MolNFT v1 · #26775 · protein
Crystal structure of an artificial metalloprotein: FE(10-CH2CH2COOH- SALOPHEN)/WILD type heme oxygenase
1WZD: “Crystal structure of an artificial metalloprotein: FE(10-CH2CH2COOH- SALOPHEN)/WILD type heme oxygenase”. X-ray diffraction, 2 ligands (YOK, SO4), 3 pockets (best druggability 0.71). MolNFT v1 #26775 on GenesisL1: 3D structure…
- PDB
- 1WZD
- Type
- protein
- Length
- 416 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heme oxygenase
- EC
- 1.14.99.3
- UniProt
- P71119
- Ligands
- YOK, SO4
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heme oxygenase (EC 1.14.99.3) | protein | 209 | 77% helix, 0% strand | P71119 |
| B | Heme oxygenase (EC 1.14.99.3) | protein | 207 | 77% helix, 0% strand | P71119 |
Ligands and binding sites
- YOK · [[2,2'-[4-carboxyethyl-1,2-phenylenebis(nitrilomethylidyne)]bis[phenolato]](2-)-N,N',O,O']-iron · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.71 | 0.85 | 30 | YOK |
| 2 | 249 | 0.69 | 0.85 | 34 | YOK, GOL |
| 3 | 96 | 0.38 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 430 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1WZD · Crystal Structure Of An Artificial Metalloprotein: Fe(10-CH2CH2COOH-Salophen)/Wild Type… · 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 B against A, TM-score 0.99
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 1WZD · PDBe 1WZD · UniProt P71119
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