Research workbench
Crystal structure of the D181E variant of catalase hpii from E. COLI
Analyse Crystal structure of the D181E variant of catalase hpii from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P81
- Type
- protein
- Length
- 2,908 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
- HDD
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Catalase hpii (EC 1.11.1.6) | protein | 727 | 32% helix, 18% strand | P21179 |
Ligands and binding sites
- HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.89 | 0.96 | 55 | empty |
| 2 | 499 | 0.88 | 0.95 | 58 | empty |
| 3 | 393 | 0.86 | 0.95 | 50 | empty |
| 4 | 289 | 0.85 | 0.95 | 48 | HDD |
| 5 | 257 | 0.84 | 0.96 | 34 | HDD |
Interfaces
6 interfaces between chains.
- A–D · 6219 Ų buried · 118 hydrogen bonds · protein-protein
- B–C · 6181 Ų buried · 115 hydrogen bonds · protein-protein
- B–D · 5993 Ų buried · 82 hydrogen bonds · protein-protein
- A–C · 5944 Ų buried · 87 hydrogen bonds · protein-protein
- A–B · 2274 Ų buried · 42 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 1P81 · PDBe 1P81 · UniProt P21179
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