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
- 4B7A
- Type
- protein
- Length
- 2,688 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase-phenol oxidase
- EC
- 1.11.1.6
- Ligands
- 3TR, HDD, CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catalase-phenol oxidase (EC 1.11.1.6) | protein | 673 | 32% helix, 20% strand | — |
| B | Catalase-phenol oxidase (EC 1.11.1.6) | protein | 674 | 34% helix, 18% strand | — |
| C | Catalase-phenol oxidase (EC 1.11.1.6) | protein | 671 | 34% helix, 20% strand | — |
| D | Catalase-phenol oxidase (EC 1.11.1.6) | protein | 670 | 34% helix, 19% strand | — |
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 | 496 | 0.87 | 0.94 | 93 | 3TR |
| 2 | 613 | 0.87 | 0.92 | 119 | 3TR |
| 3 | 1132 | 0.86 | 0.87 | 115 | CA |
| 4 | 280 | 0.86 | 0.97 | 51 | HDD |
| 5 | 283 | 0.86 | 0.96 | 54 | HDD |
Interfaces
6 interfaces between chains.
- A–C · 5744 Ų buried · 78 hydrogen bonds · protein-protein
- B–D · 5743 Ų buried · 88 hydrogen bonds · protein-protein
- A–D · 5101 Ų buried · 68 hydrogen bonds · protein-protein
- B–C · 5067 Ų buried · 66 hydrogen bonds · protein-protein
- C–D · 2074 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4B7A · 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
- Elsewhere: RCSB PDB 4B7A · PDBe 4B7A
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