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Title :   CRYSTAL STRUCTURE OF THE P- AND N-DOMAINS OF HIS462GLN MUTANT COPA, A COPPER-TRANSPORTING P-TYPE ATPASE, BOUND WITH AMPPCP-MG

Authors :   T. Tsuda, C. Toyoshima

Date :   31 Mar 09 (Deposition) - 21 Jul 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   P-Type Atpase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Tsuda, C. Toyoshima
Nucleotide Recognition By Copa, A Cu+-Transporting P-Type Atpase.
Embo J. V. 28 1782 2009
PubMed-ID: 19478797 | Reference-DOI: 10.1038/EMBOJ.2009.143

Molecule 1 - PROBABLE COPPER-EXPORTING P-TYPE ATPASE A
	Chains	:	A, B
	EC Number	:	3.6.3.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBAD
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 387-673
	Gene	:	COPA, PACS, AF_0473
	Mutation	:	YES
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	ACP	2	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:424 , LYS A:425 , THR A:426 , GLU A:457 , GLN A:462 , ILE A:464 , GLY A:490 , GLU A:491 , GLY A:492 , VAL A:500 , GLY A:501 , ASN A:502 , VAL A:532 , THR A:572 , GLY A:573 , ASP A:574 , PRO A:597 , LYS A:600 , MG A:998 , HOH A:1121 , HOH A:1127 , HOH A:1141 , HOH A:1150	BINDING SITE FOR RESIDUE ACP A 997
2	AC2	SOFTWARE	ASP A:424 , THR A:426 , ACP A:997 , HOH A:1001	BINDING SITE FOR RESIDUE MG A 998
3	AC3	SOFTWARE	ASP B:424 , LYS B:425 , THR B:426 , GLU B:457 , GLN B:462 , GLY B:490 , GLU B:491 , VAL B:493 , VAL B:500 , GLY B:501 , ASN B:502 , THR B:572 , GLY B:573 , ASP B:574 , LYS B:600 , HOH B:1391	BINDING SITE FOR RESIDUE ACP B 997

(no "SS Bond" information available for 3A1E)

(no "Cis Peptide Bond" information available for 3A1E)

(no "SAP(SNP)/Variant" information available for 3A1E)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ATPASE_E1_E2	PS00154	E1-E2 ATPases phosphorylation site.	COPA_ARCFU	424-430	2	A:424-430 B:424-430

(no "Exon" information available for 3A1E)

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:268
 aligned with COPA_ARCFU | O29777 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:268
                                   409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659        
           COPA_ARCFU   400 AELGILIKNADALEVAEKVTAVIFDKTGTLTKGKPEVTDLVPLNGDERELLRLAAIAERRSEHPIAEAIVKKALEHGIELGEPEKVEVIAGEGVVADGILVGNKRLMEDFGVAVSNEVELALEKLEREAKTAVIVARNGRVEGIIAVSDTLKESAKPAVQELKRMGIKVGMITGDNWRSAEAISRELNLDLVIAEVLPHQKSEEVKKLQAKEVVAFVGDGINDAPALAQADLGIAVGSGSDVAVESGDIVLIRDDLRDVVAAIQLSRK 667
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...hhhhhhhhh.eeeee..........eeeeeee...hhhhhhhhhhhhh....hhhhhhhhhhhhhh.........eeee...eeee..eeeehhhhhhhh....hhhhhhhhhhhhhh..eeeeeee..eeeeeeeee.....hhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh..eee...hhhhhhhhhhhhh....eeeee....hhhhhhhh.eeeee............eee....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------ATPASE_--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a1e A 400 AELGILIKNADALEVAEKVTAVIFDKTGTLTKGKPEVTDLVPLNGDERELLRLAAIAERRSEQPIAEAIVKKALEHGIELGEPEKVEVIAGEGVVADGILVGNKRLMEDFGVAVSNEVELALEKLEREAKTAVIVARNGRVEGIIAVSDTLKESAKPAVQELKRMGIKVGMITGDNWRSAEAISRELNLDLVIAEVLPHQKSEEVKKLQAKEVVAFVGDGINDAPALAQADLGIAVGSGSDVAVESGDIVLIRDDLRDVVAAIQLSRK 667
                                   409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659

Chain B from PDB  Type:PROTEIN  Length:272
 aligned with COPA_ARCFU | O29777 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:272
                                   408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668  
           COPA_ARCFU   399 GAELGILIKNADALEVAEKVTAVIFDKTGTLTKGKPEVTDLVPLNGDERELLRLAAIAERRSEHPIAEAIVKKALEHGIELGEPEKVEVIAGEGVVADGILVGNKRLMEDFGVAVSNEVELALEKLEREAKTAVIVARNGRVEGIIAVSDTLKESAKPAVQELKRMGIKVGMITGDNWRSAEAISRELNLDLVIAEVLPHQKSEEVKKLQAKEVVAFVGDGINDAPALAQADLGIAVGSGSDVAVESGDIVLIRDDLRDVVAAIQLSRKTMS 670
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...hhhhhhhhh.eeeee..........eeeeeee...hhhhhhhhhhhhh....hhhhhhhhhhhhhhh...............eeee..eeeehhhhhhhh....hhhhhhhhhhhhh...eeeeeee..eeeeeeeee.....hhhhhhhhhhhh..eeeee...hhhhhhhhhhhhh..eee......hhhhhhhhhh....eeeee....hhhhhhhh.eeeee............eee....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------ATPASE_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a1e B 399 GAELGILIKNADALEVAEKVTAVIFDKTGTLTKGKPEVTDLVPLNGDERELLRLAAIAERRSEQPIAEAIVKKALEHGIELGEPEKVEVIAGEGVVADGILVGNKRLMEDFGVAVSNEVELALEKLEREAKTAVIVARNGRVEGIIAVSDTLKESAKPAVQELKRMGIKVGMITGDNWRSAEAISRELNLDLVIAEVLPHQKSEEVKKLQAKEVVAFVGDGINDAPALAQADLGIAVGSGSDVAVESGDIVLIRDDLRDVVAAIQLSRKTMS 670
                                   408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668

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 3A1E)

(no "CATH Domain" information available for 3A1E)

(no "Pfam Domain" information available for 3A1E)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (COPA_ARCFU | O29777)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0019829	cation-transporting ATPase activity	Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + cation(out) = ADP + phosphate + cation(in).
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0098655	cation transmembrane transport	A process in which a cation is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0006812	cation transport	The directed movement of cations, atoms or small molecules with a net positive charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006825	copper ion transport	The directed movement of copper (Cu) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0030001	metal ion transport	The directed movement of metal ions, any metal ion with an electric charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3a1e)

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	3a1e
		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)
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	COPA_ARCFU \| O29777
		Comparative Protein Structure Models	:	ModBase
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	3.6.3.-
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		Interatomic Contacts of Structural Units	:	CSU
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	COPA_ARCFU \| O29777
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UniProtKB/Swiss-Prot
	COPA_ARCFU \| O29777	:	2b8e 2hc8 2voy 3a1c 3a1d 3fry 3j08 3j09

2arf	NMR STRUCTURE OF THE N-DOMAIN OF ATP7B
2b8e	NUCLEOTIDE UNBOUND FORM
2iye	SO4 BOUND FORM
3a1c	AMPPCP-MG BOUND FORM (WILD TYPE)
3a1d	ADP-MG BOUND FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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