Research workbench
Crystal structure of catalase hpii from E. COLI in space group P1
Analyse Crystal structure of catalase hpii from E. COLI in space group P1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BY0
- Type
- protein
- Length
- 2,895 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase hpii
- EC
- 1.11.1.6
- UniProt
- P21179
- Ligands
- HEM
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Catalase hpii (EC 1.11.1.6) | protein | 726 | 32% helix, 18% strand | P21179 |
| B | Catalase hpii (EC 1.11.1.6) | protein | 721 | 33% helix, 18% strand | P21179 |
| C | Catalase hpii (EC 1.11.1.6) | protein | 722 | 33% helix, 18% strand | P21179 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.89 | 0.96 | 60 | empty |
| 2 | 507 | 0.89 | 0.96 | 60 | empty |
| 3 | 421 | 0.87 | 0.94 | 44 | empty |
| 4 | 302 | 0.86 | 0.96 | 58 | HEM |
| 5 | 285 | 0.86 | 0.96 | 50 | HEM |
Interfaces
6 interfaces between chains.
- C–D · 6258 Ų buried · 128 hydrogen bonds · protein-protein
- A–B · 6252 Ų buried · 130 hydrogen bonds · protein-protein
- A–C · 5954 Ų buried · 85 hydrogen bonds · protein-protein
- B–D · 5901 Ų buried · 81 hydrogen bonds · protein-protein
- B–C · 2269 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
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 P21179
- Elsewhere: RCSB PDB 6BY0 · PDBe 6BY0 · UniProt P21179
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