Research workbench
Structural and kinetic analysis of the beef liver catalase complexed with nitric oxide
Analyse Structural and kinetic analysis of the beef liver catalase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RGP
- 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, NO
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Catalase (EC 1.11.1.6) | protein | 499 | 33% helix, 19% strand | P00432 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, D, B, C
- NO · Nitric oxide · 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.88 | 0.92 | 51 | empty |
| 2 | 383 | 0.87 | 0.96 | 46 | empty |
| 3 | 399 | 0.87 | 0.96 | 50 | empty |
| 4 | 272 | 0.85 | 0.96 | 48 | HEM, NO |
| 5 | 260 | 0.85 | 0.96 | 44 | HEM, NO |
Interfaces
6 interfaces between chains.
- A–D · 4947 Ų buried · 77 hydrogen bonds · protein-protein
- B–C · 4941 Ų buried · 70 hydrogen bonds · protein-protein
- A–C · 4790 Ų buried · 57 hydrogen bonds · protein-protein
- B–D · 4736 Ų buried · 59 hydrogen bonds · protein-protein
- C–D · 2159 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3RGP · Structural and Kinetic Analysis of the Beef liver Catalase complexed with Nitric Oxide · 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 3RGP · PDBe 3RGP · UniProt P00432
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