1W5T - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF THE AEROPYRUM PERNIX ORC2 PROTEIN (ADPNP-ADP COMPLEXES)

Authors :   M. R. Singleton, R. Morales, I. Grainge, N. Cook, M. N. Isupov, D. B. Wigley

Date :   09 Aug 04 (Deposition) - 05 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Orc, Cdc6, Dna Replication Initiation, Dna Binding Protein, Aaa+ Atpase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. R. Singleton, R. Morales, I. Grainge, N. Cook, M. N. Isupov, D. B. Wigley
Conformational Changes Induced By Nucleotide Binding In Cdc6/Orc From Aeropyrum Pernix
J. Mol. Biol. V. 343 547 2004
PubMed-ID: 15465044 | Reference-DOI: 10.1016/J.JMB.2004.08.044

Molecule 1 - ORC2
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	K1
	Expression System Taxid	:	562
	Organism Scientific	:	AEROPYRUM PERNIX
	Organism Taxid	:	56636
	Synonym	:	HYPOTHETICAL PROTEIN APE0152

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3	MG	3	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ADP	-1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ADP	-1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	ANP	-1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:66 , ANP A:700 , HOH A:2029 , HOH A:2063	BINDING SITE FOR RESIDUE MG A 701
2	AC2	SOFTWARE	THR B:66 , ANP B:700 , HOH B:2014 , HOH B:2015 , HOH B:2040	BINDING SITE FOR RESIDUE MG B 701
3	AC3	SOFTWARE	THR C:66 , ADP C:700	BINDING SITE FOR RESIDUE MG C 701
4	AC4	SOFTWARE	TYR A:19 , LEU A:24 , VAL A:26 , VAL A:61 , GLY A:62 , ILE A:63 , GLY A:64 , LYS A:65 , THR A:66 , THR A:67 , TYR A:215 , ARG A:227 , ALA A:259 , ARG A:260 , MG A:701 , HOH A:2003 , HOH A:2007 , HOH A:2063	BINDING SITE FOR RESIDUE ANP A 700
5	AC5	SOFTWARE	GLU B:17 , TYR B:19 , LEU B:24 , VAL B:26 , VAL B:61 , GLY B:62 , ILE B:63 , GLY B:64 , LYS B:65 , THR B:66 , THR B:67 , TYR B:215 , ARG B:227 , ALA B:259 , ARG B:260 , ILE B:263 , MG B:701 , HOH B:2025 , HOH B:2040	BINDING SITE FOR RESIDUE ANP B 700
6	AC6	SOFTWARE	TYR C:19 , LEU C:24 , VAL C:26 , GLY C:62 , ILE C:63 , GLY C:64 , LYS C:65 , THR C:66 , THR C:67 , TYR C:215 , ILE C:223 , GLN C:226 , ARG C:227 , ALA C:259 , ARG C:260 , ILE C:263 , MG C:701 , HOH C:2047	BINDING SITE FOR RESIDUE ADP C 700

(no "SS Bond" information available for 1W5T)

(no "Cis Peptide Bond" information available for 1W5T)

(no "SAP(SNP)/Variant" information available for 1W5T)

(no "PROSITE Motif" information available for 1W5T)

(no "Exon" information available for 1W5T)

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:395
 aligned with CDC62_AERPE | Q9YFU8 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:404
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404    
          CDC62_AERPE     5 GLFKDRRVFDENYIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENEAASIQTHELEALSIHELIILRLIAEATLGGMEWINAGLLRQRYEDASLTMYNVKPRGYTQYHIYLKHLTSLGLVDAKPSGRGMRGRTTLFRLAPHLPADRLIEVVDNIIQAKMASG 408
               SCOP domains d1w5ta2 A:7-293 CDC6-like protein APE0152, N-terminal domain                                                                                                                                                                                                                                     ----d1w5ta1 A:300-409 CDC6-like protein APE0152, C-terminal domain                                                - SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..........hhhhhhhhhhhhhhhhhh......eeeeee.......hhhhhhhhhhhhhhhhhhhh...eeeeeee.hhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.eeeeeee.hhhhhh....hhhhhhhhhhhhhhh........eeeeeee..hhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh--...hhhhhhh.hhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..eeeee.-------.eeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w5t A   7 GLFKDRRVFDENYIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSEN--ASIQTHELEALSIHELIILRLIAEATLGGMEWINAGLLRQRYEDASLTMYNVKPRGYTQYHIYLKHLTSLGLVDAKPS-------TTLFRLAPHLPADRLIEVVDNIIQAKMASG 410
                                    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       366      |  -    |  386       396       406    
                                                                                                                                                                                                                                                                                                                        293  |                                                                          373     381                             
                                                                                                                                                                                                                                                                                                                           296

Chain B from PDB  Type:PROTEIN  Length:397
 aligned with CDC62_AERPE | Q9YFU8 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:404
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404    
          CDC62_AERPE     5 GLFKDRRVFDENYIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENEAASIQTHELEALSIHELIILRLIAEATLGGMEWINAGLLRQRYEDASLTMYNVKPRGYTQYHIYLKHLTSLGLVDAKPSGRGMRGRTTLFRLAPHLPADRLIEVVDNIIQAKMASG 408
               SCOP domains d1w5tb2 B:7-293 CDC6-like protein APE0152, N-terminal domain                                                                                                                                                                                                                                   ------d1w5tb1 B:300-409 CDC6-like protein APE0152, C-terminal domain                                                - SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..........hhhhhhhhhhhhhhhhhh......eeeeee.......hhhhhhhhhhhhhhhhhhhh...eeeeeee.hhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh.eeeeeeehhhhhh.....hhhhhhhhhhhhhhh........eeeeeee..hhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.....hhhhhhh.hhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..eeeee.-------.eeeee....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w5t B   7 GLFKDRRVFDENYIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENEAASIQTHELEALSIHELIILRLIAEATLGGMEWINAGLLRQRYEDASLTMYNVKPRGYTQYHIYLKHLTSLGLVDAKPS-------TTLFRLAPHLPADRLIEVVDNIIQAKMASG 410
                                    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       366      |  -    |  386       396       406    
                                                                                                                                                                                                                                                                                                                                                                                                        373     381

Chain C from PDB  Type:PROTEIN  Length:394
 aligned with CDC62_AERPE | Q9YFU8 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:404
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404    
          CDC62_AERPE     5 GLFKDRRVFDENYIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENEAASIQTHELEALSIHELIILRLIAEATLGGMEWINAGLLRQRYEDASLTMYNVKPRGYTQYHIYLKHLTSLGLVDAKPSGRGMRGRTTLFRLAPHLPADRLIEVVDNIIQAKMASG 408
               SCOP domains d1w5tc2 C:7-293 CDC6-like protein APE0152, N-terminal domain                                                                                                                                                                                                                                   -   --d1w5tc1 C:300-409 CDC6-like protein APE0152, C-terminal domain                                                - SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..........hhhhhhhhhhhhhhhhhh.......eeee........hhhhhhhhhhhhhhhhhhh...eeeeeeee.....hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhheeeeeeeehhhhhhh....hhhhhhhhhhhhhh.........eeeeeee.hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.---.hhhhhh..hhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eee...-------..eeee....hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w5t C   7 GLFKDRRVFDENYIPPELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENE---IQTHELEALSIHELIILRLIAEATLGGMEWINAGLLRQRYEDASLTMYNVKPRGYTQYHIYLKHLTSLGLVDAKPS-------TTLFRLAPHLPADRLIEVVDNIIQAKMASG 410
                                    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       | - |     306       316       326       336       346       356       366      |  -    |  386       396       406    
                                                                                                                                                                                                                                                                                                                         294 298                                                                        373     381

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 "CATH Domain" information available for 1W5T)

(no "Pfam Domain" information available for 1W5T)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (CDC62_AERPE | Q9YFU8)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1w5t)

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	1w5t
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	CDC62_AERPE \| Q9YFU8	:	1w5s

1w5s	STRUCTURE OF THE AEROPYRUM PERNIX ORC2 PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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