MolNFT v1 · #104902 · protein
Structure of bacillus pumilus catalase with resorcinol bound.
4QOO: “Structure of bacillus pumilus catalase with resorcinol bound.”. X-ray diffraction, 4 ligands (HEM, RCO, NA), 20 pockets (best druggability 0.87). MolNFT v1 #104902 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4QOO
- 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, RCO, 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
- RCO · Resorcinol · ligand · 4 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.87 | 0.97 | 57 | empty |
| 2 | 472 | 0.86 | 0.93 | 41 | CL |
| 3 | 306 | 0.86 | 0.96 | 47 | empty |
| 4 | 658 | 0.83 | 0.87 | 75 | HEM, RCO |
| 5 | 609 | 0.83 | 0.87 | 69 | HEM, RCO |
Interfaces
6 interfaces between chains.
- B–D · 4705 Ų buried · 48 hydrogen bonds · protein-protein
- A–C · 4695 Ų buried · 50 hydrogen bonds · protein-protein
- A–D · 4659 Ų buried · 75 hydrogen bonds · protein-protein
- B–C · 4627 Ų buried · 81 hydrogen bonds · protein-protein
- C–D · 2499 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- 4QOO · Structure of Bacillus pumilus catalase with resorcinol bound. · 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 4QOO · PDBe 4QOO · UniProt W8QL66
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