Research workbench
Structure of hmuo, heme oxygenase from corynebacterium diphtheriae, in complex with the putative reaction intermediates between FE3+- biliverdin and biliverdin (data set IV)
Analyse Structure of hmuo, heme oxygenase from corynebacterium diphtheriae, in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GPH
- Type
- protein
- Length
- 630 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heme oxygenase
- EC
- 1.14.99.3
- UniProt
- Q54AI1
- Ligands
- BLA, ASC, FE, SO4
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heme oxygenase (EC 1.14.99.3) | protein | 209 | 78% helix, 0% strand | Q54AI1 |
| B | Heme oxygenase (EC 1.14.99.3) | protein | 209 | 78% helix, 0% strand | Q54AI1 |
| C | Heme oxygenase (EC 1.14.99.3) | protein | 212 | 75% helix, 0% strand | Q54AI1 |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · 3 copies · chains A, B, C
- ASC · Ascorbic acid · ligand · chains C
- FE · Fe (III) ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 8 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 | 304 | 0.69 | 0.83 | 34 | FE, BLA |
| 2 | 285 | 0.69 | 0.83 | 32 | BLA |
| 3 | 305 | 0.66 | 0.81 | 30 | FE, BLA, ASC |
| 4 | 300 | 0.61 | 0.79 | 35 | SO4 |
| 5 | 282 | 0.56 | 0.77 | 35 | empty |
Interfaces
2 interfaces between chains.
- B–C · 714 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 595 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4GPH · Structure of HmuO, heme oxygenase from Corynebacterium diphtheriae, in complex with the… · 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 4GPH · PDBe 4GPH · UniProt Q54AI1
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