3ULP - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   PLASMODIUM FALCIPARUM SSB COMPLEX WITH SSDNA

Authors :   E. Antony, T. M. Lohman, S. Korolev

Date :   11 Nov 11 (Deposition) - 09 May 12 (Release) - 25 Jul 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B,C,D,Q,R

Keywords :   Ob-Fold, Dna Binding, Single-Stranded Dna, Apicoplast, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Antony, E. A. Weiland, S. Korolev, T. M. Lohman
Plasmodium Falciparum Ssb Tetramer Wraps Single-Stranded Dn With Similar Topology But Opposite Polarity To E. Coli Ssb.
J. Mol. Biol. V. 420 269 2012
PubMed-ID: 22543099 | Reference-DOI: 10.1016/J.JMB.2012.04.021

Molecule 1 - SINGLE-STRAND BINDING PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PET21A
	Fragment	:	UNP RESIDUES 77-200
	Gene	:	PFE0435C
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	5833

Molecule 2 - DNA (35-MER)
	Chains	:	R, Q
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC DNA
	Organism Taxid	:	32630
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	Q	R

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3ULP)

(no "Site" information available for 3ULP)

(no "SS Bond" information available for 3ULP)

Asymmetric/Biological Unit

No.	Residues
1	His C:167	-	Thr C:168
2	Thr C:168	-	Asn C:169

(no "SAP(SNP)/Variant" information available for 3ULP)

(no "PROSITE Motif" information available for 3ULP)

(no "Exon" information available for 3ULP)

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:114
 aligned with Q8I415_PLAF7 | Q8I415 from UniProtKB/TrEMBL  Length:284

    Alignment length:118
                                    86        96       106       116       126       136       146       156       166       176       186        
         Q8I415_PLAF7    77 MNEKSLNKIMLIGRVGCEPDIKILNGGDKVATFSLATNEFWRDRNTNELKSKTDWHRIVVYDQNIVDLIDKYLRKGRRVYVQGSLHTRKWHTNDMNSQPKQITEIILSYNKGDLIFLD 194
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee....eeee.....eeeeeeeeeeeeee......eeeeeeeeeeee.hhhhhhhhhhhh....eeeeeeeeeeeee..----...eeeeeeee.....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3ulp A  77 MNEKSLNKIMLIGRVGCEPDIKILNGGDKVATFSLATNEFWRDRNTNELKSKTDWHRIVVYDQNIVDLIDKYLRKGRRVYVQGSLHTRKWHT----SQPKQITEIILSYNKGDLIFLD 194
                                    86        96       106       116       126       136       146       156       166 |    |176       186        
                                                                                                                     168  173

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with Q8I415_PLAF7 | Q8I415 from UniProtKB/TrEMBL  Length:284

    Alignment length:118
                                    86        96       106       116       126       136       146       156       166       176       186        
         Q8I415_PLAF7    77 MNEKSLNKIMLIGRVGCEPDIKILNGGDKVATFSLATNEFWRDRNTNELKSKTDWHRIVVYDQNIVDLIDKYLRKGRRVYVQGSLHTRKWHTNDMNSQPKQITEIILSYNKGDLIFLD 194
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee....eeee.....eeeeeeeeeeeeee..-...eeeeeeeeeeee.hhhhhhhhhhhh....eeeeeeeeeeeee....---..eeeeeeee.....eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3ulp B  77 MNEKSLNKIMLIGRVGCEPDIKILNGGDKVATFSLATNEFWRDR-TNELKSKTDWHRIVVYDQNIVDLIDKYLRKGRRVYVQGSLHTRKWHTND---QPKQITEIILSYNKGDLIFLD 194
                                    86        96       106       116   | | 126       136       146       156       166   |   176       186        
                                                                     120 |                                             170 174                    
                                                                       122

Chain C from PDB  Type:PROTEIN  Length:116
 aligned with Q8I415_PLAF7 | Q8I415 from UniProtKB/TrEMBL  Length:284

    Alignment length:118
                                    86        96       106       116       126       136       146       156       166       176       186        
         Q8I415_PLAF7    77 MNEKSLNKIMLIGRVGCEPDIKILNGGDKVATFSLATNEFWRDRNTNELKSKTDWHRIVVYDQNIVDLIDKYLRKGRRVYVQGSLHTRKWHTNDMNSQPKQITEIILSYNKGDLIFLD 194
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee....eeee.....eeeeeeeeeeeeee......eeeeeeeeeeee.hhhhhhhhhhhh....eeeeeeeeeeeee...--....eeeeeeee.....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3ulp C  77 MNEKSLNKIMLIGRVGCEPDIKILNGGDKVATFSLATNEFWRDRNTNELKSKTDWHRIVVYDQNIVDLIDKYLRKGRRVYVQGSLHTRKWHTN--NSQPKQITEIILSYNKGDLIFLD 194
                                    86        96       106       116       126       136       146       156       166  |  | 176       186        
                                                                                                                      169  |                      
                                                                                                                         172

Chain D from PDB  Type:PROTEIN  Length:113
 aligned with Q8I415_PLAF7 | Q8I415 from UniProtKB/TrEMBL  Length:284

    Alignment length:118
                                    86        96       106       116       126       136       146       156       166       176       186        
         Q8I415_PLAF7    77 MNEKSLNKIMLIGRVGCEPDIKILNGGDKVATFSLATNEFWRDRNTNELKSKTDWHRIVVYDQNIVDLIDKYLRKGRRVYVQGSLHTRKWHTNDMNSQPKQITEIILSYNKGDLIFLD 194
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee....eeee.....eeeeeeeeeeeee...--...eeeeeeeeeee.hhhhhhhhhhhh....eeeeeeeeeeeeee.---...eeeeeeeee.....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3ulp D  77 MNEKSLNKIMLIGRVGCEPDIKILNGGDKVATFSLATNEFWRDR--NELKSKTDWHRIVVYDQNIVDLIDKYLRKGRRVYVQGSLHTRKWHT---NSQPKQITEIILSYNKGDLIFLD 194
                                    86        96       106       116   |  |126       136       146       156       166 |   | 176       186        
                                                                     120  |                                          168 172                      
                                                                        123

Chain Q from PDB  Type:DNA  Length:25
                                                         
                 3ulp Q   1 TTTTTTTTTTTTTTTTTTTTTTTTT  29
                                    10  ||    24     
                                       13|           
                                        18

Chain R from PDB  Type:DNA  Length:25
                                                         
                 3ulp R   1 TTTTTTTTTTTTTTTTTTTTTTTTT  28
                                    10   ||   23     
                                        14|          
                                         18

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 '\|'

(no "SCOP Domain" information available for 3ULP)

(no "CATH Domain" information available for 3ULP)

(no "Pfam Domain" information available for 3ULP)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (Q8I415_PLAF7 | Q8I415)

molecular function
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
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.
cellular component
	GO:0020011	apicoplast	The plastid organelle found in apicomplexans.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3ulp)

	Sites
(no "Sites" information available for 3ulp)

	Cis Peptide Bonds
		His C:167 - Thr C:168	[ RasMol ]
		Thr C:168 - Asn C:169	[ RasMol ]

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	3ulp
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		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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	Q8I415_PLAF7 \| Q8I415
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Gene Ontology (4, 4)

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