1D9U - JenaLib

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU B:19 , VAL B:37 , GLY B:38 , GLN B:68 , SER B:126 , GLN B:134 , PHE B:135 , HOH B:301 , NAG B:1402	BINDING SITE FOR RESIDUE NAG B 1401
02	AC2	SOFTWARE	GLU A:101 , PHE B:135 , HOH B:321 , NAG B:1401 , NAG B:1403	BINDING SITE FOR RESIDUE NAG B 1402
03	AC3	SOFTWARE	GLU A:101 , ARG B:25 , NAG B:1402 , NDG B:1404	BINDING SITE FOR RESIDUE NAG B 1403
04	AC4	SOFTWARE	TRP A:73 , TYR A:77 , ASN A:122 , ILE A:123 , NAG B:1403 , NAG B:1405	BINDING SITE FOR RESIDUE NDG B 1404
05	AC5	SOFTWARE	GLN A:68 , LEU A:70 , TRP A:73 , GLN A:98 , ILE A:123 , TYR A:132 , NDG B:1404 , NAG B:1406	BINDING SITE FOR RESIDUE NAG B 1405
06	AC6	SOFTWARE	LEU A:70 , ILE A:123 , TRP A:124 , ALA A:125 , NAG B:1405	BINDING SITE FOR RESIDUE NAG B 1406
07	AC7	SOFTWARE	NDG B:2402	BINDING SITE FOR RESIDUE NAG B 2401
08	AC8	SOFTWARE	GLU B:101 , HOH B:308 , HOH B:322 , NAG B:2401 , NDG B:2403	BINDING SITE FOR RESIDUE NDG B 2402
09	AC9	SOFTWARE	TRP B:73 , HOH B:319 , NDG B:2402 , NAG B:2404	BINDING SITE FOR RESIDUE NDG B 2403
10	BC1	SOFTWARE	TRP B:73 , TYR B:77 , GLN B:98 , GLU B:101 , ASN B:122 , NDG B:2403 , NAG B:2405	BINDING SITE FOR RESIDUE NAG B 2404
11	BC2	SOFTWARE	GLN B:68 , LEU B:70 , TRP B:73 , GLN B:98 , ASN B:122 , ILE B:123 , TYR B:132 , NAG B:2404 , NAG B:2406	BINDING SITE FOR RESIDUE NAG B 2405
12	BC3	SOFTWARE	LEU B:70 , TRP B:124 , ALA B:125 , TYR B:132 , HOH B:307 , NAG B:2405	BINDING SITE FOR RESIDUE NAG B 2406
13	BC4	SOFTWARE	GLU A:3 , ARG A:8 , LEU A:105 , LYS B:138	BINDING SITE FOR RESIDUE SO4 A 200
14	BC5	SOFTWARE	TRP A:17 , HIS A:137 , LYS A:138 , SER A:141	BINDING SITE FOR RESIDUE SO4 A 201
15	BC6	SOFTWARE	GLN A:97 , LYS A:100 , HIS B:137 , LYS B:138 , SER B:141 , HOH B:305	BINDING SITE FOR RESIDUE SO4 B 202
16	BC7	SOFTWARE	LYS A:138	BINDING SITE FOR RESIDUE SO4 A 203

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

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 d1d9ua_ A: Lambda lysozyme                                                                                                                                 SCOP domains
               CATH domains 1d9uA00 A:1-154  [code=1.10.530.10, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.................................eeee..eee........hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.................hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d9u A   1 MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRWWDAYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAGGTVR 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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 d1d9ub_ B: Lambda lysozyme                                                                                                                                 SCOP domains
               CATH domains 1d9uB00 B:1-154  [code=1.10.530.10, no name defined]                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.................................ee.....ee........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhhhh................hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d9u B   1 MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRWWDAYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAGGTVR 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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 (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

Visualization

Interactive Views

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
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NDG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1d9u)

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

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1d9u
		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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 16)

Sites (16, 16)