MolNFT v1 · #10588 · protein
Crystal structure of a heme oxygenase (hmuo) from corynebacterium diphtheriae complexed with heme in the ferrous state
1IW1: “Crystal structure of a heme oxygenase (hmuo) from corynebacterium diphtheriae complexed with heme in the…”. X-ray diffraction, 4 ligands (HEM, GLC, FRU), 5 pockets (best druggability 0.72). MolNFT v1 #10588 on GenesisL1: 3D…
- PDB
- 1IW1
- Type
- protein
- Length
- 629 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
- Pockets
- 5 · best druggability 0.72
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 | 76% 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 | 77% 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 · 10 copies · chains A, B
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 | 320 | 0.72 | 0.84 | 32 | HEM |
| 2 | 267 | 0.71 | 0.85 | 34 | HEM |
| 3 | 292 | 0.70 | 0.84 | 35 | HEM |
| 4 | 395 | 0.69 | 0.81 | 47 | empty |
| 5 | 312 | 0.58 | 0.77 | 37 | empty |
Interfaces
2 interfaces between chains.
- B–C · 754 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 583 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1IW1 · Crystal structure of a heme oxygenase (HmuO) from Corynebacterium diphtheriae complexed… · 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 1IW1 · PDBe 1IW1 · UniProt P71119
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