1AM7 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   LYSOZYME FROM BACTERIOPHAGE LAMBDA

Authors :   C. Evrard, J. Fastrez, J. P. Declercq

Date :   24 Jun 97 (Deposition) - 24 Dec 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)
Biol. Unit 4: C  (1x)

Keywords :   Glycosidase, Transglycosylase, Evolution, Lysozyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Evrard, J. Fastrez, J. P. Declercq
Crystal Structure Of The Lysozyme From Bacteriophage Lambda And Its Relationship With V And C-Type Lysozymes.
J. Mol. Biol. V. 276 151 1998
PubMed-ID: 9514719 | Reference-DOI: 10.1006/JMBI.1997.1499
(for further references see the PDB file header)

Molecule 1 - LYSOZYME
	Cellular Location	:	CYTOPLASM
	Chains	:	A, B, C
	EC Number	:	3.2.1.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Plasmid	:	PLJ05
	Expression System Strain	:	M5219
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID, PL CONTROL
	Gene	:	R
	Organism Scientific	:	ENTEROBACTERIA PHAGE LAMBDA
	Organism Taxid	:	10710

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B
Biological Unit 4 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 15)

No.	Name	Count	Type	Full Name
1	IPA	3	Ligand/Ion	ISOPROPYL ALCOHOL
2	TRN	12	Mod. Amino Acid	NZ2-TRYPTOPHAN

Biological Unit 1 (2, 15)

No.	Name	Count	Type	Full Name
1	IPA	3	Ligand/Ion	ISOPROPYL ALCOHOL
2	TRN	12	Mod. Amino Acid	NZ2-TRYPTOPHAN

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
2	TRN	4	Mod. Amino Acid	NZ2-TRYPTOPHAN

Biological Unit 3 (2, 5)

No.	Name	Count	Type	Full Name
1	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
2	TRN	4	Mod. Amino Acid	NZ2-TRYPTOPHAN

Biological Unit 4 (2, 5)

No.	Name	Count	Type	Full Name
1	IPA	1	Ligand/Ion	ISOPROPYL ALCOHOL
2	TRN	4	Mod. Amino Acid	NZ2-TRYPTOPHAN

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:19 , VAL A:35 , GLY A:38 , GLN A:68	BINDING SITE FOR RESIDUE IPA A 350
2	AC2	SOFTWARE	GLN B:26 , GLY B:38 , GLN B:68	BINDING SITE FOR RESIDUE IPA B 350
3	AC3	SOFTWARE	GLU C:19 , VAL C:35 , GLY C:38 , GLN C:68	BINDING SITE FOR RESIDUE IPA C 350
4	CAA	UNKNOWN	GLU A:19	CATALYTIC SITE.
5	CAB	UNKNOWN	GLU B:19	CATALYTIC SITE.
6	CAC	UNKNOWN	GLU C:19	CATALYTIC SITE.

(no "SS Bond" information available for 1AM7)

(no "Cis Peptide Bond" information available for 1AM7)

(no "SAP(SNP)/Variant" information available for 1AM7)

(no "PROSITE Motif" information available for 1AM7)

(no "Exon" information available for 1AM7)

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
	(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:154
 aligned with ENLYS_LAMBD | P03706 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
          ENLYS_LAMBD     1 MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRWWDAYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAGGTVR 154
               SCOP domains d1am7a_ A: Lambda lysozyme                                                                                                                                 SCOP domains
               CATH domains 1am7A00 A:1-154  [code=1.10.530.10, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh..............eeee..eee.........eeee...eee.eee..eeehhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhh.............hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1am7 A   1 MVEINNQRKAFLDMLAwSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRwwDAYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIwASLPGAGYGQFEHKADSLIAKFKEAGGTVR 154
                                    10      | 20        30        40        50        60        70  ||    80        90       100       110       120   |   130       140       150    
                                           17-TRN                                                  73-TRN                                            124-TRN                          
                                                                                                    74-TRN

Chain B from PDB  Type:PROTEIN  Length:154
 aligned with ENLYS_LAMBD | P03706 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
          ENLYS_LAMBD     1 MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRWWDAYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAGGTVR 154
               SCOP domains d1am7b_ B: Lambda lysozyme                                                                                                                                 SCOP domains
               CATH domains 1am7B00 B:1-154  [code=1.10.530.10, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh..............eeee..eee....................eee..eeehhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhh.................hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1am7 B   1 MVEINNQRKAFLDMLAwSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRwwDAYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIwASLPGAGYGQFEHKADSLIAKFKEAGGTVR 154
                                    10      | 20        30        40        50        60        70  ||    80        90       100       110       120   |   130       140       150    
                                           17-TRN                                                  73-TRN                                            124-TRN                          
                                                                                                    74-TRN

Chain C from PDB  Type:PROTEIN  Length:154
 aligned with ENLYS_LAMBD | P03706 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
          ENLYS_LAMBD     1 MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRWWDAYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAGGTVR 154
               SCOP domains d1am7c_ C: Lambda lysozyme                                                                                                                                 SCOP domains
               CATH domains 1am7C00 C:1-154  [code=1.10.530.10, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh..............eeee..eee.........eeee...eee.eee..eeehhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhh.............hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1am7 C   1 MVEINNQRKAFLDMLAwSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRwwDAYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIwASLPGAGYGQFEHKADSLIAKFKEAGGTVR 154
                                    10      | 20        30        40        50        60        70  ||    80        90       100       110       120   |   130       140       150    
                                           17-TRN                                                  73-TRN                                            124-TRN                          
                                                                                                    74-TRN

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 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: Lambda lysozyme (3)

Protein domain: Lambda lysozyme (3)

Bacteriophage lambda [TaxId: 10710] (3)

1a	d1am7a_	A:
1b	d1am7b_	B:
1c	d1am7c_	C:

Asymmetric 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)

Enterobacteria phage lambda. Organism_taxid: 10710. (1)

1a	1am7A00	A:1-154
1b	1am7B00	B:1-154
1c	1am7C00	C:1-154

(no "Pfam Domain" information available for 1AM7)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (ENLYS_LAMBD | P03706)

molecular function
	GO:0016837	carbon-oxygen lyase activity, acting on polysaccharides	Catalysis of the cleavage of a carbon-oxygen bond by the elimination of an alcohol from a polysaccharide.
	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:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	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:0016998	cell wall macromolecule catabolic process	The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
	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.
	GO:0009253	peptidoglycan catabolic process	The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
	GO:0019076	viral release from host cell	The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
	GO:0030430	host cell cytoplasm	The cytoplasm of a host cell.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		IPA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TRN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		CAA	[ RasMol ]	+environment [ RasMol ]
		CAB	[ RasMol ]	+environment [ RasMol ]
		CAC	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1am7)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1am7
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	ENLYS_LAMBD \| P03706
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.2.1.17
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	ENLYS_LAMBD \| P03706
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ENLYS_LAMBD \| P03706	:	1d9u 3d3d

(no "Related Entries Specified in the PDB File" available for 1AM7)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 15)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File