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
- 4B2Y
- Type
- protein
- Length
- 2,693 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
- HEM, CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catalase-phenol oxidase (EC 1.11.1.6) | protein | 675 | 33% helix, 20% strand | — |
| B | Catalase-phenol oxidase (EC 1.11.1.6) | protein | 674 | 34% helix, 19% strand | — |
| C, D | Catalase-phenol oxidase (EC 1.11.1.6) | protein | 672 | 33% helix, 19% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, C, B, D
- CA · Calcium ion · metal · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 295 | 0.86 | 0.97 | 45 | HEM |
| 2 | 290 | 0.86 | 0.96 | 46 | HEM |
| 3 | 298 | 0.86 | 0.96 | 52 | HEM |
| 4 | 1122 | 0.86 | 0.87 | 114 | CA |
| 5 | 1121 | 0.85 | 0.86 | 112 | CA |
Interfaces
6 interfaces between chains.
- B–D · 5733 Ų buried · 86 hydrogen bonds · protein-protein
- A–C · 5700 Ų buried · 85 hydrogen bonds · protein-protein
- B–C · 5087 Ų buried · 66 hydrogen bonds · protein-protein
- A–D · 5076 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 2074 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4B2Y · 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 4B2Y · PDBe 4B2Y
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