5AW7 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   KINETICS BY X-RAY CRYSTALLOGRAPHY: RB+-SUBSTITUTION OF BOUND K+ IN THE E2.MGF42-.2K+ CRYSTAL AFTER 11.3 MIN

Authors :   H. Ogawa, F. Cornelius, A. Hirata, C. Toyoshima

Date :   01 Jul 15 (Deposition) - 02 Sep 15 (Release) - 02 Sep 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Membrane Protein, Ion Pump, Atpase, K+ Binding, Haloacid Dehydrogenease Superfamily, Phosphate Analogue, Atp-Binding, Hydrolase, Ion Transport, Nucleotide-Binding, Phosphoprotein, Hydrolase-Transport Protein Complex, Kinetics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Ogawa, F. Cornelius, A. Hirata, C. Toyoshima
Sequential Substitution Of K(+) Bound To Na(+), K(+)-Atpase Visualized By X-Ray Crystallography.
Nat Commun V. 6 8004 2015
PubMed-ID: 26258479 | Reference-DOI: 10.1038/NCOMMS9004

Molecule 1 - NA, K-ATPASE ALPHA SUBUNIT
	Chains	:	A
	Organism Common	:	SPINY DOGFISH
	Organism Scientific	:	SQUALUS ACANTHIAS
	Organism Taxid	:	7797

Molecule 2 - NA+,K+-ATPASE BETA SUBUNIT
	Chains	:	B
	Organism Common	:	SPINY DOGFISH
	Organism Scientific	:	SQUALUS ACANTHIAS
	Organism Taxid	:	7797
	Synonym	:	SODIUM/POTASSIUM-TRANSPORTING ATPASE SUBUNIT BETA-1

Molecule 3 - PHOSPHOLEMMAN-LIKE PROTEIN
	Chains	:	G
	Organism Common	:	SPINY DOGFISH
	Organism Scientific	:	SQUALUS ACANTHIAS
	Organism Taxid	:	7797

		1	2	3
Asymmetric/Biological Unit	:	A	B	G

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 11)

No.	Name	Count	Type	Full Name
1	CLR	1	Ligand/Ion	CHOLESTEROL
2	K	2	Ligand/Ion	POTASSIUM ION
3	MF4	1	Ligand/Ion	TETRAFLUOROMAGNESATE(2-)
4	MG	1	Ligand/Ion	MAGNESIUM ION
5	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
6	RB	3	Ligand/Ion	RUBIDIUM ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:219 , GLY A:220 , GLU A:221 , ASP A:376 , LYS A:377 , THR A:378 , THR A:617 , GLY A:618 , ASP A:619 , LYS A:698 , ASN A:720 , MG A:2002	binding site for residue MF4 A 2001
02	AC2	SOFTWARE	ASP A:376 , THR A:378 , ASP A:717 , MF4 A:2001	binding site for residue MG A 2002
03	AC3	SOFTWARE	THR A:779 , SER A:782 , ASN A:783 , ASP A:811 , HOH A:2101	binding site for residue K A 2003
04	AC4	SOFTWARE	THR A:779 , SER A:782 , ASN A:783 , ASP A:811 , HOH A:2101	binding site for residue RB A 2004
05	AC5	SOFTWARE	VAL A:329 , ALA A:330 , VAL A:332 , GLU A:334 , ASN A:783 , GLU A:786 , ASP A:811	binding site for residue RB A 2005
06	AC6	SOFTWARE	LEU A:725 , LYS A:726 , ALA A:728 , ASP A:747	binding site for residue K A 2006
07	AC7	SOFTWARE	LEU A:725 , LYS A:726 , ALA A:728 , ASP A:747	binding site for residue RB A 2007
08	AC8	SOFTWARE	GLU A:847 , SER A:851 , ARG B:28 , TYR B:44	binding site for residue CLR B 3001
09	AC9	SOFTWARE	ASP B:111 , ASN B:114 , SER B:116 , ARG B:154	binding site for Poly-Saccharide residues NAG B 4001 through NAG B 4002 bound to ASN B 114
10	AD1	SOFTWARE	ASN B:159 , GLU B:230	binding site for Mono-Saccharide NAG B 4021 bound to ASN B 159

Asymmetric/Biological Unit

No.	Residues
1	B:127	-	B:150
2	B:160	-	B:176
3	B:215	-	B:278

Asymmetric/Biological Unit

No.	Residues
1	Ser B:122	-	Pro B:123
2	Tyr B:245	-	Pro B:246

(no "SAP(SNP)/Variant" information available for 5AW7)

(no "PROSITE Motif" information available for 5AW7)

(no "Exon" information available for 5AW7)

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:992
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhh.......hhhhhhhhhhhhh..........hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh....eeeeee..eeeeee.hhh....eeeee.......eeeeeeeeeeeeehhhhhh....ee...............ee....eeeeeeeeeeeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhh.eeee...........eeeeeee..eeee...............hhhhhhhhhhhhhh...ee.......hhhhh.ee.hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.......eeeeeee........eeeeeeehhhhhhh.eeee.........hhhhhhhhhhhhhhhhhh..eeeeeeeee.......................eeeeeeeeee.....hhhhhhhhhhhh..eeeee...hhhhhhhhhhhh........hhhhhhhhh..hhhhhhhhhh.eeeeehhhhh..hhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhh.eeeee....hhhhhhhh.eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh..hhhhhhhhhhh....hhhhh...........hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhh......ee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5aw7 A   32 LDELKKEVSMDDHKLSLDELHNKYGTDLTRGLTNARAKEILARDGPNSLTPPPTTPEWIKFCRQLFGGFSILLWIGAILCFLAYGIQAATEDEPANDNLYLGVVLSTVVIVTGCFSYYQEAKSSRIMDSFKNMVPQQALVIRDGEKSTINAEFVVAGDLVEVKGGDRIPADLRIISAHGCKVDNSSLTGESEPQTRSPEFSSENPLETRNIAFFSTNCVEGTARGVVVYTGDRTVMGRIATLASGLEVGRTPIAIEIEHFIHIITGVAVFLGVSFFILSLILGYSWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGSTSTICSDKTGTLTQNRMTVAHMWFDNQIHEADTTENQSGAAFDKTSATWSALSRIAALCNRAVFQAGQDNVPILKRSVAGDASESALLKCIELCCGSVQGMRDRNPKIVEIPFNSTNKYQLSIHENEKSSESRYLLVMKGAPERILDRCSTILLNGAEEPLKEDMKEAFQNAYLELGGLGERVLGFCHFALPEDKYNEGYPFDADEPNFPTTDLCFVGLMAMIDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETIEDIAARLNIPIGQVNPRDAKACVVHGSDLKDLSTEVLDDILHYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPALKKADIGVAMGISGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEITPFLVFIIGNVPLPLGTVTILCIDLGTDMVPAISLAYEQAESDIMKRQPRNPKTDKLVNERLISMAYGQIGMIQALGGFFSYFVILAENGFLPMDLIGKRVRWDDRWISDVEDSFGQQWTYEQRKIVEFTCHTSFFISIVVVQWADLIICKTRRNSIFQQGMKNKILIFGLFEETALAAFLSYCPGTDVALRMYPLKPSWWFCAFPYSLIIFLYDEMRRFIIRRSPGGWVEQETYY 1023
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011      1021

Chain B from PDB  Type:PROTEIN  Length:268
                                                                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........................eeee...hhhhhhhhhhhhhhhhhhhhhhhh.....ee.......................ee..hhhhh............eee.............................eeeeeee.......eeeehhhhh.eee.hhh..............eeeeee........eeeeeee..................eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5aw7 B   25 FLGRTGSSWFKIFLFYLIFYGCLAGIFIGTIQVLLLTLSDFEPKYQDRVAPPGLSHAPYAIKTEISFSISNPKSYESFVKSMHKLMDLYNESSQAGNSPFEDCSDTPADYIKRGDLDDSQGQKKACRFSRMWLKNCGYAEGKPCVVAKLNRIIGFYPKPLKNTTDLPEELQANYNQYVLPLRCAAREKIGSIEYFGLGGYAGFPLQYYPYYGKRLQKKYLQPLLAIQFTNLTQNMELRIECKVYGENIDYSEKDRFRGRFEVKIEVKS  305
                                    34        44        54        64        74        84        94       104       114       124       134       144       154     ||172       182       192       202       212    || 227       237       247       257       267       277       287       297        
                                                                                                                                                                 160|                                             217|                                                                                  
                                                                                                                                                                  169                                              223

Chain G from PDB  Type:PROTEIN  Length:39
                                                                        
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                5aw7 G    4 EGPDNDERFTYDYYRLRVVGLIVAAVLCVIGIIILLAGK   42
                                    13        23        33

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 5AW7)

(no "CATH Domain" information available for 5AW7)

(no "Pfam Domain" information available for 5AW7)

Asymmetric/Biological Unit(hide GO term definitions)

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
		CLR	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MF4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		RB	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		AD1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ser B:122 - Pro B:123	[ RasMol ]
		Tyr B:245 - Pro B:246	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites 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
	5aw7
		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
	C4IX13_SQUAC \| C4IX13
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL
	Q4H132_SQUAC \| Q4H132
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL
	Q70Q12_SQUAC \| Q70Q12
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

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
	C4IX13_SQUAC \| C4IX13
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	Q4H132_SQUAC \| Q4H132
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	Q70Q12_SQUAC \| Q70Q12
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 11)

Sites (10, 10)

SS Bonds (3, 3)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 25)

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