Research workbench
Crystal structure of P. aeruginosa catalase, kata tetramer
Analyse Crystal structure of P. aeruginosa catalase, kata tetramer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E37
- Type
- protein
- Length
- 1,918 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase
- EC
- 1.11.1.6
- UniProt
- O52762
- Ligands
- HEM, NDP
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catalase (EC 1.11.1.6) | protein | 479 | 33% helix, 19% strand | O52762 |
| B, D | Catalase (EC 1.11.1.6) | protein | 480 | 33% helix, 19% strand | O52762 |
| C | Catalase (EC 1.11.1.6) | protein | 479 | 32% helix, 19% strand | O52762 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 884 | 0.87 | 0.89 | 56 | empty |
| 2 | 294 | 0.85 | 0.96 | 43 | HEM |
| 3 | 283 | 0.85 | 0.96 | 43 | HEM |
| 4 | 289 | 0.84 | 0.95 | 41 | HEM |
| 5 | 831 | 0.84 | 0.87 | 91 | HEM |
Interfaces
6 interfaces between chains.
- A–B · 4578 Ų buried · 75 hydrogen bonds · protein-protein
- C–D · 4563 Ų buried · 68 hydrogen bonds · protein-protein
- A–D · 4270 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 4254 Ų buried · 54 hydrogen bonds · protein-protein
- B–D · 2201 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
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 O52762
- Elsewhere: RCSB PDB 4E37 · PDBe 4E37 · UniProt O52762
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