Research workbench
Probing the active center of catalase-phenol oxidase from scytalidium thermophilum
Analyse Probing the active center of catalase-phenol oxidase from scytalidium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZZ1
- Type
- protein
- Length
- 2,711 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase
- EC
- 1.11.1.6
- UniProt
- M4GGR7
- Ligands
- 3TR, HDD, CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catalase (EC 1.11.1.6) | protein | 677 | 34% helix, 19% strand | M4GGR7 |
| B, C, D | Catalase (EC 1.11.1.6) | protein | 678 | 33% helix, 19% strand | M4GGR7 |
Ligands and binding sites
- 3TR · 3-amino-1,2,4-triazole · ligand · 8 copies · chains A, C, B, D
- HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · 4 copies · chains A, C, B, D
- CA · Calcium ion · metal · 5 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 | 488 | 0.87 | 0.94 | 93 | 3TR |
| 2 | 379 | 0.86 | 0.94 | 51 | CA |
| 3 | 356 | 0.85 | 0.95 | 57 | 3TR |
| 4 | 1064 | 0.85 | 0.86 | 113 | CA |
| 5 | 274 | 0.85 | 0.96 | 47 | HDD |
Interfaces
6 interfaces between chains.
- B–D · 5811 Ų buried · 84 hydrogen bonds · protein-protein
- A–C · 5791 Ų buried · 81 hydrogen bonds · protein-protein
- B–C · 5066 Ų buried · 68 hydrogen bonds · protein-protein
- A–D · 5065 Ų buried · 69 hydrogen bonds · protein-protein
- C–D · 2046 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5ZZ1 · Probing the active center of catalase-phenol oxidase from Scytalidium thermophilum · 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 M4GGR7
- Elsewhere: RCSB PDB 5ZZ1 · PDBe 5ZZ1 · UniProt M4GGR7
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