands
- HEM, DTV, SO4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Heme oxygenase | protein | 207 | 79% helix, 0% strand | Q54AI1 |
| B | Heme oxygenase | protein | 209 | 76% helix, 0% strand | Q54AI1 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- DTV · (2S,3S)-1,4-dimercaptobutane-2,3-diol · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.74 | 0.85 | 37 | HEM, DTV |
| 2 | 346 | 0.72 | 0.84 | 35 | HEM, DTV |
| 3 | 329 | 0.71 | 0.84 | 36 | HEM, DTV |
| 4 | 357 | 0.66 | 0.80 | 42 | SO4 |
| 5 | 274 | 0.56 | 0.77 | 33 | empty |
Interfaces
3 interfaces between chains.
- B–C · 742 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 552 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3I8R · Crystal structure of the heme oxygenase from Corynebacterium diphtheriae (HmuO) in… · 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 Q54AI1
- Elsewhere: RCSB PDB 3I8R · PDBe 3I8R · UniProt Q54AI1
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