7MK4: Soluble cytochrome b562

Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2. Determined by X-ray diffraction at 1.27 Å resolution. Released 27 Apr 2022.

Method: X-ray diffraction
Resolution: 1.27 Å
Organism: Escherichia coli
Chains: 2
Atoms: 2,123
Mol. weight: 25.19 kDa
Ligands: CO, HEC
Released: 27 Apr 2022

Explore 7MK4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7MK4 contains 13 α-helices and 0 β-strands across 2 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: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	3-19	17
α-helix	23-41	19
α-helix	44-45	2
α-helix	46-48	3
α-helix	56-80	25
α-helix	84-93	10
α-helix	95-105	11

Chain B: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	3-19	17
α-helix	24-40	17
α-helix	46-48	3
α-helix	56-80	25
α-helix	84-93	10
α-helix	95-105	11

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>7MK4_1 Soluble cytochrome b562 (chains A, B)
ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMWH
FRHGFDHLVGHIDDALKLANEGKVKEAQAAAEQLKCHCNHCHQHYR

Ligands and cofactors

ID	Name	Formula	Copies
CO	Cobalt (II) ion	Co	2
HEC	Heme C	C34 H36 Fe N4 O4	2

Primary citation

Overcoming universal restrictions on metal selectivity by protein design. Choi, T.S., Tezcan, F.A. Nature (2022) 603:522-527. DOI 10.1038/s41586-022-04469-8 · 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,…
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
6OT8 1.5 Å, Bimetallic hexameric cage design 4 (BMC4) from cytochrome cb562

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