7YRK: Lysozyme C

Crystal structure of the hen egg lysozyme-2-oxidobenzylidene-threoninato-copper (II) complex. Determined by X-ray diffraction at 0.92 Å resolution. Released 10 May 2023.

Method: X-ray diffraction
Resolution: 0.92 Å
Organism: Gallus gallus
Chains: 1
Atoms: 1,400
Mol. weight: 16.91 kDa
Ligands: JI6
Released: 10 May 2023

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

Secondary structure: helices and β-sheets

7YRK contains 7 α-helices and 9 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: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
α-helix	5-14	10
β-strand	20	1	2
β-strand	23	1	2
α-helix	25-36	12
β-strand	39	1	1
β-strand	43-45	3	3
β-strand	51-53	3	3
β-strand	58-59	2	3
β-strand	65	1	4
β-strand	79	1	4
α-helix	80-84	5
α-helix	89-99	11
α-helix	104-107	4
α-helix	109-114	6
α-helix	120-124	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysozyme C	A	protein	147	Gallus gallus	P00698 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7YRK_1 Lysozyme C (chains A)
MRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQA
TNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDG
NGMNAWVAWRNRCKGTDVQAWIRGCRL

Ligands and cofactors

ID	Name	Formula	Copies
JI6	(6~{S})-3-$l^{3}-oxidanyl-6-[(1~{R})-1-oxidanylethyl]-2,4-dioxa-7$l^{4}-aza-3$l…	C11 H13 Cu N O5	1

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

Primary citation

A novel hybrid protein composed of superoxide-dismutase-active Cu(II) complex and lysozyme. Furuya, T., Nakane, D., Kitanishi, K. et al. Sci Rep (2023) 13:6892-6892. DOI 10.1038/s41598-023-33926-1 · PubMed

Other PDB entries of the same protein (UniProt P00698 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2VB1 0.65 Å, HEWL at 0.65 angstrom resolution
8ZST 0.8 Å, Lysozyme Crystallized with Bioassembler on Earth
9QUM 0.83 Å, Structure of lysozyme by continuous serial electron diffraction (SerialED)
7SKW 0.87 Å, Ab initio structure of triclinic lysozyme from electron-counted MicroED data
7ULY 0.87 Å, MicroED structure of triclinic lysozyme
7P6M 0.89 Å, Hydrogenated refolded hen egg-white lysozyme
9RZL 0.9 Å, Hen egg-white lysozyme (HEWL)
8RLI 0.91 Å, Neutron structure of perdeuterated hen egg-white lysozyme at room temperature
3LZT 0.93 Å, Refinement of triclinic lysozyme at atomic resolution
1IEE 0.94 Å, Structure of tetragonal hen egg white lysozyme at 0.94 a from crystals grown by the…
7OL5 0.94 Å, Crystal structure of Lysozyme in complex with Hepes
4LZT 0.95 Å, Atomic resolution refinement of triclinic hew lysozyme at 295K

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