1B77 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   BUILDING A REPLISOME STRUCTURE FROM INTERACTING PIECES: A SLIDING CLAMP COMPLEXED WITH AN INTERACTION PEPTIDE FROM DNA POLYMERASE

Authors :   Y. Shamoo, T. A. Steitz

Date :   27 Jan 99 (Deposition) - 08 Feb 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Sliding Clamp, Gp45, Replisome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Shamoo, T. A. Steitz
Building A Replisome From Interacting Pieces: Sliding Clamp Complexed To A Peptide From Dna Polymerase And A Polymerase Editing Complex.
Cell(Cambridge, Mass. ) V. 99 155 1999
PubMed-ID: 10535734 | Reference-DOI: 10.1016/S0092-8674(00)81647-5
(for further references see the PDB file header)

Molecule 1 - PROTEIN (SLIDING CLAMP)
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	BL21(DE3)
	Expression System Taxid	:	562
	Gene	:	GENE 45
	Organism Scientific	:	ENTEROBACTERIA PHAGE RB69
	Organism Taxid	:	12353
	Synonym	:	GP45

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1B77)

(no "Site" information available for 1B77)

(no "SS Bond" information available for 1B77)

(no "Cis Peptide Bond" information available for 1B77)

(no "SAP(SNP)/Variant" information available for 1B77)

(no "PROSITE Motif" information available for 1B77)

(no "Exon" information available for 1B77)

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:228
 aligned with DPA5_BPR69 | O80164 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        
           DPA5_BPR69     1 MKLSKDTIAILKNFASINSGILLSQGKFIMTRAVNGTTYAEANISDEIDFDVALYDLNSFLSILSLVSDDAEISMHTDGNIKIADTRSTVYWPAADKSTIVFPNKPIQFPVASVITEIKAEDLQQLLRVSRGLQIDTIAITNKDGKIVINGYNKVEDSGLTRPKYSLTLTDYDGSNNFNFVINMANMKIQPGNYKVMLWGAGDKVAAKFESSQVSYVIAMEADSTHDF 228
               SCOP domains d1b77a1 A:1-110 gp45 sliding clamp                                                                            d1b77a2 A:111-228 gp45 sliding clamp                                                                                   SCOP domains
               CATH domains 1b77A00 A:1-228  [code=3.70.10.10, no name defined]                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh....eee....eeeee.....eeeeee........eee..hhhhhhhhhh.....eeee.....eeee....eeee....hhh..............eeeee.hhhhhhhhhhhhh....eeeeeee..eeeeeee............eeee..........eeeeehhh.......eeeeeeee..eeeeeee....eeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1b77 A   1 MKLSKDTIAILKNFASINSGILLSQGKFIMTRAVNGTTYAEANISDEIDFDVALYDLNSFLSILSLVSDDAEISMHTDGNIKIADTRSTVYWPAADKSTIVFPNKPIQFPVASVITEIKAEDLQQLLRVSRGLQIDTIAITNKDGKIVINGYNKVEDSGLTRPKYSLTLTDYDGSNNFNFVINMANMKIQPGNYKVMLWGAGDKVAAKFESSQVSYVIAMEADSTHDF 228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:228
 aligned with DPA5_BPR69 | O80164 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        
           DPA5_BPR69     1 MKLSKDTIAILKNFASINSGILLSQGKFIMTRAVNGTTYAEANISDEIDFDVALYDLNSFLSILSLVSDDAEISMHTDGNIKIADTRSTVYWPAADKSTIVFPNKPIQFPVASVITEIKAEDLQQLLRVSRGLQIDTIAITNKDGKIVINGYNKVEDSGLTRPKYSLTLTDYDGSNNFNFVINMANMKIQPGNYKVMLWGAGDKVAAKFESSQVSYVIAMEADSTHDF 228
               SCOP domains d1b77b1 B:1-110 gp45 sliding clamp                                                                            d1b77b2 B:111-228 gp45 sliding clamp                                                                                   SCOP domains
               CATH domains 1b77B00 B:1-228  [code=3.70.10.10, no name defined]                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh...eee....eeeee.....eeeeee........eee..hhhhhhhhhh.....eeee.....eeee....eeee....hhh..............eeeee.hhhhhhhhhhhhhh...eeeeeee..eeeeeee............eeee..........eeeeehhh.......eeeeeeee..eeeeeee....eeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1b77 B   1 MKLSKDTIAILKNFASINSGILLSQGKFIMTRAVNGTTYAEANISDEIDFDVALYDLNSFLSILSLVSDDAEISMHTDGNIKIADTRSTVYWPAADKSTIVFPNKPIQFPVASVITEIKAEDLQQLLRVSRGLQIDTIAITNKDGKIVINGYNKVEDSGLTRPKYSLTLTDYDGSNNFNFVINMANMKIQPGNYKVMLWGAGDKVAAKFESSQVSYVIAMEADSTHDF 228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain C from PDB  Type:PROTEIN  Length:228
 aligned with DPA5_BPR69 | O80164 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        
           DPA5_BPR69     1 MKLSKDTIAILKNFASINSGILLSQGKFIMTRAVNGTTYAEANISDEIDFDVALYDLNSFLSILSLVSDDAEISMHTDGNIKIADTRSTVYWPAADKSTIVFPNKPIQFPVASVITEIKAEDLQQLLRVSRGLQIDTIAITNKDGKIVINGYNKVEDSGLTRPKYSLTLTDYDGSNNFNFVINMANMKIQPGNYKVMLWGAGDKVAAKFESSQVSYVIAMEADSTHDF 228
               SCOP domains d1b77c1 C:1-110 gp45 sliding clamp                                                                            d1b77c2 C:111-228 gp45 sliding clamp                                                                                   SCOP domains
               CATH domains 1b77C00 C:1-228  [code=3.70.10.10, no name defined]                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh...eee....eeeee.....eeeeee........eee..hhhhhhhhhh.....eeee.....eeee....eeee....hhh..............eeeee.hhhhhhhhhhhhh....eeeeeee..eeeeeee............eeeeeee.......eeeeehhh.......eeeeeeee..eeeeeee....eeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1b77 C   1 MKLSKDTIAILKNFASINSGILLSQGKFIMTRAVNGTTYAEANISDEIDFDVALYDLNSFLSILSLVSDDAEISMHTDGNIKIADTRSTVYWPAADKSTIVFPNKPIQFPVASVITEIKAEDLQQLLRVSRGLQIDTIAITNKDGKIVINGYNKVEDSGLTRPKYSLTLTDYDGSNNFNFVINMANMKIQPGNYKVMLWGAGDKVAAKFESSQVSYVIAMEADSTHDF 228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

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: DNA clamp (88)

Superfamily: DNA clamp (88)

Family: DNA polymerase processivity factor (40)

Protein domain: gp45 sliding clamp (3)

Bacteriophage RB69 [TaxId: 12353] (2)

1a	d1b77a1	A:1-110
1b	d1b77a2	A:111-228
1c	d1b77b1	B:1-110
1d	d1b77b2	B:111-228
1e	d1b77c1	C:1-110
1f	d1b77c2	C:111-228

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Box (41)

Topology: Proliferating Cell Nuclear Antigen (41)

Homologous Superfamily: [code=3.70.10.10, no name defined] (41)

Enterobacteria phage rb69. Organism_taxid: 12353. (2)

1a	1b77A00	A:1-228
1b	1b77B00	B:1-228
1c	1b77C00	C:1-228

(no "Pfam Domain" information available for 1B77)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (DPA5_BPR69 | O80164)

biological process
	GO:0006260		DNA replication		The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0039693		viral DNA genome replication		The replication of a viral DNA genome.

Asymmetric/Biological 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 1b77)

	Sites
(no "Sites" information available for 1b77)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1b77)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit 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
	1b77
		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
	DPA5_BPR69 \| O80164
		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
	DPA5_BPR69 \| O80164
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	DPA5_BPR69 \| O80164	:	1b8h 1qe4

(no "Related Entries Specified in the PDB File" available for 1B77)

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, 6)

CATH Domains (1, 3)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

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