1ZBY: Native (Resting) Cytochrome c Peroxidase

High-Resolution Crystal Structure of Native (Resting) Cytochrome c Peroxidase (CcP). Determined by X-ray diffraction at 1.2 Å resolution. Released 3 May 2005.

Method: X-ray diffraction
Resolution: 1.2 Å
Organism: Saccharomyces cerevisiae
Chains: 1
Atoms: 3,289
Mol. weight: 34.19 kDa
Ligands: HEM
Released: 3 May 2005

Explore 1ZBY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1ZBY contains 24 α-helices and 11 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 24 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	1
α-helix	10-11	2
α-helix	16-32	17
α-helix	36-39	4
α-helix	43-54	12
β-strand	58	1	2
β-strand	63	1	2
α-helix	70-72	3
α-helix	74-77	4
α-helix	80-82	3
α-helix	86-98	13
α-helix	104-118	15
β-strand	126	1	3
α-helix	135-137	3
α-helix	138-140	3
α-helix	145-146	2
α-helix	151-159	9
α-helix	165-172	8
α-helix	173-176	4
β-strand	179-180	2	4
α-helix	182-185	4
β-strand	189-190	2	4
α-helix	201-208	8
β-strand	211-215	5	5
β-strand	221-225	5	5
β-strand	230-231	2	5
α-helix	233-240	8
α-helix	242-252	11
α-helix	255-271	17
β-strand	274-275	2	1
α-helix	276-277	2
α-helix	281-283	3
β-strand	284	1	3
α-helix	286-288	3
α-helix	289-292	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytochrome c peroxidase	A	protein	294	Saccharomyces cerevisiae	P00431 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1ZBY_1 Cytochrome c peroxidase (chains A)
TTPLVHVASVEKGRSYEDFQKVYNAIALKLREDDEYDNYIGYGPVLVRLAWHTSGTWDKH
DNTGGSYGGTYRFKKEFNDPSNAGLQNGFKFLEPIHKEFPWISSGDLFSLGGVTAVQEMQ
GPKIPWRCGRVDTPEDTTPDNGRLPDADKDADYVRTFFQRLNMNDREVVALMGAHALGKT
HLKNSGYEGPWGAANNVFTNEFYLNLLNEDWKLEKNDANNEQWDSKSGYMMLPTDYSLIQ
DPKYLSIVKEYANDQDKFFKDFSKAFEKLLENGITFPKDAPSPFIFKTLEEQGL

Ligands and cofactors

ID	Name	Formula	Copies
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	1

Primary citation

High-resolution crystal structures and spectroscopy of native and compound I cytochrome c peroxidase. Bonagura, C.A., Bhaskar, B., Shimizu, H. et al. Biochemistry (2003) 42:5600-5608. DOI 10.1021/bi034058c · PubMed

Other PDB entries of the same protein (UniProt P00431 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3E2O 1.06 Å, Crystal structure of cytochrome c peroxidase, N184R mutant
7BIU 1.06 Å, XFEL crystal structure of cytochrome c peroxidase compound II
2EUT 1.12 Å, Cytochrome c peroxidase (CCP) in complex with 2-amino-4-picoline
1Z53 1.13 Å, The 1.13 Angstrom Structure of Iron-free Cytochrome c Peroxidase
2RBT 1.24 Å, n-methylbenzylamine in complex with Cytochrome C Peroxidase W191G
2Y5A 1.25 Å, Cytochrome c peroxidase (CCP) W191G bound to 3-aminopyridine
1ZBZ 1.29 Å, High-Resolution Crystal Structure of Compound I intermediate of Cytochrome c Peroxidase…
2AS4 1.3 Å, cytochrome c peroxidase in complex with 3-fluorocatechol
2EUQ 1.3 Å, Cytochrome c peroxydase (CCP) in complex with 3-thienylmethylamine
3E2N 1.3 Å, Engineering ascorbate peroxidase activity into cytochrome c peroxidase
2AQD 1.35 Å, cytochrome c peroxidase (CCP) in complex with 2,5-diaminopyridine
2EUR 1.39 Å, Cytochrome c peroxidase (CCP) in complex with 4-pyridylcarbinol

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