Research workbench
Crystal structure of heme oxygenase-1 from cyanobacterium synechocystis sp. PCC6803 in complex with heme
Analyse Crystal structure of heme oxygenase-1 from cyanobacterium synechocystis sp.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WE1
- Type
- protein
- Length
- 887 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heme oxygenase 1
- EC
- 1.14.99.3
- UniProt
- P72849
- Ligands
- HEM, CL, PO4
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Heme oxygenase 1 (EC 1.14.99.3) | protein | 222 | 76% helix, 0% strand | P72849 |
| D | Heme oxygenase 1 (EC 1.14.99.3) | protein | 221 | 74% helix, 0% strand | P72849 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.77 | 0.86 | 38 | CL, HEM, IPA |
| 2 | 414 | 0.77 | 0.86 | 40 | CL, HEM, IPA |
| 3 | 410 | 0.77 | 0.85 | 40 | CL, HEM, IPA |
| 4 | 367 | 0.76 | 0.86 | 38 | CL, HEM, IPA |
| 5 | 431 | 0.75 | 0.84 | 48 | CL, IPA |
Interfaces
4 interfaces between chains.
- A–C · 564 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 526 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 521 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 419 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1WE1 · Crystal structure of heme oxygenase-1 from cyanobacterium Synechocystis sp. PCC6803 in… · the same entry in another collection · chain A against A, TM-score 1.00
- P72849 · AlphaFold monomer V2.0 prediction for heme oxygenase 1 (P72849) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 P72849
- Elsewhere: RCSB PDB 1WE1 · PDBe 1WE1 · UniProt P72849
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