Research workbench
Electron crystallographic structure of catalase using a direct electron detector at 300 kv
Analyse Electron crystallographic structure of catalase using a direct electron… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DI8
- Type
- protein
- Length
- 1,996 residues
- Chains
- 4
- Method
- electron crystallography
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase
- EC
- 1.11.1.6
- UniProt
- P00432
- Ligands
- HEM, NDP
- Pockets
- 20 · best druggability 0.88
Structure
electron crystallography · 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
- 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 | 419 | 0.88 | 0.96 | 50 | empty |
| 2 | 436 | 0.88 | 0.95 | 55 | empty |
| 3 | 767 | 0.87 | 0.91 | 53 | empty |
| 4 | 326 | 0.86 | 0.95 | 50 | HEM |
| 5 | 555 | 0.85 | 0.90 | 106 | empty |
Interfaces
6 interfaces between chains.
- B–C · 4891 Ų buried · 65 hydrogen bonds · protein-protein
- A–D · 4873 Ų buried · 63 hydrogen bonds · protein-protein
- A–C · 4593 Ų buried · 48 hydrogen bonds · protein-protein
- B–D · 4563 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 2019 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7DI8 · Electron crystallographic structure of Catalase using a direct electron detector at 300 kV · 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 A 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 7DI8 · PDBe 7DI8 · UniProt P00432
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