5V94: Lysozyme isoform III

Pekin duck egg lysozyme isoform III (DEL-III), cubic form. Determined by X-ray diffraction at 1.65 Å resolution. Released 15 Nov 2017.

Method: X-ray diffraction
Resolution: 1.65 Å
Organism: Anas platyrhynchos
Chains: 2
Atoms: 2,182
Mol. weight: 30.16 kDa
Ligands: PO4, MRD
Released: 15 Nov 2017

Explore 5V94 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V94 contains 14 α-helices and 18 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, 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	80-83	4
α-helix	89-100	12
α-helix	104-107	4
α-helix	109-114	6
α-helix	120-124	5

Chain B: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	5
α-helix	5-14	10
β-strand	20	1	6
β-strand	23	1	6
α-helix	25-36	12
β-strand	39	1	5
β-strand	43-45	3	7
β-strand	51-53	3	7
β-strand	58-59	2	7
β-strand	65	1	8
β-strand	79	1	8
α-helix	80-84	5
α-helix	89-100	12
α-helix	105-107	3
α-helix	109-114	6
α-helix	120-124	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
lysozyme isoform III	A, B	protein	129	Anas platyrhynchos	P00705 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5V94_1 lysozyme isoform III (chains A, B)
KVYSRCELAAAMKRLGLDNYRGYSLGNWVCAANYESGFNTQATNRNTDGSTDYGILQINS
RWWCDDGKTPRSKNACGIRCSVLLRSDITEAVRCAKRIVRDGNGMNAWVAWRNRCRGTDV
SKWIRGCRL

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	7
MRD	(4R)-2-methylpentane-2,4-diol	C6 H14 O2	1

Water and common crystallization additives (TRS) are not listed.

Primary citation

Structural basis of antigen recognition: crystal structure of duck egg lysozyme. Langley, D.B., Crossett, B., Schofield, P. et al. Acta Crystallogr D Struct Biol (2017) 73:910-920. DOI 10.1107/S2059798317013730 · PubMed

Other PDB entries of the same protein (UniProt P00705 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5V92 1.11 Å, Pekin duck egg lysozyme isoform III (DEL-III), orthorhombic form
6D9I 1.15 Å, Pekin duck egg lysozyme isoform II (DEL-II)
5V8G 1.2 Å, Pekin duck lysozyme isoform I (DEL-I)
5VAS 1.4 Å, Pekin duck egg lysozyme isoform III (DEL-III), orthorhombic form
5VJQ 1.9 Å, Complex between HyHEL10 Fab fragment heavy chain mutant (I29F, S52T, Y53F) and Pekin…
5VJO 2.43 Å, Complex between HyHEL10 Fab fragment heavy chain mutant I29F and Pekin duck egg lysozyme…

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