1RE2 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   HUMAN LYSOZYME LABELLED WITH TWO 2',3'-EPOXYPROPYL BETA-GLYCOSIDE OF N-ACETYLLACTOSAMINE

Authors :   M. Muraki, K. Harata, N. Sugita, K. Sato

Date :   05 Nov 98 (Deposition) - 05 May 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A

Keywords :   Lysozyme, Muramidase, Ec 3. 2. 1. 17, Hydrolase(O-Glycosyl), N- Acetyllactosamine, Affinity Labeling (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Muraki, K. Harata, N. Sugita, K. Sato
Dual Affinity Labeling Of The Active Site Of Human Lysozyme With An N-Acetyllactosamine Derivative: First Ligand Assisted Recognition Of The Second Ligand.
Biochemistry V. 38 540 1999
PubMed-ID: 9888793 | Reference-DOI: 10.1021/BI981779G

Molecule 1 - PROTEIN (LYSOZYME)
	Chains	:	A
	EC Number	:	3.2.1.17
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
2	GOL	2	Ligand/Ion	GLYCEROL
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:64 , ASP A:102 , GLN A:104 , NAG A:132 , GAL A:133 , HOH A:219	BINDING SITE FOR RESIDUE GAL A 131
2	AC2	SOFTWARE	GLN A:58 , ILE A:59 , ASN A:60 , TYR A:63 , TRP A:64 , GLN A:104 , ALA A:108 , TRP A:109 , GAL A:131 , GAL A:133 , NAG A:134 , GOL A:135 , HOH A:174 , HOH A:219	BINDING SITE FOR RESIDUE NAG A 132
3	AC3	SOFTWARE	GLN A:104 , GAL A:131 , NAG A:132 , NAG A:134 , HOH A:167 , HOH A:168 , HOH A:220	BINDING SITE FOR RESIDUE GAL A 133
4	AC4	SOFTWARE	ARG A:107 , ALA A:108 , TRP A:109 , VAL A:110 , NAG A:132 , GAL A:133 , GOL A:135 , GOL A:136 , HOH A:191	BINDING SITE FOR RESIDUE NAG A 134
5	AC5	SOFTWARE	ASP A:53 , GLN A:58 , NAG A:132 , NAG A:134 , GOL A:136	BINDING SITE FOR RESIDUE GOL A 135
6	AC6	SOFTWARE	GLU A:35 , GLN A:58 , TRP A:109 , VAL A:110 , NAG A:134 , GOL A:135	BINDING SITE FOR RESIDUE GOL A 136

Asymmetric/Biological Unit

No.	Residues
1	A:6	-	A:128
2	A:30	-	A:116
3	A:65	-	A:81
4	A:77	-	A:95

(no "Cis Peptide Bond" information available for 1RE2)

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_004280	I	74	T	LYSC_HUMAN	Disease (AMYL8)	121913547	A	I	56	T
2	UniProt	VAR_004281	D	85	H	LYSC_HUMAN	Disease (AMYL8)	121913548	A	D	67	H
3	UniProt	VAR_012050	T	88	N	LYSC_HUMAN	Polymorphism	1800973	A	T	70	N

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (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_PANPA	19-148	1	A:1-130
				LYSC_PANTR	19-148	1	A:1-130
				LYSC_HUMAN	19-148	1	A:1-130
2	LACTALBUMIN_LYSOZYME_1	PS00128	Alpha-lactalbumin / lysozyme C signature.	LYSC_PANPA	95-113	1	A:77-95
				LYSC_PANTR	95-113	1	A:77-95
				LYSC_HUMAN	95-113	1	A:77-95

(no "Exon" information available for 1RE2)

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:130
 aligned with LYSC_HUMAN | P61626 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:130
                                    28        38        48        58        68        78        88        98       108       118       128       138       148
           LYSC_HUMAN    19 KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV 148
               SCOP domains d1re2a_ A: Lysozyme                                                                                                                SCOP domains
               CATH domains 1re2A00 A:1-130  [code=1.10.530.10, no name defined]                                                                               CATH domains
               Pfam domains Lys-1re2A01 A:1-128                                                                                                             -- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.....hhh..hhhhhhhhhhhh......eeee....eeee..........................hhhh.....hhhhhhhhhhhh...hhhh.hhhhhh.....hhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------T----------H--N------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) LACTALBUMIN_LYSOZYME_2  PDB: A:1-130 UniProt: 19-148                                                                               PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ---------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ----------------------------------------------------------------------------LACTALBUMIN_LYSOZYM----------------------------------- PROSITE (5)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1re2 A   1 KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain A from PDB  Type:PROTEIN  Length:130
 aligned with LYSC_PANPA | P61627 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:130
                                    28        38        48        58        68        78        88        98       108       118       128       138       148
           LYSC_PANPA    19 KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV 148
               SCOP domains d1re2a_ A: Lysozyme                                                                                                                SCOP domains
               CATH domains 1re2A00 A:1-130  [code=1.10.530.10, no name defined]                                                                               CATH domains
               Pfam domains Lys-1re2A01 A:1-128                                                                                                             -- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.....hhh..hhhhhhhhhhhh......eeee....eeee..........................hhhh.....hhhhhhhhhhhh...hhhh.hhhhhh.....hhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------T----------H--N------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) LACTALBUMIN_LYSOZYME_2  PDB: A:1-130 UniProt: 19-148                                                                               PROSITE (3)
                PROSITE (4) ----------------------------------------------------------------------------LACTALBUMIN_LYSOZYM----------------------------------- PROSITE (4)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1re2 A   1 KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain A from PDB  Type:PROTEIN  Length:130
 aligned with LYSC_PANTR | P61628 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:130
                                    28        38        48        58        68        78        88        98       108       118       128       138       148
           LYSC_PANTR    19 KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV 148
               SCOP domains d1re2a_ A: Lysozyme                                                                                                                SCOP domains
               CATH domains 1re2A00 A:1-130  [code=1.10.530.10, no name defined]                                                                               CATH domains
               Pfam domains Lys-1re2A01 A:1-128                                                                                                             -- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.....hhh..hhhhhhhhhhhh......eeee....eeee..........................hhhh.....hhhhhhhhhhhh...hhhh.hhhhhh.....hhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------T----------H--N------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) LACTALBUMIN_LYSOZYME_2  PDB: A:1-130 UniProt: 19-148                                                                               PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ---------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ---------------------------------------------------------------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) ----------------------------------------------------------------------------LACTALBUMIN_LYSOZYM----------------------------------- PROSITE (6)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1re2 A   1 KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Lysozyme-like (1361)

Superfamily: Lysozyme-like (1361)

Family: C-type lysozyme (738)

Protein domain: Lysozyme (696)

Human (Homo sapiens) [TaxId: 9606] (200)

d1re2a_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Lysozyme (1131)

Homologous Superfamily: [code=1.10.530.10, no name defined] (605)

Human (Homo sapiens) (206)

1re2A00

A:1-130

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Lysozyme (266)

Family: Lys (245)

Homo sapiens (Human) (62)

Lys-1re2A01

A:1-128

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (LYSC_PANPA | P61627)

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.

Chain A (LYSC_PANTR | P61628)

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.

Chain A (LYSC_HUMAN | P61626)

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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0044267	cellular protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
	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:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	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.
	GO:0001895	retina homeostasis	A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1re2)

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	1re2
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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (4, 4)

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