MolNFT v1 · #104899 · protein
Structure of bacillus pumilus catalase
4QOL: “Structure of bacillus pumilus catalase”. X-ray diffraction, 3 ligands (HEM, NA, CL), 20 pockets (best druggability 0.87). MolNFT v1 #104899 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4QOL
- Type
- protein
- Length
- 1,920 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, NA, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Catalase (EC 1.11.1.6) | protein | 480 | 32% helix, 18% strand | W8QL66 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, D, B, C
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 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 | 317 | 0.87 | 0.97 | 49 | empty |
| 2 | 479 | 0.86 | 0.93 | 42 | CL |
| 3 | 331 | 0.86 | 0.96 | 55 | empty |
| 4 | 240 | 0.85 | 0.96 | 41 | HEM |
| 5 | 627 | 0.82 | 0.87 | 73 | HEM, ACT |
Interfaces
6 interfaces between chains.
- A–D · 4673 Ų buried · 77 hydrogen bonds · protein-protein
- B–D · 4666 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 4662 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 4642 Ų buried · 75 hydrogen bonds · protein-protein
- C–D · 2492 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 4QOL · Structure of Bacillus pumilus catalase · 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 W8QL66
- Elsewhere: RCSB PDB 4QOL · PDBe 4QOL · UniProt W8QL66
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