Research workbench
The cryo-EM structure of the catalase-peroxidase from escherichia COLI
Analyse The cryo-EM structure of the catalase-peroxidase from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JZ6
- Type
- protein
- Length
- 2,646 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase-peroxidase
- EC
- 1.11.1.21
- UniProt
- A0A037YMJ1
- Ligands
- HEM
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 45% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catalase-peroxidase (EC 1.11.1.21) | protein | 660 | 45% helix, 8% strand | A0A037YMJ1 |
| B, C, D | Catalase-peroxidase (EC 1.11.1.21) | protein | 662 | 45% helix, 8% strand | A0A037YMJ1 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · 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 | 583 | 0.83 | 0.88 | 62 | HEM |
| 2 | 560 | 0.83 | 0.88 | 60 | HEM |
| 3 | 561 | 0.83 | 0.88 | 61 | HEM |
| 4 | 558 | 0.83 | 0.88 | 64 | HEM |
| 5 | 114 | 0.78 | 0.97 | 22 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2837 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2801 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 785 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 784 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7JZ6 · The Cryo-EM structure of the Catalase-peroxidase from Escherichia coli · the same entry in another collection · 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 A0A037YMJ1
- Elsewhere: RCSB PDB 7JZ6 · PDBe 7JZ6 · UniProt A0A037YMJ1
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