168L - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   PROTEIN FLEXIBILITY AND ADAPTABILITY SEEN IN 25 CRYSTAL FORMS OF T4 LYSOZYME

Authors :   X. -J. Zhang, B. W. Matthews

Date :   24 Mar 95 (Deposition) - 10 Jul 95 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: E  (1x)

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

Reference :   X. J. Zhang, J. A. Wozniak, B. W. Matthews
Protein Flexibility And Adaptability Seen In 25 Crystal Forms Of T4 Lysozyme.
J. Mol. Biol. V. 250 527 1995
PubMed-ID: 7616572 | Reference-DOI: 10.1006/JMBI.1995.0396
(for further references see the PDB file header)

Molecule 1 - T4 LYSOZYME
	Chains	:	A, B, C, D, E
	EC Number	:	3.2.1.17
	Engineered	:	YES
	Expression System Plasmid	:	M13
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ENTEROBACTERIA PHAGE T4
	Organism Taxid	:	10665

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:					E

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 168L)

(no "Site" information available for 168L)

(no "SS Bond" information available for 168L)

(no "Cis Peptide Bond" information available for 168L)

(no "SAP(SNP)/Variant" information available for 168L)

(no "PROSITE Motif" information available for 168L)

(no "Exon" information available for 168L)

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:164
 aligned with ENLYS_BPT4 | P00720 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
           ENLYS_BPT4     1 MNIFEMLRIDERLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYKNL 164
               SCOP domains d168la_ A: Phage T4 lysozyme                                                                                                                                         SCOP domains
               CATH domains 168lA00 A:1-164  [code=1.10.530.40, no name defined]                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.............eee...eeee....hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhh.hhhhhh.hhhhhhhhh..hhhhhhhhh..hhhhh.hhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 168l A   1 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDAAAAALAAAAWYNQTPNRAKRVITTFRTGTWDAYKNL 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:164
 aligned with ENLYS_BPT4 | P00720 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
           ENLYS_BPT4     1 MNIFEMLRIDERLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYKNL 164
               SCOP domains d168lb_ B: Phage T4 lysozyme                                                                                                                                         SCOP domains
               CATH domains 168lB00 B:1-164  [code=1.10.530.40, no name defined]                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.............eee...eeee....hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhh.hhhhhh.hhhhhhhhh..hhhhhhhhh..hhhhh.hhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 168l B   1 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDAAAAALAAAAWYNQTPNRAKRVITTFRTGTWDAYKNL 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain C from PDB  Type:PROTEIN  Length:164
 aligned with ENLYS_BPT4 | P00720 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
           ENLYS_BPT4     1 MNIFEMLRIDERLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYKNL 164
               SCOP domains d168lc_ C: Phage T4 lysozyme                                                                                                                                         SCOP domains
               CATH domains 168lC00 C:1-164  [code=1.10.530.40, no name defined]                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.............eee...eeee....hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhh.hhhhhh.hhhhhhhhh..hhhhhhhhh..hhhhh.hhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 168l C   1 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDAAAAALAAAAWYNQTPNRAKRVITTFRTGTWDAYKNL 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain D from PDB  Type:PROTEIN  Length:164
 aligned with ENLYS_BPT4 | P00720 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
           ENLYS_BPT4     1 MNIFEMLRIDERLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYKNL 164
               SCOP domains d168ld_ D: Phage T4 lysozyme                                                                                                                                         SCOP domains
               CATH domains 168lD00 D:1-164  [code=1.10.530.40, no name defined]                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.............eee...eeee....hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhh.hhhhhh.hhhhhhhhh..hhhhhhhhh..hhhhh.hhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 168l D   1 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDAAAAALAAAAWYNQTPNRAKRVITTFRTGTWDAYKNL 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain E from PDB  Type:PROTEIN  Length:164
 aligned with ENLYS_BPT4 | P00720 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160    
           ENLYS_BPT4     1 MNIFEMLRIDERLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYKNL 164
               SCOP domains d168le_ E: Phage T4 lysozyme                                                                                                                                         SCOP domains
               CATH domains 168lE00 E:1-164  [code=1.10.530.40, no name defined]                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.............eee...eeee....hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhh.hhhhhh.hhhhhhhhh..hhhhhhhhh..hhhhh.hhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 168l E   1 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDAAAAALAAAAWYNQTPNRAKRVITTFRTGTWDAYKNL 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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: Phage lysozyme (550)

Protein domain: Phage T4 lysozyme (546)

Bacteriophage T4 [TaxId: 10665] (546)

1a	d168la_	A:
1b	d168lb_	B:
1c	d168lc_	C:
1d	d168ld_	D:
1e	d168le_	E:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Lysozyme (1131)

Homologous Superfamily: [code=1.10.530.40, no name defined] (526)

Enterobacteria phage t4. Organism_taxid: 10665. Expression_system_vector_type: plasmid. (108)

1a	168lA00	A:1-164
1b	168lB00	B:1-164
1c	168lC00	C:1-164
1d	168lD00	D:1-164
1e	168lE00	E:1-164

(no "Pfam Domain" information available for 168L)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (ENLYS_BPT4 | P00720)

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: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
(no "Ligands, Modified Residues, Ions" information available for 168l)

	Sites
(no "Sites" information available for 168l)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 168l)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]
		Biological Unit 5	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 PNG format \| Biol. Unit 5 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
	168l
		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_BPT4 \| P00720
		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_BPT4 \| P00720
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 168L)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

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, 5)

CATH Domains (1, 5)

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