Research workbench
Structure of bacillus pumilus catalase with guaiacol bound
Analyse Structure of bacillus pumilus catalase with guaiacol bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QOQ
- Type
- protein
- Length
- 1,924 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase
- EC
- 1.11.1.6
- UniProt
- W8QL66
- Ligands
- HEM, JZ3, NA, CL
- Pockets
- 20 · best druggability 0.87
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 | 481 | 33% helix, 19% strand | W8QL66 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, D, B, C
- JZ3 · Guaiacol · ligand · 6 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 6 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 | 324 | 0.87 | 0.97 | 57 | empty |
| 2 | 476 | 0.86 | 0.92 | 37 | CL |
| 3 | 317 | 0.85 | 0.96 | 53 | empty |
| 4 | 611 | 0.83 | 0.87 | 68 | HEM, JZ3 |
| 5 | 624 | 0.83 | 0.87 | 69 | HEM, JZ3 |
Interfaces
6 interfaces between chains.
- B–D · 4673 Ų buried · 49 hydrogen bonds · protein-protein
- A–D · 4666 Ų buried · 76 hydrogen bonds · protein-protein
- A–C · 4663 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 4641 Ų buried · 83 hydrogen bonds · protein-protein
- C–D · 2488 Ų buried · 55 hydrogen bonds · protein-protein
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 W8QL66
- Elsewhere: RCSB PDB 4QOQ · PDBe 4QOQ · UniProt W8QL66
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