MolNFT v1 · #64686 · protein
Crystal structure of helicobacter pylori heme oxygenase hugz in complex with heme
3GAS: “Crystal structure of helicobacter pylori heme oxygenase hugz in complex with heme”. X-ray diffraction, 2 ligands (HEM, AZI), 20 pockets (best druggability 0.81). MolNFT v1 #64686 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3GAS
- Type
- protein
- Length
- 1,484 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heme oxygenase
- EC
- 1.14.99.3
- UniProt
- C0LU01
- Ligands
- HEM, AZI
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | Heme oxygenase (EC 1.14.99.3) | protein | 248 | 33% helix, 35% strand | C0LU01 |
| B | Heme oxygenase (EC 1.14.99.3) | protein | 247 | 32% helix, 36% strand | C0LU01 |
| D | Heme oxygenase (EC 1.14.99.3) | protein | 247 | 32% helix, 36% strand | C0LU01 |
| E | Heme oxygenase (EC 1.14.99.3) | protein | 246 | 32% helix, 36% strand | C0LU01 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
- AZI · Azide ion · ion · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.81 | 0.87 | 62 | HEM, AZI, EDO |
| 2 | 606 | 0.81 | 0.86 | 64 | HEM, AZI, EDO |
| 3 | 647 | 0.81 | 0.86 | 66 | HEM, AZI, EDO |
| 4 | 635 | 0.80 | 0.85 | 66 | HEM, AZI, EDO |
| 5 | 604 | 0.80 | 0.85 | 64 | HEM, AZI, EDO |
Interfaces
9 interfaces between chains.
- C–D · 2796 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 2764 Ų buried · 53 hydrogen bonds · protein-protein
- E–F · 2724 Ų buried · 51 hydrogen bonds · protein-protein
- A–F · 413 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 322 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 3GAS · Crystal Structure of Helicobacter pylori Heme Oxygenase Hugz in Complex with Heme · the same entry in another collection · chain B against B, 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 C0LU01
- Elsewhere: RCSB PDB 3GAS · PDBe 3GAS · UniProt C0LU01
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