1Z1B | PD0636 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A LAMBDA INTEGRASE DIMER BOUND TO A COC' CORE SITE

Authors :   T. Biswas, H. Aihara, M. Radman-Livaja, D. Filman, A. Landy, T. Ellenberger

Date :   03 Mar 05 (Deposition) - 28 Jun 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.80

Chains :   Asym. Unit : A,B,C,D,E,F,G
Biol. Unit 1: A,B,C,D,E,F,G  (2x)

Keywords :   Protein-Dna Complex, Dna Binding Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Biswas, H. Aihara, M. Radman-Livaja, D. Filman, A. Landy, T. Ellenberger
A Structural Basis For Allosteric Control Of Dna Recombination By Lambda Integrase.
Nature V. 435 1059 2005
PubMed-ID: 15973401 | Reference-DOI: 10.1038/NATURE03657
(for further references see the PDB file header)

*Molecule 1 - 5'- D(CPTCPGPTPTPCPAPGPCPTPTPTPTPTPT)-3'*
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'- D(TPTPTPAPTPAPCPTPAPAPGPTPTPGPGPCPAPT)- 3'*
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - 29-MER
	Chains	:	E
	Engineered	:	YES
	Synthetic	:	YES

Molecule 4 - 25-MER
	Chains	:	F
	Engineered	:	YES
	Synthetic	:	YES

Molecule 5 - 25-MER
	Chains	:	G
	Engineered	:	YES
	Synthetic	:	YES

Molecule 6 - INTEGRASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	INT
	Mutation	:	YES
	Organism Scientific	:	ENTEROBACTERIA PHAGE LAMBDA
	Organism Taxid	:	10710

		1	2	3	4	5	6	7
Asymmetric Unit	:	A	B	C	D	E	F	G
Biological Unit 1 (2x)	:	A	B	C	D	E	F	G

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	PTR	2	Mod. Amino Acid	O-PHOSPHOTYROSINE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	PTR	4	Mod. Amino Acid	O-PHOSPHOTYROSINE

(no "Site" information available for 1Z1B)

(no "SS Bond" information available for 1Z1B)

(no "Cis Peptide Bond" information available for 1Z1B)

(no "SAP(SNP)/Variant" information available for 1Z1B)

(no "PROSITE Motif" information available for 1Z1B)

(no "Exon" information available for 1Z1B)

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:349
 aligned with VINT_LAMBD | P03700 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:349
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347         
           VINT_LAMBD     8 ERRDLPPNLYIRNNGYYCYRDPRTGKEFGLGRDRRIAITEAIQANIELFSGHKHKPLTARINSDNSVTLHSWLDRYEKILASRGIKQKTLINYMSKIKAIRRGLPDAPLEDITTKEIAAMLNGYIDEGKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAKSEVRRSRLTADEYLKIYQAAESSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIPTALHIDALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTMASQYRDDRGREWDKIEIK 356
               SCOP domains ---d1z1ba1 A:11-59                                  --------------d1z1ba2 A:74-356 Integrase (Int)                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1z1bA01 A:8-64 Classic Zinc Finger                       ---------1z1bA02 A:74-174  [code=1.10.150.130, no name defined]                                               --1z1bA03 A:177-355 Intergrase catalytic core                                                                                                                                        - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee...eeeee......eeeee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhh.ee..eeeee......eeeee...ee....eehhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z1b A   8 ERRDLPPNLYIRNNGYYCYRDPRTGKEFGLGRDRRIAITEAIQANIELFSGHKHKPLTARINSDNSVTLHSWLDRYEKILASRGIKQKTLINYMSKIKAIRRGLPDAPLEDITTKEIAAMLNGYIDEGKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAKSKVRRSRLTADEYLKIYQAAESSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIPTALHIDALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTMASQyRDDRGREWDKIEIK 356
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337    |  347         
                                                                                                                                                                                                                                                                                                                                                                        342-PTR

Chain B from PDB  Type:PROTEIN  Length:350
 aligned with VINT_LAMBD | P03700 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:350
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356
           VINT_LAMBD     7 HERRDLPPNLYIRNNGYYCYRDPRTGKEFGLGRDRRIAITEAIQANIELFSGHKHKPLTARINSDNSVTLHSWLDRYEKILASRGIKQKTLINYMSKIKAIRRGLPDAPLEDITTKEIAAMLNGYIDEGKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAKSEVRRSRLTADEYLKIYQAAESSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIPTALHIDALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTMASQYRDDRGREWDKIEIK 356
               SCOP domains ----d1z1bb1 B:11-59                                  --------------d1z1bb2 B:74-356 Integrase (Int)                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1z1bB01 B:7-64 Classic Zinc Finger                        ---------1z1bB02 B:74-174  [code=1.10.150.130, no name defined]                                               --1z1bB03 B:177-355 Intergrase catalytic core                                                                                                                                        - CATH domains
           Pfam domains (1) Phage_integ_N-1z1bB05 B:7-76                                          ---Phage_integr_N-1z1bB03 B:80-158                                                -------------------Phage_integrase-1z1bB01 B:178-349                                                                                                                                           ------- Pfam domains (1)
           Pfam domains (2) Phage_integ_N-1z1bB06 B:7-76                                          ---Phage_integr_N-1z1bB04 B:80-158                                                -------------------Phage_integrase-1z1bB02 B:178-349                                                                                                                                           ------- Pfam domains (2)
         Sec.struct. author .........eee.....eeee......eeeee.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.ee..eeeee......eeeee...ee....eehhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z1b B   7 HERRDLPPNLYIRNNGYYCYRDPRTGKEFGLGRDRRIAITEAIQANIELFSGHKHKPLTARINSDNSVTLHSWLDRYEKILASRGIKQKTLINYMSKIKAIRRGLPDAPLEDITTKEIAAMLNGYIDEGKAASAKLIRSTLSDAFREAIAEGHITTNHVAATRAAKSKVRRSRLTADEYLKIYQAAESSPCWLRLAMELAVVTGQRVGDLCEMKWSDIVDGYLYVEQSKTGVKIAIPTALHIDALGISMKETLDKCKEILGGETIIASTRREPLSSGTVSRYFMRARKASGLSFEGDPPTFHELRSLSARLYEKQISDKFAQHLLGHKSDTMASQyRDDRGREWDKIEIK 356
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336     | 346       356
                                                                                                                                                                                                                                                                                                                                                                         342-PTR

Chain C from PDB  Type:DNA  Length:11
                                           
                 1z1b C   3 CGTTCAGCTTT  13
                                    12

Chain D from PDB  Type:DNA  Length:18
                                                  
                 1z1b D  14 TTTATACTAAGTTGGCAT  31
                                    23

Chain E from PDB  Type:DNA  Length:29
                                                             
                 1z1b E  36 ATGCCAACTTAGTATAAAAAAGCTGAACG  64
                                    45        55

Chain F from PDB  Type:DNA  Length:25
                                                         
                 1z1b F   1 ACAGGTCACTATCAGTCAAAATACC  25
                                    10        20

Chain G from PDB  Type:DNA  Length:25
                                                         
                 1z1b G  28 GGTATTTTGACTGATAGTGACCTGT  52
                                    37        47

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Double Stranded RNA Binding Domain (204)

Homologous Superfamily: Classic Zinc Finger (45)

[unclassified] (29)

1a	1z1bA01	A:8-64
1b	1z1bB01	B:7-64

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: DNA polymerase; domain 1 (617)

Homologous Superfamily: [code=1.10.150.130, no name defined] (26)

[unclassified] (23)

2a	1z1bA02	A:74-174
2b	1z1bB02	B:74-174

Topology: hpI Integrase; Chain A (31)

Homologous Superfamily: Intergrase catalytic core (31)

[unclassified] (26)

3a	1z1bA03	A:177-355
3b	1z1bB03	B:177-355

Asymmetric Unit(hide GO term definitions)

Chain A,B (VINT_LAMBD | P03700)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0008907	integrase activity	Catalysis of the integration of one segment of DNA into another.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0015074	DNA integration	The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
	GO:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	GO:0075713	establishment of integrated proviral latency	A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.

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
		PTR	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 1z1b)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1z1b)

Biological Unit
	Complete Structure
		Biological Unit 1	[ 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 ](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
	1z1b
		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
	VINT_LAMBD \| P03700
		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)
	(no 'Enzyme Classificator' available)
		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
	VINT_LAMBD \| P03700
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	VINT_LAMBD \| P03700	:	1ae9 1kjk 1m97 1p7d 1z19 1z1g 2oxo 2wcc 5j0n

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

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 (2, 4)

CATH Domains (3, 6)

Pfam Domains (3, 6)

Gene Ontology (9, 9)

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