3LX2 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE ANALYSIS OF PCNA FROM THERMOCOCCUS KODAKARAENSIS TK0582

Authors :   J. E. Ladner, Z. Kelman, M. Pan

Date :   24 Feb 10 (Deposition) - 26 Jan 11 (Release) - 20 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Pcna, Dna Processivity Factor, Trimer, Toroidal, Dna Replication, Dna-Binding, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. E. Ladner, M. Pan, J. Hurwitz, Z. Kelman
Crystal Structures Of Two Active Proliferating Cell Nuclear Antigens (Pcnas) Encoded By Thermococcus Kodakaraensis.
Proc. Natl. Acad. Sci. Usa V. 108 2711 2011
PubMed-ID: 21270332 | Reference-DOI: 10.1073/PNAS.1019179108

Molecule 1 - DNA POLYMERASE SLIDING CLAMP 2
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3) ROSETTA
	Expression System Taxid	:	562
	Gene	:	PCN2, TK0535, TK0582
	Organism Common	:	THERMOCOCCUS KODAKARAENSIS
	Organism Scientific	:	THERMOCOCCUS KODAKARENSIS
	Organism Taxid	:	311400
	Synonym	:	PROLIFERATING CELL NUCLEAR ANTIGEN HOMOLOG 2, PCNA 2

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 6)

No.	Name	Count	Type	Full Name
1	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:213 , ASP A:214	BINDING SITE FOR RESIDUE SO4 A 260
2	AC2	SOFTWARE	SER A:9 , ARG A:11 , SER A:85 , ARG A:86 , HOH A:268	BINDING SITE FOR RESIDUE SO4 A 261
3	AC3	SOFTWARE	GLU A:4 , VAL A:90	BINDING SITE FOR RESIDUE SO4 A 262
4	AC4	SOFTWARE	ALA B:213 , ASP B:214	BINDING SITE FOR RESIDUE SO4 B 260
5	AC5	SOFTWARE	SER B:9 , ARG B:11 , SER B:85 , HOH B:278	BINDING SITE FOR RESIDUE SO4 B 261
6	AC6	SOFTWARE	SER C:9 , SER C:85	BINDING SITE FOR RESIDUE SO4 C 260

(no "SS Bond" information available for 3LX2)

(no "Cis Peptide Bond" information available for 3LX2)

(no "SAP(SNP)/Variant" information available for 3LX2)

Asymmetric/Biological Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PCNA_1	PS01251	Proliferating cell nuclear antigen signature 1.	PCNA2_THEKO	35-58	3	A:35-58 B:35-58 C:35-58

(no "Exon" information available for 3LX2)

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:247
 aligned with PCNA2_THEKO | Q5JFD3 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       
          PCNA2_THEKO     2 TFEIVFDSAREFESLIATLEKFFDEAVFQVNMEGIQMRAIDPSRVVLVDLNLPEMLFSKYSVESEEAIAFDLKRFLKVLKLARSRDTLVLRKGGENFLEVGLLGDENTWFKLPLIDANTPEIEIPSLPWTVKAVVLAGALKRAVKAAKLVSDSIYFMATPEKLTFKAEGNDSEVRTVLTMEDPGLLDLEHKMTKAKSAYGVAYLEDILRSLADADEVIIRFGFDIPLLLKYMVRDAGEVSFLIAPRV 248
               SCOP domains d3lx2a1 A:2-117 automated matches                                                                                   d3lx2a2 A:118-248 automated matches                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhh...eeeeee...eeeeeee.....eeeeeeee.hhh.eeee...eeeeeehhhhhhhhh......eeeeee....eeeeeee...eeeeeee.................eeeeeehhhhhhhhhhhhhhh.eeeeee....eeeeee....eeeeee......eeeeee....eeeeeehhhhhhhhh......eeeeee.....eeeeeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------PCNA_1  PDB: A:35-58    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lx2 A   2 TFEIVFDSAREFESLIATLEKFFDEAVFQVNMEGIQMRAIDPSRVVLVDLNLPEMLFSKYSVESEEAIAFDLKRFLKVLKLARSRDTLVLRKGGENFLEVGLLGDENTWFKLPLIDANTPEIEIPSLPWTVKAVVLAGALKRAVKAAKLVSDSIYFMATPEKLTFKAEGNDSEVRTVLTMEDPGLLDLEHKMTKAKSAYGVAYLEDILRSLADADEVIIRFGFDIPLLLKYMVRDAGEVSFLIAPRV 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain B from PDB  Type:PROTEIN  Length:246
 aligned with PCNA2_THEKO | Q5JFD3 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:246
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      
          PCNA2_THEKO     2 TFEIVFDSAREFESLIATLEKFFDEAVFQVNMEGIQMRAIDPSRVVLVDLNLPEMLFSKYSVESEEAIAFDLKRFLKVLKLARSRDTLVLRKGGENFLEVGLLGDENTWFKLPLIDANTPEIEIPSLPWTVKAVVLAGALKRAVKAAKLVSDSIYFMATPEKLTFKAEGNDSEVRTVLTMEDPGLLDLEHKMTKAKSAYGVAYLEDILRSLADADEVIIRFGFDIPLLLKYMVRDAGEVSFLIAPR 247
               SCOP domains d3lx2b1 B:2-117 automated matches                                                                                   d3lx2b2 B:118-247 automated matches                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhh.eeeeee...eeeeeee.....eeeeeeee.hhh.eeee....eeeeehhhhhhhhh......eeeeee....eeeeeee...eeeeeee.................eeeeeehhhhhhhhhhhhh...eeeeee...eeeeeee....eeeeeee.....eeeeee....eeeeeehhhhhhhhh......eeeeee.....eeeeeee...eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------PCNA_1  PDB: B:35-58    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lx2 B   2 TFEIVFDSAREFESLIATLEKFFDEAVFQVNMEGIQMRAIDPSRVVLVDLNLPEMLFSKYSVESEEAIAFDLKRFLKVLKLARSRDTLVLRKGGENFLEVGLLGDENTWFKLPLIDANTPEIEIPSLPWTVKAVVLAGALKRAVKAAKLVSDSIYFMATPEKLTFKAEGNDSEVRTVLTMEDPGLLDLEHKMTKAKSAYGVAYLEDILRSLADADEVIIRFGFDIPLLLKYMVRDAGEVSFLIAPR 247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain C from PDB  Type:PROTEIN  Length:246
 aligned with PCNA2_THEKO | Q5JFD3 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:246
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      
          PCNA2_THEKO     2 TFEIVFDSAREFESLIATLEKFFDEAVFQVNMEGIQMRAIDPSRVVLVDLNLPEMLFSKYSVESEEAIAFDLKRFLKVLKLARSRDTLVLRKGGENFLEVGLLGDENTWFKLPLIDANTPEIEIPSLPWTVKAVVLAGALKRAVKAAKLVSDSIYFMATPEKLTFKAEGNDSEVRTVLTMEDPGLLDLEHKMTKAKSAYGVAYLEDILRSLADADEVIIRFGFDIPLLLKYMVRDAGEVSFLIAPR 247
               SCOP domains d3lx2c1 C:2-117 automated matches                                                                                   d3lx2c2 C:118-247 automated matches                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhh...eeeeee...eeeeeee.....eeeeeeee.hhh..eee...eeeeeehhhhhhhhh......eeeeee....eeeeeee...eeeeeee.................eeeeeehhhhhhhhhhhhh...eeeeee...eeeeeee....eeeeeee.....eeeeee....eeeeeehhhhhhhhh......eeeeee.....eeeeeee...eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------PCNA_1  PDB: C:35-58    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lx2 C   2 TFEIVFDSAREFESLIATLEKFFDEAVFQVNMEGIQMRAIDPSRVVLVDLNLPEMLFSKYSVESEEAIAFDLKRFLKVLKLARSRDTLVLRKGGENFLEVGLLGDENTWFKLPLIDANTPEIEIPSLPWTVKAVVLAGALKRAVKAAKLVSDSIYFMATPEKLTFKAEGNDSEVRTVLTMEDPGLLDLEHKMTKAKSAYGVAYLEDILRSLADADEVIIRFGFDIPLLLKYMVRDAGEVSFLIAPR 247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

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( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: DNA clamp (88)

Superfamily: DNA clamp (88)

Family: automated matches (17)

Protein domain: automated matches (17)

Thermococcus kodakarensis [TaxId: 311400] (1)

1a	d3lx2a1	A:2-117
1b	d3lx2a2	A:118-248
1c	d3lx2b1	B:2-117
1d	d3lx2b2	B:118-247
1e	d3lx2c1	C:2-117
1f	d3lx2c2	C:118-247

(no "CATH Domain" information available for 3LX2)

(no "Pfam Domain" information available for 3LX2)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (PCNA2_THEKO | Q5JFD3)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0030337	DNA polymerase processivity factor activity	An enzyme regulator activity that increases the processivity of polymerization by DNA polymerase, by allowing the polymerase to move rapidly along DNA while remaining topologically bound to it.
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:0006275	regulation of DNA replication	Any process that modulates the frequency, rate or extent of DNA replication.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3lx2)

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Description

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Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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