Research workbench
Crystal structure of cytochrome C peroxidase with a proposed electron pathway excised in a complex with a peptide wire
Analyse Crystal structure of cytochrome C peroxidase with a proposed electron pathway… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EXB
- Type
- protein
- Length
- 292 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C peroxidase; N-[3-(1H-benzimidazol-1-YL)PROPANOYL]GLYCYL-L-alanyl-L…
- EC
- 1.11.1.5
- UniProt
- P00431
- Ligands
- EXB, HEM, NH2
- Pockets
- 2 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C peroxidase (EC 1.11.1.5) | protein | 289 | 51% helix, 7% strand | P00431 |
| B | N-[3-(1H-benzimidazol-1-YL)PROPANOYL]GLYCYL-L-alanyl-L- alaninamide | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- EXB · 3-(1H-benzimidazol-1-yl)propanoic acid · ligand · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- NH2 · Amino group · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.82 | 0.89 | 61 | EXB, HEM |
| 2 | 98 | 0.42 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 210 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3EXB · Crystal structure of Cytochrome C Peroxidase with a Proposed Electron Pathway Excised in… · the same entry in another collection · chain B against B, 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 0.99
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 3EXB · PDBe 3EXB · UniProt P00431
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