Research workbench
Structural and kinetic analysis of the beef liver catalase with the ammonia as a ligand
Analyse Structural and kinetic analysis of the beef liver catalase with the ammonia as… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RGS
- Type
- protein
- Length
- 1,996 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase
- EC
- 1.11.1.6
- UniProt
- P00432
- Ligands
- HEM, NH3
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Catalase (EC 1.11.1.6) | protein | 499 | 34% helix, 19% strand | P00432 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, D, B, C
- NH3 · Ammonia · ion · 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 | 671 | 0.88 | 0.92 | 53 | empty |
| 2 | 387 | 0.87 | 0.96 | 52 | empty |
| 3 | 387 | 0.87 | 0.95 | 48 | empty |
| 4 | 251 | 0.85 | 0.96 | 40 | HEM, NH3 |
| 5 | 261 | 0.85 | 0.96 | 45 | HEM, NH3 |
Interfaces
6 interfaces between chains.
- A–D · 4961 Ų buried · 77 hydrogen bonds · protein-protein
- B–C · 4913 Ų buried · 81 hydrogen bonds · protein-protein
- A–C · 4783 Ų buried · 56 hydrogen bonds · protein-protein
- B–D · 4773 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 2171 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 3RGS · Structural and kinetic analysis of the beef liver catalase with the ammonia as a ligand · the same entry in another collection · chain D against D, TM-score 1.00
- P00432 · AlphaFold monomer V2.0 prediction for catalase (P00432) · a predicted model of the same protein · chain C against A, 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 P00432
- Elsewhere: RCSB PDB 3RGS · PDBe 3RGS · UniProt P00432
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