Research workbench
Crystal structure of KatE from atypical E. coli
Analyse Crystal structure of KatE from atypical E. coli in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LFK
- Type
- protein
- Length
- 2,883 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Escherichia coli
- Molecule
- eKatE catalase
- Ligands
- HEM
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · resolution 2.1 · 4 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | eKatE catalase | protein | 719 | 34% helix, 18% strand | — |
| B | eKatE catalase | protein | 721 | 34% helix, 18% strand | — |
| C | eKatE catalase | protein | 723 | 33% helix, 18% strand | — |
| D | eKatE catalase | protein | 720 | 33% helix, 18% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, C, B, 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 | 1196 | 0.87 | 0.88 | 127 | empty |
| 2 | 441 | 0.86 | 0.94 | 46 | empty |
| 3 | 287 | 0.86 | 0.97 | 50 | HEM |
| 4 | 288 | 0.86 | 0.96 | 50 | HEM |
| 5 | 287 | 0.86 | 0.96 | 48 | HEM |
Interfaces
6 interfaces between chains.
- A–C · 6658 Ų buried · 113 hydrogen bonds · protein-protein
- B–D · 6525 Ų buried · 113 hydrogen bonds · protein-protein
- C–D · 5929 Ų buried · 92 hydrogen bonds · protein-protein
- A–B · 5920 Ų buried · 86 hydrogen bonds · protein-protein
- A–D · 2161 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 6LFK · Crystal structure of kate from atypical E. 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
- Elsewhere: RCSB PDB 6LFK · PDBe 6LFK
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