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Crystal structure of Cytochrome c Peroxidase with a Proposed Electron Transfer Pathway Excised to Form a Ligand Binding Channel.

Analyse Crystal structure of Cytochrome c Peroxidase with a Proposed Electron Transfer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KXM
Type: protein
Length: 290 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.74
Source: Saccharomyces cerevisiae
Molecule: Cytochrome c Peroxidase
EC: 1.11.1.5
UniProt: P00431
Ligands: HEM, BZI
Pockets: 2 · best druggability 0.81

Structure

x-ray diffraction · resolution 1.74 · 1 distinct chain · 51% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytochrome c Peroxidase (EC 1.11.1.5)	protein	290	51% helix, 6% strand	P00431

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · chains A
BZI · Benzimidazole · ligand · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	464	0.81	0.88	58	HEM, BZI
2	95	0.41	0.77	18	empty

Compared structures

1KXM · Crystal structure of cytochrome C peroxidase with a proposed electron transfer pathway… · 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 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 1KXM · PDBe 1KXM · UniProt P00431

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