Research workbench
Crystal structure of helicobacter pylori heme oxygenase hugz in complex with heme
Analyse Crystal structure of helicobacter pylori heme oxygenase hugz in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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