3AB6 - JenaLib

Title :   CRYSTAL STRUCTURE OF NAG3 BOUND LYSOZYME FROM MERETRIX LUSORIA

Authors :   K. Yoneda, Y. Kuwano, T. Araki

Date :   01 Dec 09 (Deposition) - 01 Dec 10 (Release) - 20 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.78

Chains :   Asym./Biol. Unit : A

Keywords :   Lysozyme, Meretrix Lusoria, Antibiotic, Antimicrobial, Bacteriolytic Enzyme, Glycosidase, Hydrolase, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kuwano, K. Yoneda, Y. Kawaguchi, T. Araki
The Tertiary Structure Of An I-Type Lysozyme Isolated From The Common Orient Clam (Meretrix Lusoria)
Acta Crystallogr. , Sect. F V. 69 1202 2013
PubMed-ID: 24192349 | Reference-DOI: 10.1107/S1744309113028170

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:39 , ILE A:40 , LYS A:41 , TYR A:44 , HIS A:93 , ASN A:94 , GLY A:96 , NAG A:124 , HOH A:154 , HOH A:192 , HOH A:250 , HOH A:258 , HOH A:267	BINDING SITE FOR RESIDUE NAG A 123
2	AC2	SOFTWARE	ASP A:47 , TYR A:72 , GLY A:95 , PRO A:97 , LYS A:102 , NAG A:123 , NAG A:125 , HOH A:154 , HOH A:157 , HOH A:179 , HOH A:292	BINDING SITE FOR RESIDUE NAG A 124
3	AC3	SOFTWARE	ALA A:43 , ASP A:47 , LYS A:56 , NAG A:124 , HOH A:151 , HOH A:159 , HOH A:160 , HOH A:236 , HOH A:291	BINDING SITE FOR RESIDUE NAG A 125

SS Bonds (7, 7)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:122
 aligned with LYS_MERLU | P86383 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:122
                                    10        20        30        40        50        60        70        80        90       100       110       120  
            LYS_MERLU     1 FAGGIVSQRCLSCICKMESGCRNVGCKMDMGSLSCGYFQIKEAYWIDCGRPGSSWKSCAASSYCASLCVQNYMKRYAKWAGCPLRCEGFAREHNGGPRGCKKGSTIGYWNRLQKISGCHGVQ 122
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh.....eeee..eeee....eehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.hhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----T--------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ab6 A   1 FAGGTVSQRCLSCICKMESGCRNVGCKMDMGSLSCGYFQIKEAYWIDCGRPGSSWKSCAASSYCASLCVQNYMKRYAKWAGCPLRCEGFAREHNGGPRGCKKGSTIGYWNRLQKISGCHGVQ 122
                                    10        20        30        40        50        60        70        80        90       100       110       120

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (LYS_MERLU | P86383)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0003796	lysozyme activity	Catalysis of the hydrolysis of the beta-(1->4) linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan.
biological process
	GO:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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