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Title :   THE 2.1 STRUCTURE OF T. CALIFORNICA CREATINE KINASE COMPLEXED WITH THE TRANSITION-STATE ANALOGUE COMPLEX, ADP-MG 2+ /NO3-/CREATINE

Authors :   S. D. Lahiri, P. F. Wang, P. C. Babbitt, M. J. Mcleish, G. L. Kenyon, K. N. Allen

Date :   25 Apr 05 (Deposition) - 03 May 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Creatine Kinase, Transition-State Analogue Complex, Guanidino Kinases, Phosphocreatine, Arginine Kinases, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. D. Lahiri, P. F. Wang, P. C. Babbitt, M. J. Mcleish, G. L. Kenyon, K. N. Allen
The 2. 1 A Structure Of Torpedo Californica Creatine Kinase Complexed With The Adp-Mg(2+)-No3(-)-Creatine Transition-State Analogue Complex
Biochemistry V. 41 13861 2002
PubMed-ID: 12437342 | Reference-DOI: 10.1021/BI026655P
(for further references see the PDB file header)

Molecule 1 - CREATINE KINASE, M CHAIN
	Chains	:	A, B
	EC Number	:	2.7.3.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET17B
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	FSCCKPA
	Organism Common	:	PACIFIC ELECTRIC RAY
	Organism Scientific	:	TORPEDO CALIFORNICA
	Organism Taxid	:	7787
	Synonym	:	M-CK

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 6)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	IOM	1	Ligand/Ion	(DIAMINOMETHYL-METHYL-AMINO)-ACETIC ACID
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	NO3	1	Ligand/Ion	NITRATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ADP B:401 , NO3 B:405 , HOH B:474 , HOH B:475 , HOH B:479 , HOH B:484	BINDING SITE FOR RESIDUE MG B 403
2	AC2	SOFTWARE	GLU A:232 , ADP A:400 , HOH A:459 , HOH A:461 , HOH A:462 , HOH A:463	BINDING SITE FOR RESIDUE MG A 404
3	AC3	SOFTWARE	GLU B:232 , ARG B:236 , ASN B:286 , ARG B:320 , ADP B:401 , IOM B:402 , MG B:403 , HOH B:469	BINDING SITE FOR RESIDUE NO3 B 405
4	AC4	SOFTWARE	SER A:128 , ARG A:130 , ARG A:132 , HIS A:191 , TRP A:228 , ARG A:292 , GLY A:294 , VAL A:295 , HIS A:296 , ARG A:320 , THR A:322 , ASP A:335 , MG A:404 , HOH A:446 , HOH A:458 , HOH A:459 , HOH A:462	BINDING SITE FOR RESIDUE ADP A 400
5	AC5	SOFTWARE	SER B:128 , ARG B:130 , ARG B:132 , HIS B:191 , TRP B:228 , ARG B:236 , ARG B:292 , GLY B:294 , VAL B:295 , HIS B:296 , ARG B:320 , THR B:322 , GLY B:323 , GLY B:324 , VAL B:325 , ASP B:335 , MG B:403 , NO3 B:405 , HOH B:424 , HOH B:442 , HOH B:460 , HOH B:480 , HOH B:484	BINDING SITE FOR RESIDUE ADP B 401
6	AC6	SOFTWARE	ILE B:69 , THR B:71 , VAL B:72 , LEU B:201 , GLU B:232 , CYS B:283 , VAL B:325 , NO3 B:405 , HOH B:426 , HOH B:462 , HOH B:481	BINDING SITE FOR RESIDUE IOM B 402

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

Asymmetric/Biological Unit

No.	Residues
1	Trp A:211	-	Pro A:212
2	Trp B:211	-	Pro B:212

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

Asymmetric/Biological Unit (3, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHOSPHAGEN_KINASE_N	PS51509	Phosphagen kinase N-terminal domain profile.	KCRM_TETCF	11-98	1	B:11-98
2	PHOSPHAGEN_KINASE_C	PS51510	Phosphagen kinase C-terminal domain profile.	KCRM_TETCF	125-367	2	A:125-367 B:125-367
3	PHOSPHAGEN_KINASE	PS00112	Phosphagen kinase active site signature.	KCRM_TETCF	283-289	2	A:283-289 B:283-289

(no "Exon" information available for 1VRP)

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:370
 aligned with KCRM_TETCF | P04414 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:370
                                    21        31        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
           KCRM_TETCF    12 LNYSAAEEFPDLSKHNNHMAKALTLDIYKKLRDKETPSGFTLDDIIQTGVDNPGHPFIMTVGCVAGDEECYEVFKDLFDPVIEDRHGGYKPTDKHKTDLNQENLKGGDDLDPNYVLSSRVRTGRSIKGIALPPHCSRGERRLVEKLCIDGLATLTGEFQGKYYPLSSMSDAEQQQLIDDHFLFDKPISPLLLASGMARDWPDGRGIWHNNDKTFLVWVNEEDHLRVISMQKGGNMKEVFRRFCVGLKKIEDIFVKAGRGFMWNEHLGYVLTCPSNLGTGLRGGVHVKIPHLCKHEKFSEVLKRTRLQKRGTGGVDTAAVGSIYDISNADRLGFSEVEQVQMVVDGVKLMVEMEKRLENGKSIDDLMPAQK 381
               SCOP domains d1vrpa1 A:12-102 Creatine kinase, N-domain                                                 d1vrpa2 A:103-381 Creatine kinase, C-terminal domain                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1vrpA01 A:12-102 Transferase Creatine Kinase, Chain A, domain 1                            --1vrpA02 A:105-381 Creatine Kinase; Chain                                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh.............hhhhh..........eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhh........hhhhhh...........eeeee....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh.....ee...ee...hhhhh....eeeeeee..hhhhh.hhhhhhhhhheeeee...........eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PHOSPHAGEN_KINASE_N  PDB: - UniProt: 11-98                                             --------------------------PHOSPHAGEN_KINASE_C  PDB: A:125-367 UniProt: 125-367                                                                                                                                                                                               -------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PHOSPHA-------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vrp A  12 LNYSAAEEFPDLSKHNNHMAKALTLDIYKKLRDKETPSGFTLDDIIQTGVDNPGHPFIMTVGCVAGDEECYEVFKDLFDPVIEDRHGGYKPTDKHKTDLNQENLKGGDDLDPNYVLSSRVRTGRSIKGIALPPHCSRGERRLVEKLCIDGLATLTGEFQGKYYPLSSMSDAEQQQLIDDHFLFDKPISPLLLASGMARDWPDGRGIWHNNDKTFLVWVNEEDHLRVISMQKGGNMKEVFRRFCVGLKKIEDIFVKAGRGFMWNEHLGYVLTCPSNLGTGLRGGVHVKIPHLCKHEKFSEVLKRTRLQKRGTGGVDTAAVGSIYDISNADRLGFSEVEQVQMVVDGVKLMVEMEKRLENGKSIDDLMPAQK 381
                                    21        31        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

Chain B from PDB  Type:PROTEIN  Length:374
 aligned with KCRM_TETCF | P04414 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:374
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377    
           KCRM_TETCF     8 NKWKLNYSAAEEFPDLSKHNNHMAKALTLDIYKKLRDKETPSGFTLDDIIQTGVDNPGHPFIMTVGCVAGDEECYEVFKDLFDPVIEDRHGGYKPTDKHKTDLNQENLKGGDDLDPNYVLSSRVRTGRSIKGIALPPHCSRGERRLVEKLCIDGLATLTGEFQGKYYPLSSMSDAEQQQLIDDHFLFDKPISPLLLASGMARDWPDGRGIWHNNDKTFLVWVNEEDHLRVISMQKGGNMKEVFRRFCVGLKKIEDIFVKAGRGFMWNEHLGYVLTCPSNLGTGLRGGVHVKIPHLCKHEKFSEVLKRTRLQKRGTGGVDTAAVGSIYDISNADRLGFSEVEQVQMVVDGVKLMVEMEKRLENGKSIDDLMPAQK 381
               SCOP domains d1vrpb1 B:8-102 Creatine kinase, N-domain                                                      d1vrpb2 B:103-381 Creatine kinase, C-terminal domain                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1vrpB01 B:8-102 Transferase Creatine Kinase, Chain A, domain 1                                 --1vrpB02 B:105-381 Creatine Kinase; Chain                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh.............hhhhh..........eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhh........hhhhhhh..........eeeee....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhh.....ee...ee...hhhhh....eeeeeee..hhhhh.hhhhhhhhhheeee............eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---PHOSPHAGEN_KINASE_N  PDB: B:11-98 UniProt: 11-98                                        --------------------------PHOSPHAGEN_KINASE_C  PDB: B:125-367 UniProt: 125-367                                                                                                                                                                                               -------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PHOSPHA-------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vrp B   8 NKWKLNYSAAEEFPDLSKHNNHMAKALTLDIYKKLRDKETPSGFTLDDIIQTGVDNPGHPFIMTVGCVAGDEECYEVFKDLFDPVIEDRHGGYKPTDKHKTDLNQENLKGGDDLDPNYVLSSRVRTGRSIKGIALPPHCSRGERRLVEKLCIDGLATLTGEFQGKYYPLSSMSDAEQQQLIDDHFLFDKPISPLLLASGMARDWPDGRGIWHNNDKTFLVWVNEEDHLRVISMQKGGNMKEVFRRFCVGLKKIEDIFVKAGRGFMWNEHLGYVLTCPSNLGTGLRGGVHVKIPHLCKHEKFSEVLKRTRLQKRGTGGVDTAAVGSIYDISNADRLGFSEVEQVQMVVDGVKLMVEMEKRLENGKSIDDLMPAQK 381
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377

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: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Creatine Kinase; Chain A, domain 2 (27)

Homologous Superfamily: Creatine Kinase; Chain (27)

Pacific electric ray (Torpedo californica) (1)

1a	1vrpA02	A:105-381
1b	1vrpB02	B:105-381

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Transferase Creatine Kinase; Chain A, domain 1 (26)

Homologous Superfamily: Transferase Creatine Kinase, Chain A, domain 1 (26)

Pacific electric ray (Torpedo californica) (1)

2a	1vrpB01	B:8-102
2b	1vrpA01	A:12-102

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (KCRM_TETCF | P04414)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004111	creatine kinase activity	Catalysis of the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+).
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016772	transferase activity, transferring phosphorus-containing groups	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Trp A:211 - Pro A:212	[ RasMol ]
		Trp B:211 - Pro B:212	[ RasMol ]

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	2.7.3.2
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1bg0	TRANSITION STATE STRUCTURE OF ARGININE KINASE
1g0w	CRYSTAL STRUCTURE OF BOVINE RETINAL CREATINE KINASE
1qh4	CHICKEN BRAIN CREATINE KINASE
2crk	MUSCLE CREATINE KINASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 5)

Exons (0, 0)

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SCOP Domains (2, 4)

CATH Domains (2, 4)

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Gene Ontology (9, 9)

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