8DRM: Soluble cytochrome b562

Zn(II)-bound B2 dimer (H60/H100/H104) formed in Zn(II)//Cu(II) (M1 // M2) condition. Determined by X-ray diffraction at 1.55 Å resolution. Released 12 Oct 2022.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Escherichia coli
Chains: 1
Atoms: 999
Mol. weight: 12.66 kDa
Ligands: ZN, HEC
Released: 12 Oct 2022

Explore 8DRM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DRM contains 5 α-helices and 0 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: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	3-18	16
α-helix	23-40	18
α-helix	56-80	25
α-helix	84-92	9
α-helix	95-105	11

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>8DRM_1 Soluble cytochrome b562 (chains A)
ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMWH
FRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKCTCNHCHQHYR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
HEC	Heme C	C34 H36 Fe N4 O4	1

Primary citation

Design of a Flexible, Zn-Selective Protein Scaffold that Displays Anti-Irving-Williams Behavior. Choi, T.S., Tezcan, F.A. J Am Chem Soc (2022) 144:18090-18100. DOI 10.1021/jacs.2c08050 · 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

Browse structure collections

About this viewer

MolViewer shows 8DRM directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.