Research workbench
Structure of a bacterial catalase
Analyse Structure of a bacterial catalase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B7G
- Type
- protein
- Length
- 2,054 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase
- EC
- 1.11.1.6
- UniProt
- Q6M8A6
- Ligands
- NDP, HEM, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Catalase (EC 1.11.1.6) | protein | 513 | 30% helix, 18% strand | Q6M8A6 |
| B, D | Catalase (EC 1.11.1.6) | protein | 514 | 30% helix, 18% strand | Q6M8A6 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, C, B, D
- CL · Chloride ion · ion · 2 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 | 551 | 0.87 | 0.92 | 47 | CL |
| 2 | 242 | 0.84 | 0.96 | 39 | HEM |
| 3 | 238 | 0.84 | 0.96 | 37 | HEM |
| 4 | 236 | 0.84 | 0.96 | 36 | HEM |
| 5 | 242 | 0.84 | 0.96 | 38 | HEM |
Interfaces
6 interfaces between chains.
- C–D · 5402 Ų buried · 77 hydrogen bonds · protein-protein
- A–B · 5356 Ų buried · 82 hydrogen bonds · protein-protein
- B–D · 4270 Ų buried · 69 hydrogen bonds · protein-protein
- A–C · 4190 Ų buried · 67 hydrogen bonds · protein-protein
- B–C · 3205 Ų buried · 64 hydrogen bonds · protein-protein
Compared structures
- 4B7G · Structure of a bacterial 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 Q6M8A6
- Elsewhere: RCSB PDB 4B7G · PDBe 4B7G · UniProt Q6M8A6
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