Research workbench
Crystal structure analysis of catalase from exiguobacterium oxidotolerans
Analyse Crystal structure analysis of catalase from exiguobacterium oxidotolerans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J2M
- 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
- Ligands
- HEM
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Catalase (EC 1.11.1.6) | protein | 480 | 32% helix, 19% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 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 | 399 | 0.88 | 0.97 | 50 | empty |
| 2 | 716 | 0.86 | 0.90 | 51 | empty |
| 3 | 240 | 0.85 | 0.97 | 43 | HEM |
| 4 | 208 | 0.83 | 0.96 | 26 | empty |
| 5 | 601 | 0.82 | 0.87 | 70 | HEM |
Interfaces
6 interfaces between chains.
- C–D · 4906 Ų buried · 91 hydrogen bonds · protein-protein
- A–B · 4856 Ų buried · 89 hydrogen bonds · protein-protein
- A–C · 4369 Ų buried · 54 hydrogen bonds · protein-protein
- B–D · 4357 Ų buried · 53 hydrogen bonds · protein-protein
- B–C · 2236 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 2J2M · Crystal Structure Analysis of Catalase from Exiguobacterium oxidotolerans · 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 2J2M · PDBe 2J2M
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