Structure of PDB 2ybi Chain A

Receptor sequence

>2ybiA (length=129) Species: 9031 (Gallus gallus)

KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGS
TDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVS
DGNGMNAWVAWRNRCKGTDVQAWIRGCRL

3D structure

• PDB: 2ybi Effective Scavenging at Cryotemperatures: Further Increasing the Dose Tolerance of Protein Crystals.
• Chain: A
• Resolution: 2.0 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): E35 N46 D48 S50 D52 N59
• Catalytic site (residue number reindexed from 1): E35 N46 D48 S50 D52 N59
• Enzyme Commision number: 3.2.1.17: lysozyme.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	NO3	A	N65 D66 G67 R68 T69 S72	N65 D66 G67 R68 T69 S72
BS02	NO2	A	G4 R5 C6 E7	G4 R5 C6 E7
BS03	NO2	A	R14 D87 I88	R14 D87 I88
BS04	NO3	A	S24 L25 G26 Q121	S24 L25 G26 Q121

Gene Ontology

Molecular Function

• GO:0003796 lysozyme activity
• GO:0005515 protein binding
• GO:0016231 beta-N-acetylglucosaminidase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0042802 identical protein binding

Biological Process

• GO:0016998 cell wall macromolecule catabolic process
• GO:0031640 killing of cells of another organism
• GO:0042742 defense response to bacterium
• GO:0050829 defense response to Gram-negative bacterium
• GO:0050830 defense response to Gram-positive bacterium

Cellular Component

• GO:0005576 extracellular region
• GO:0005615 extracellular space
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum

External links

• PDB: RCSB:2ybi, PDBe:2ybi, PDBj:2ybi
• PDBsum: 2ybi
• PubMed: 21525642
• UniProt: P00698|LYSC_CHICK Lysozyme C (Gene Name=LYZ)