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Structure of the biliverdin-hmuo, heme oxygenase from corynebacterium diphtheriae
Analyse Structure of the biliverdin-hmuo, heme oxygenase from corynebacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GPC
- Type
- protein
- Length
- 631 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, 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 | 212 | 77% helix, 0% strand | Q54AI1 |
| B | Heme oxygenase (EC 1.14.99.3) | protein | 211 | 77% helix, 0% strand | Q54AI1 |
| C | Heme oxygenase (EC 1.14.99.3) | protein | 208 | 77% 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
- SO4 · Sulfate ion · ion · 6 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 | 286 | 0.69 | 0.83 | 34 | BLA |
| 2 | 292 | 0.68 | 0.83 | 30 | BLA |
| 3 | 298 | 0.67 | 0.82 | 30 | BLA, ASC |
| 4 | 271 | 0.59 | 0.79 | 34 | SO4 |
| 5 | 307 | 0.59 | 0.78 | 42 | empty |
Interfaces
2 interfaces between chains.
- B–C · 730 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 600 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4GPC · Structure of the biliverdin-HmuO, heme oxygenase from Corynebacterium diphtheriae · 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 4GPC · PDBe 4GPC · UniProt Q54AI1
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