Research workbench
Expression, purification, characterization, and solution NMR study of highly deuterated yeast cytochrome C peroxidase with enhanced solubility
Analyse Expression, purification, characterization, and solution NMR study of highly… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JB4
- Type
- protein
- Length
- 582 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C peroxidase, mitochondrial
- EC
- 1.11.1.5
- UniProt
- P00431
- Ligands
- HEM, F
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cytochrome C peroxidase, mitochondrial (EC 1.11.1.5) | protein | 291 | 49% helix, 8% strand | P00431 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, C
- F · Fluoride ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.80 | 0.89 | 44 | HEM, F |
| 2 | 560 | 0.78 | 0.84 | 65 | HEM, F |
| 3 | 137 | 0.45 | 0.77 | 20 | empty |
| 4 | 126 | 0.40 | 0.75 | 22 | empty |
| 5 | 88 | 0.39 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–C · 451 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4JB4 · Expression, Purification, Characterization, and Solution NMR Study of Highly Deuterated… · the same entry in another collection · chain A against A, TM-score 1.00
- P00431 · AlphaFold monomer V2.0 prediction for cytochrome C peroxidase, mitochondrial (P00431) · 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 P00431
- Elsewhere: RCSB PDB 4JB4 · PDBe 4JB4 · UniProt P00431
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