Research workbench
Crystal structure of the dioxygen-bound heme oxygenase from corynebacterium diphtheriae
Analyse Crystal structure of the dioxygen-bound 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
- 1V8X
- Type
- protein
- Length
- 627 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heme oxygenase
- EC
- 1.14.99.3
- UniProt
- P71119
- Ligands
- HEM, GLC, FRU, SO4, OXY
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heme oxygenase (EC 1.14.99.3) | protein | 210 | 78% helix, 0% strand | P71119 |
| B | Heme oxygenase (EC 1.14.99.3) | protein | 209 | 77% helix, 0% strand | P71119 |
| C | Heme oxygenase (EC 1.14.99.3) | protein | 208 | 78% helix, 0% strand | P71119 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- GLC · alpha-D-glucopyranose · sugar
- FRU · beta-D-fructofuranose · sugar · chains A
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C
- OXY · Oxygen molecule · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.72 | 0.85 | 35 | HEM, OXY |
| 2 | 294 | 0.70 | 0.84 | 34 | HEM, OXY |
| 3 | 279 | 0.69 | 0.84 | 34 | HEM, OXY |
| 4 | 373 | 0.66 | 0.80 | 43 | SO4 |
| 5 | 306 | 0.57 | 0.77 | 36 | empty |
Interfaces
3 interfaces between chains.
- B–C · 750 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 555 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1V8X · Crystal Structure of the Dioxygen-bound Heme Oxygenase from Corynebacterium diphtheriae · the same entry in another collection · chain A against A, TM-score 1.00
- P71119 · AlphaFold monomer V2.0 prediction for heme oxygenase (P71119) · a predicted model of the same protein · 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 P71119
- Elsewhere: RCSB PDB 1V8X · PDBe 1V8X · UniProt P71119
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