Research workbench
Heme ligand mutant of recombinant horseradish peroxidase in complex with benzhydroxamic acid
Analyse Heme ligand mutant of recombinant horseradish peroxidase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ATJ
- Type
- protein
- Length
- 614 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (horseradish peroxidase C1A)
- EC
- 1.11.1.7
- UniProt
- P00433
- Ligands
- HEM, BHO, CA
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (horseradish peroxidase C1A) (EC 1.11.1.7) | protein | 307 | 49% helix, 5% strand | P00433 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- BHO · Benzhydroxamic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.82 | 0.83 | 85 | HEM, BHO |
| 2 | 384 | 0.82 | 0.91 | 49 | HEM, BHO |
| 3 | 372 | 0.58 | 0.75 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 466 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3ATJ · Heme ligand mutant of recombinant horseradish peroxidase in complex with benzhydroxamic… · the same entry in another collection · chain A against A, TM-score 1.00
- P00433 · AlphaFold monomer V2.0 prediction for peroxidase C1A (P00433) · a predicted model of the same protein · 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 P00433
- Elsewhere: RCSB PDB 3ATJ · PDBe 3ATJ · UniProt P00433
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