9PPR: Soluble cytochrome b562

Zn- and Bi-bound structure of the H77C variant of TriCyt2. Determined by X-ray diffraction at 1.57 Å resolution. Released 22 Oct 2025.

Method: X-ray diffraction
Resolution: 1.57 Å
Organism: Escherichia coli BL21(DE3)
Chains: 3
Atoms: 2,949
Mol. weight: 36.18 kDa
Ligands: ZN, BS3
Released: 22 Oct 2025

Explore 9PPR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PPR contains 15 α-helices and 0 β-strands across 3 chains. 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: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	3-18	16
α-helix	23-40	18
α-helix	46-48	3
α-helix	56-80	25
α-helix	84-105	22

Chain B: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	3-19	17
α-helix	23-41	19
α-helix	46-48	3
α-helix	56-80	25
α-helix	84-105	22

Chain C: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	3-18	16
α-helix	23-41	19
α-helix	46-48	3
α-helix	56-80	25
α-helix	84-105	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562	A, B, C	protein	106	Escherichia coli BL21(DE3)	P0ABE7 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>9PPR_1 Soluble cytochrome b562 (chains A, B, C)
ADWEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAKKATPPKLEDKSPASPEMID
FRVGFDILLWQIHDALCLANEGKVKEAQAAAEQLKTTVNAHWQKYR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
BS3	Bismuth(III) ION	Bi	1

Water and common crystallization additives (CL, NA) are not listed.

Primary citation

Design of a protein scaffold with a selective, Bi-containing heterodinuclear metal coordination motif. Eng, V.H., Gascon, M., Kakkis, A. et al. J Inorg Biochem (2025) 274:113104-113104. DOI 10.1016/j.jinorgbio.2025.113104 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

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