1DKK - JenaLib

Title :   BOBWHITE QUAIL LYSOZYME WITH NITRATE

Authors :   P. D. Jeffrey, S. Sheriff

Date :   10 Jan 96 (Deposition) - 11 Jul 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Hydrolase, Glycosidase, Bacteriolytic Enzyme, Hydrolase (O- Glycosyl) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Chacko, E. W. Silverton, S. J. Smith-Gill, D. R. Davies, K. A. Shick, K. A. Xavier, R. C. Willson, P. D. Jeffrey, C. Y. Chang, L. C. Sieker, S. Sheriff
Refined Structures Of Bobwhite Quail Lysozyme Uncomplexed And Complexed With The Hyhel-5 Fab Fragment.
Proteins V. 26 55 1996
PubMed-ID: 8880929 | Reference-DOI: 10.1002/(SICI)1097-0134(199609)26:1<55::AID-PROT5>3 .0.CO;2-F
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (8, 8)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LACTALBUMIN_LYSOZYME_2	PS51348	Alpha-lactalbumin / lysozyme C family profile.	LYSC_COLVI	1-129	2	A:1-129 B:1-129
2	LACTALBUMIN_LYSOZYME_1	PS00128	Alpha-lactalbumin / lysozyme C signature.	LYSC_COLVI	76-94	2	A:76-94 B:76-94

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LACTALBUMIN_LYSOZYME_2	PS51348	Alpha-lactalbumin / lysozyme C family profile.	LYSC_COLVI	1-129	1	A:1-129 -
2	LACTALBUMIN_LYSOZYME_1	PS00128	Alpha-lactalbumin / lysozyme C signature.	LYSC_COLVI	76-94	1	A:76-94 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LACTALBUMIN_LYSOZYME_2	PS51348	Alpha-lactalbumin / lysozyme C family profile.	LYSC_COLVI	1-129	1	- B:1-129
2	LACTALBUMIN_LYSOZYME_1	PS00128	Alpha-lactalbumin / lysozyme C signature.	LYSC_COLVI	76-94	1	- B:76-94

Exons (0, 0)

Sequences/Alignments

Asymmetric 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:129
 aligned with LYSC_COLVI | P00700 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
           LYSC_COLVI     1 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNSQATNRNTDGSTDYGVLQINSRWWCNDGKTPGSRNLCNIPCSALLSSDITATVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL 129
               SCOP domains d1dkka_ A: Lysozyme                                                                                                               SCOP domains
               CATH domains 1dkkA00 A:1-129  [code=1.10.530.10, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.....hhh..hhhhhhhhhhhh......eee.....eee..........................hhhhh....hhhhhhhhhhh....hhhh.hhhhhh.....hhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LACTALBUMIN_LYSOZYME_2  PDB: A:1-129 UniProt: 1-129                                                                               PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------LACTALBUMIN_LYSOZYM----------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dkk A   1 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNSQATNRNTDGSTDYGVLQINSRWWCNDGKTPGSRNLCNIPCSALLSSDITATVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:129
 aligned with LYSC_COLVI | P00700 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
           LYSC_COLVI     1 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNSQATNRNTDGSTDYGVLQINSRWWCNDGKTPGSRNLCNIPCSALLSSDITATVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL 129
               SCOP domains d1dkkb_ B: Lysozyme                                                                                                               SCOP domains
               CATH domains 1dkkB00 B:1-129  [code=1.10.530.10, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.....hhh..hhhhhhhhhhhh......eee.....eee..........................hhhh.....hhhhhhhhhhhhh..hhhh.hhhhhh.....hhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LACTALBUMIN_LYSOZYME_2  PDB: B:1-129 UniProt: 1-129                                                                               PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------LACTALBUMIN_LYSOZYM----------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dkk B   1 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNSQATNRNTDGSTDYGVLQINSRWWCNDGKTPGSRNLCNIPCSALLSSDITATVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL 129
                                    10        20        30        40        50        60        70        80        90       100       110       120

Legend:		→ Mismatch	(orange background)
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	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 (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LYSC_COLVI | P00700)

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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