1KQM - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   SCALLOP MYOSIN S1-AMPPNP IN THE ACTIN-DETACHED CONFORMATION

Authors :   D. M. Himmel, S. Gourinath, L. Reshetnikova, Y. Shen, G. Szent- Gyorgyi, C. Cohen

Date :   07 Jan 02 (Deposition) - 20 Nov 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Actin-Detached, Myosin, Mechanics Of Motor, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. M. Himmel, S. Gourinath, L. Reshetnikova, Y. Shen, A. G. Szent-Gyorgyi, C. Cohen
Crystallographic Findings On The Internally Uncoupled And Near-Rigor States Of Myosin: Further Insights Into The Mechanics Of The Motor
Proc. Natl. Acad. Sci. Usa V. 99 12645 2002
PubMed-ID: 12297624 | Reference-DOI: 10.1073/PNAS.202476799
(for further references see the PDB file header)

Molecule 1 - MYOSIN HEAVY CHAIN
	Chains	:	A
	Fragment	:	SUBFRAGMENT 1(S1)
	Organism Scientific	:	ARGOPECTEN IRRADIANS
	Organism Taxid	:	31199
	Other Details	:	PAPAIN DIGESTED
	Tissue	:	MUSCLE

Molecule 2 - MYOSIN REGULATORY LIGHT CHAIN
	Chains	:	B
	Organism Scientific	:	ARGOPECTEN IRRADIANS
	Organism Taxid	:	31199
	Synonym	:	R-LC
	Tissue	:	MUSCLE

Molecule 3 - MYOSIN ESSENTIAL LIGHT CHAIN
	Chains	:	C
	Organism Scientific	:	ARGOPECTEN IRRADIANS
	Organism Taxid	:	31199
	Synonym	:	E-LC
	Tissue	:	MUSCLE

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	CA	1	Ligand/Ion	CALCIUM ION
3	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP C:19 , ASP C:22 , GLY C:23 , ASP C:25 , ALA C:27	BINDING SITE FOR RESIDUE CA C 501
2	AC2	SOFTWARE	ASP B:28 , ASP B:30 , ASP B:32 , PHE B:34 , ASP B:39 , HOH B:503	BINDING SITE FOR RESIDUE MG B 502
3	AC3	SOFTWARE	THR A:183 , ASN A:239 , SER A:241 , ANP A:999 , HOH A:1003	BINDING SITE FOR RESIDUE MG A 903
4	AC4	SOFTWARE	ASN A:124 , PRO A:125 , TYR A:126 , ARG A:127 , GLU A:177 , SER A:178 , GLY A:179 , ALA A:180 , GLY A:181 , LYS A:182 , THR A:183 , GLU A:184 , ASN A:237 , ASN A:239 , SER A:240 , SER A:241 , MG A:903 , HOH A:1003	BINDING SITE FOR RESIDUE ANP A 999

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

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

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

Asymmetric/Biological Unit (4, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	MLE_ARGIR	7-44 82-117	2	C:6-43 C:81-116
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	MLR_ARGIR	16-51 85-120	2	B:15-50 B:84-119
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	MLR_ARGIR	29-41	1	B:28-40
3	MYOSIN_MOTOR	PS51456	Myosin motor domain profile.	MYS_ARGIR	83-775	1	A:83-775
4	IQ	PS50096	IQ motif profile.	MYS_ARGIR	778-805	1	A:778-805

(no "Exon" information available for 1KQM)

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:777
 aligned with MYS_ARGIR | P24733 from UniProtKB/Swiss-Prot  Length:1938

    Alignment length:831
                                    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       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834 
            MYS_ARGIR     5 FSDPDFQYLAVDRKKLMKEQTAAFDGKKNCWVPDEKEGFASAEIQSSKGDEITVKIVADSSTRTVKKDDIQSMNPPKFEKLEDMANMTYLNEASVLYNLRSRYTSGLIYTYSGLFCIAVNPYRRLPIYTDSVIAKYRGKRKTEIPPHLFSVADNAYQNMVTDRENQSCLITGESGAGKTENTKKVIMYLAKVACAVKKKDEEASDKKEGSLEDQIIQANPVLEAYGNAKTTRNNNSSRFGKFIRIHFGPTGKIAGADIETYLLEKSRVTYQQSAERNYHIFYQICSNAIPELNDVMLVTPDSGLYSFINQGCLTVDNIDDVEEFKLCDEAFDILGFTKEEKQSMFKCTASILHMGEMKFKQRPREEQAESDGTAEAEKVAFLCGINAGDLLKALLKPKVKVGTEMVTKGQNMNQVVNSVGALAKSLYDRMFNWLVRRVNKTLDTKAKRNYYIGVLDIAGFEIFDFNSFEQLCINYTNERLQQFFNHHMFILEQEEYKKEGIAWEFIDFGMDLQMCIDLIEKPMGILSILEEECMFPKADDKSFQDKLYQNHMGKNRMFTKPGKPTRPNQGPAHFELHHYAGNVPYSITGWLEKNKDPINENVVALLGASKEPLVAELFKAPEEPAGGGKKKKGKSSAFQTISAVHRESLNKLMKNLYSTHPHFVRCIIPNELKQPGLVDAELVLHQLQCNGVLEGIRICRKGFPSRLIYSEFKQRYSILAPNAIPQGFVDGKTVSEKILAGLQMDPAEYRLGTTKVFFKAGVLGNLEEMRDERLSKIISMFQAHIRGYLIRKAYKKLQDQRIGLSVIQRNIRKWLVLRNWQWWKLYSKVKP 835
               SCOP domains d1kqma2 A:      5-28,A:7d1kqma1 A:29-76                                 d1kqma2 A:5-28,A:77-835 Myosin S1, motor domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........------............eeeee.....eeeeeeeeee..eeeeee..................hhhhh...........hhhhhhhhhhhhhh....eee...eeeee.....hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhhh...------------.hhhhhhhhhhhhhhhhhh............eeeeeee..........eeeee...hhhhh........hhhhhhh....hhhhhhhhh.....................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....-----.........hhhhhhhhhh.hhhhhhhhh.......---........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........--.....hhhhhhhhhh..hhhhhhh...---....hhhhhhhhhhhh........................ee..ee......hhhhhh....hhhhhhhhhh..hhhhhhhh.......------------..hhhhhhhhhhhhhhhhhh.eeeeeeeee...........hhhhhhhhhh......------......eehhhhhhhhhhhh....-----.....hhhhhhh.......eee...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------MYOSIN_MOTOR  PDB: A:83-775 UniProt: 83-775                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          ------------------------------------------------------------ PROSITE (3)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IQ  PDB: A:778-805          ------------------------------ PROSITE (1)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kqm A   5 FSDPDFQYLA------MKEQTAAFDGKKNCWVPDEKEGFASAEIQSSKGDEITVKIVADSSTRTVKKDDIQSMNPPKFEKLEDMANMTYLNEASVLYNLRSRYTSGLIYTYSGLFCIAVNPYRRLPIYTDSVIAKYRGKRKTEIPPHLFSVADNAYQNMVTDRENQSCLITGESGAGKTENTKKVIMYLAKVACAV------------GSLEDQIIQANPVLEAYGNAKTTRNNNSSRFGKFIRIHFGPTGKIAGADIETYLLEKSRVTYQQSAERNYHIFYQICSNAIPELNDVMLVTPDSGLYSFINQGCLTVDNIDDVEEFKLCDEAFDILGFTKEEKQSMFKCTASILHMGEMKFK-----EQAESDGTAEAEKVAFLCGINAGDLLKALLKPKVKV---MVTKGQNMNQVVNSVGALAKSLYDRMFNWLVRRVNKTLDTKAKRNYYIGVLDIAGFEIFDFNSFEQLCINYTNERLQQFFNHHMFILEQEEYKKEGIAWE--DFGMDLQMCIDLIEKPMGILSILEEEC---KADDKSFQDKLYQNHMGKNRMFTKPGKPTRPNQGPAHFELHHYAGNVPYSITGWLEKNKDPINENVVALLGASKEPLVAELFKAPEEPA------------FQTISAVHRESLNKLMKNLYSTHPHFVRCIIPNELKQPGLVDAELVLHQLQCNGVLE------KGFPSRLIYSEFKQRYSILAPNAI-----DGKTVSEKILAGLQMDPAEYRLGTTKVFFKAGVLGNLEEMRDERLSKIISMFQAHIRGYLIRKAYKKLQDQRIGLSVIQRNIRKWLVLRNWQWWKLYSKVKP 835
                                    14      | 24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194     |   -       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364     | 374       384       394       404|   |  414       424       434       444       454       464       474       484       494       504   |  |514       524       534  |   |544       554       564       574       584       594       604       614       624    |    -       644       654       664       674       684       694   |     -|      714       724   |   734       744       754       764       774       784       794       804       814       824       834 
                                    14     21                                                                                                                                                                                200          213                                                                                                                                                    364   370                                405 409                                                                                                508  |                       537 541                                                                                     629          642                                                     698    705                    728   734                                                                                                     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    511

Chain B from PDB  Type:PROTEIN  Length:142
 aligned with MLR_ARGIR | P13543 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:142
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153  
            MLR_ARGIR    14 PQKQIQEMKEAFSMIDVDRDGFVSKEDIKAISEQLGRAPDDKELTAMLKEAPGPLNFTMFLSIFSDKLSGTDSEETIRNAFAMFDEQETKKLNIEYIKDLLENMGDNFNKDEMRMTFKEAPVEGGKFDYVKFTAMIKGSGEE 155
               SCOP domains d1kqmb_ B: Myosin Essential Chain                                                                                                              SCOP domains
               CATH domains 1kqmB01 B:13-81 EF-hand                                              1kqmB02 B:82-149 EF-hand                                            ----- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.......hhhhhhhhhh......hhhhhhhhhh......hhhhhhhhhhh..............hhhhh......ee..hhhhhhhhh....hhhhhhhhhh.......eehhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --EF_HAND_2  PDB: B:15-50             ---------------------------------EF_HAND_2  PDB: B:84-119            ----------------------------------- PROSITE (2)
                PROSITE (3) ---------------EF_HAND_1    ------------------------------------------------------------------------------------------------------------------ PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kqm B  13 PQKQIQEMKEAFSMIDVDRDGFVSKEDIKAISEQLGRAPDDKELTAMLKEAPGPLNFTMFLSIFSDKLSGTDSEETIRNAFAMFDEQETKKLNIEYIKDLLENMGDNFNKDEMRMTFKEAPVEGGKFDYVKFTAMIKGSGEE 154
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain C from PDB  Type:PROTEIN  Length:153
 aligned with MLE_ARGIR | P07291 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:153
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152   
            MLE_ARGIR     3 KLSQDEIDDLKDVFELFDFWDGRDGAVDAFKLGDVCRCLGINPRNEDVFAVGGTHKMGEKSLPFEEFLPAYEGLMDCEQGTFADYMEAFKTFDREGQGFISGAELRHVLTALGERLSDEDVDEIIKLTDLQEDLEGNVKYEDFVKKVMAGPYP 155
               SCOP domains d1kqmc_ C: Myosin Regulatory Chain                                                                                                                        SCOP domains
               CATH domains -1kqmC01 C:3-80 EF-hand                                                        1kqmC02 C:81-152 EF-hand                                                -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...........ee..hhhhhhhhh....hhhhhh...........eehhhhhhhhhhhh..............hhhhh......eehhhhhhhhhhh....hhhhhhhhhhhh........eehhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----EF_HAND_2  PDB: C:6-43 UniProt: 7-44  -------------------------------------EF_HAND_2  PDB: C:81-116            -------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kqm C   2 KLSQDEIDDLKDVFELFDFWDGRDGAVDAFKLGDVCRCLGINPRNEDVFAVGGTHKMGEKSLPFEEFLPAYEGLMDCEQGTFADYMEAFKTFDREGQGFISGAELRHVLTALGERLSDEDVDEIIKLTDLQEDLEGNVKYEDFVKKVMAGPYP 154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: EF-hand (412)

Argopecten irradians. Organism_taxid: 31199. (5)

1a	1kqmC02	C:81-152
1b	1kqmB01	B:13-81
1c	1kqmB02	B:82-149
1d	1kqmC01	C:3-80

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MYS_ARGIR | P24733)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0005516	calmodulin binding	Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
	GO:0003774	motor activity	Catalysis of the generation of force resulting either in movement along a microfilament or microtubule, or in torque resulting in membrane scission, coupled to the hydrolysis of a nucleoside triphosphate.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0030016	myofibril	The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism.
	GO:0016459	myosin complex	A protein complex, formed of one or more myosin heavy chains plus associated light chains and other proteins, that functions as a molecular motor; uses the energy of ATP hydrolysis to move actin filaments or to move vesicles or other cargo on fixed actin filaments; has magnesium-ATPase activity and binds actin. Myosin classes are distinguished based on sequence features of the motor, or head, domain, but also have distinct tail regions that are believed to bind specific cargoes.
	GO:0032982	myosin filament	A protein complex containing myosin heavy chains, plus associated light chains and other proteins, in which the myosin heavy chains are arranged into a filament.

Chain B (MLR_ARGIR | P13543)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
cellular component
	GO:0016459	myosin complex	A protein complex, formed of one or more myosin heavy chains plus associated light chains and other proteins, that functions as a molecular motor; uses the energy of ATP hydrolysis to move actin filaments or to move vesicles or other cargo on fixed actin filaments; has magnesium-ATPase activity and binds actin. Myosin classes are distinguished based on sequence features of the motor, or head, domain, but also have distinct tail regions that are believed to bind specific cargoes.

Chain C (MLE_ARGIR | P07291)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
cellular component
	GO:0016459	myosin complex	A protein complex, formed of one or more myosin heavy chains plus associated light chains and other proteins, that functions as a molecular motor; uses the energy of ATP hydrolysis to move actin filaments or to move vesicles or other cargo on fixed actin filaments; has magnesium-ATPase activity and binds actin. Myosin classes are distinguished based on sequence features of the motor, or head, domain, but also have distinct tail regions that are believed to bind specific cargoes.

Asymmetric/Biological Unit
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1b7t	1B7T CONTAINS THE SAME PROTEIN COMPLEXED WITH MGADP.

Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

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