4BG4 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF LITOPENAEUS VANNAMEI ARGININE KINASE IN TERNARY COMPLEX WITH ARGININE, ADP-MG AND NO3

Authors :   A. A. Lopez-Zavala, K. D. Garcia-Orozco, J. S. Carrasco-Miranda, R. Sugich-Miranda, E. F. Velazquez-Contreras, M. F. Criscitiello, L E. Rudino-Pinera, R. R. Sotelo-Mundo

Date :   22 Mar 13 (Deposition) - 04 Sep 13 (Release) - 27 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Transferase, Binary Complex, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. A. Lopez-Zavala, K. D. Garcia-Orozco, J. S. Carrasco-Miranda, R. Sugich-Miranda, E. F. Velazquez-Contreras, M. F. Criscitiello, L. G. Brieba, E. Rudino-Pinera, R. R. Sotelo-Mundo
Crystal Structure Of Shrimp Arginine Kinase In Binary Complex With Arginine-A Molecular View Of The Phosphagen Precursor Binding To The Enzyme.
J. Bioenerg. Biomembr. V. 45 511 2013
PubMed-ID: 23873077 | Reference-DOI: 10.1007/S10863-013-9521-0

Molecule 1 - ARGININE KINASE
	Chains	:	A
	EC Number	:	2.7.3.3
	Organism Common	:	PACIFIC WHITE SHRIMP
	Organism Scientific	:	LITOPENAEUS VANNAMEI
	Organism Taxid	:	6689
	Tissue	:	TAIL MUSCLE

Molecule 2 - ARGININE KINASE
	Chains	:	B
	EC Number	:	2.7.3.3
	Organism Common	:	PACIFIC WHITE SHRIMP
	Organism Scientific	:	LITOPENAEUS VANNAMEI
	Organism Taxid	:	6689
	Tissue	:	TAIL MUSCLE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 12)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	ARG	2	Mod. Amino Acid	ARGININE
3	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
4	CSO	2	Mod. Amino Acid	S-HYDROXYCYSTEINE
5	MG	2	Ligand/Ion	MAGNESIUM ION
6	NO3	2	Ligand/Ion	NITRATE ION

Biological Unit 1 (5, 5)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	ARG	1	Mod. Amino Acid	ARGININE
3	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
4	CSO	1	Mod. Amino Acid	S-HYDROXYCYSTEINE
5	MG	-1	Ligand/Ion	MAGNESIUM ION
6	NO3	1	Ligand/Ion	NITRATE ION

Biological Unit 2 (5, 5)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	ARG	1	Mod. Amino Acid	ARGININE
3	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
4	CSO	1	Mod. Amino Acid	S-HYDROXYCYSTEINE
5	MG	-1	Ligand/Ion	MAGNESIUM ION
6	NO3	1	Ligand/Ion	NITRATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:122 , ARG A:124 , ARG A:126 , HIS A:185 , TRP A:221 , ARG A:229 , MET A:233 , ARG A:280 , SER A:282 , VAL A:283 , HIS A:284 , ARG A:309 , THR A:311 , ARG A:312 , GLY A:313 , GLU A:314 , ASP A:324 , NO3 A:405 , MG A:406 , HOH A:2167 , HOH A:2233 , HOH A:2242 , HOH A:2297 , HOH A:2330	BINDING SITE FOR RESIDUE ADP A 400
02	AC2	SOFTWARE	SER A:63 , GLY A:64 , VAL A:65 , GLY A:66 , TYR A:68 , GLU A:225 , CYS A:271 , GLU A:314 , NO3 A:405 , HOH A:2077 , HOH A:2091 , HOH A:2316	BINDING SITE FOR RESIDUE ARG A 403
03	AC3	SOFTWARE	ARG A:126 , GLU A:225 , ARG A:229 , ASN A:274 , ARG A:309 , GLU A:314 , ADP A:400 , ARG A:403 , MG A:406 , HOH A:2295 , HOH A:2314	BINDING SITE FOR RESIDUE NO3 A 405
04	AC4	SOFTWARE	ADP A:400 , NO3 A:405 , HOH A:2272 , HOH A:2273 , HOH A:2314	BINDING SITE FOR RESIDUE MG A 406
05	AC5	SOFTWARE	LEU A:46 , ASP A:52 , PRO A:138 , CYS A:139	BINDING SITE FOR RESIDUE BME A 409
06	AC6	SOFTWARE	SER B:122 , ARG B:124 , ARG B:126 , HIS B:185 , TRP B:221 , ARG B:229 , MET B:233 , ARG B:280 , SER B:282 , VAL B:283 , HIS B:284 , ARG B:309 , THR B:311 , ARG B:312 , GLY B:313 , GLU B:314 , ASP B:324 , NO3 B:405 , MG B:407 , HOH B:2179 , HOH B:2185 , HOH B:2210 , HOH B:2213 , HOH B:2254	BINDING SITE FOR RESIDUE ADP B 400
07	AC7	SOFTWARE	SER B:63 , GLY B:64 , VAL B:65 , GLY B:66 , TYR B:68 , GLU B:225 , CYS B:271 , THR B:273 , GLU B:314 , NO3 B:405 , HOH B:2062 , HOH B:2076 , HOH B:2247	BINDING SITE FOR RESIDUE ARG B 403
08	AC8	SOFTWARE	ARG B:126 , GLU B:225 , ARG B:229 , ASN B:274 , ARG B:309 , GLU B:314 , ADP B:400 , ARG B:403 , MG B:407 , HOH B:2228	BINDING SITE FOR RESIDUE NO3 B 405
09	AC9	SOFTWARE	ASP B:52 , CYS B:139	BINDING SITE FOR RESIDUE BME B 406
10	BC1	SOFTWARE	ADP B:400 , NO3 B:405 , HOH B:2210 , HOH B:2211 , HOH B:2245	BINDING SITE FOR RESIDUE MG B 407

(no "SS Bond" information available for 4BG4)

Asymmetric Unit

No.	Residues
1	Trp A:204	-	Pro A:205
2	Met B:1	-	Ala B:2
3	Trp B:204	-	Pro B:205

(no "SAP(SNP)/Variant" information available for 4BG4)

(no "PROSITE Motif" information available for 4BG4)

(no "Exon" information available for 4BG4)

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:356
 aligned with Q004B5_LITVA | Q004B5 from UniProtKB/TrEMBL  Length:356

    Alignment length:356
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      
         Q004B5_LITVA     1 MADAAVIEKLEAGFKKLEAATDCKSLLKKYLTKEVFDKLKDKRTSLGATLLDVIQSGVENLDSGVGIYAPDAEAYTLFAPLFDPIIEDYHVGFKQTDKHPNKDFGDVNSFVNVDPEGKFVISTRVRCGRSLQGYPFNPCLTESQYKEMEAKVSSTLSSLEGELKGTYYPLTGMSKEVQQKLIDDHFLFKEGDRFLQAANACRYWPAGRGIYHNDNKTFLVWVNEEDHLRIISMQMGGDLGQVFRRLTSAVNEIEKRIPFSHHDRLGFLTFCPTNLGTTVRASVHIKLPKLAANREKLEEVAGKYNLQVRGTRGEHTEAEGGIYDISNKRRMGLTEFQAVKEMQDGILELIKIEKEM 356
               SCOP domains d4bg4a1 A:1-95 automated matches                                                               d4bg4a2 A:96-356 automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh........hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh...............hhhhh.........eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeee....hhhhhhhhhhh.......hhhhhhh..........eeee.....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhh.....ee...ee...hhhhh....eeeeeee..hhhhhhhhhhhhhhhh.eeee............eeeeee......hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bg4 A   1 MADAAVIEKLEAGFKKLEAATDCKSLLKKYLTKEVFDKLKDKKTSLGATLLDVIQSGVENLDSGVGIYAPDAEAYTLFAPLFDPIIEDYHVGFKQTDKHPNKDFGDVNSFVNVDPEGKFVISTRVRCGRSMQGYPFNPCLTESQYKEMEAKVSSTLSSLEGELKGTYYPLTGMSKEVQQKLIDDHFLFKEGDRFLQAANScRYWPAGRGIYHNDNKTFLVWVNEEDHLRIISMQMGGDLGQVFRRLTSAVNEIEKRIPFSHHDRLGFLTFCPTNLGTTVRASVHIKLPKLAANREKLEEVAGKYNLQVRGTRGEHTEAEGGIYDISNKRRMGLTEFQAVKEMQDGILELIKIEKEM 356
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200|      210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      
                                                                                                                                                                                                                                  201-CSO

Chain B from PDB  Type:PROTEIN  Length:356
 aligned with Q004B5_LITVA | Q004B5 from UniProtKB/TrEMBL  Length:356

    Alignment length:356
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      
         Q004B5_LITVA     1 MADAAVIEKLEAGFKKLEAATDCKSLLKKYLTKEVFDKLKDKRTSLGATLLDVIQSGVENLDSGVGIYAPDAEAYTLFAPLFDPIIEDYHVGFKQTDKHPNKDFGDVNSFVNVDPEGKFVISTRVRCGRSLQGYPFNPCLTESQYKEMEAKVSSTLSSLEGELKGTYYPLTGMSKEVQQKLIDDHFLFKEGDRFLQAANACRYWPAGRGIYHNDNKTFLVWVNEEDHLRIISMQMGGDLGQVFRRLTSAVNEIEKRIPFSHHDRLGFLTFCPTNLGTTVRASVHIKLPKLAANREKLEEVAGKYNLQVRGTRGEHTEAEGGIYDISNKRRMGLTEFQAVKEMQDGILELIKIEKEM 356
               SCOP domains d4bg4b1 B:1-95 automated matches                                                               d4bg4b2 B:96-356 automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.........hhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh...............hhhhh.........eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeee....hhhhhhhhhhh.......hhhhhhh..........eeee.....eeeee.....eeeeeeee..hhhhhhhhhhhhhhhhhh.....ee...ee...hhhhh....eeeeeeehhhhhhhhhhhhhhhhhh.eeee............eeeeee......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bg4 B   1 MADAAVIEKLEAGFKKLEAATDCRSLLKKYLTKDVFDKLKDKKTSLGATLLDVIQSGVENLDSGVGIYAPDAEAYTLFAPLFDPIIEDYHVGFKQTDKHPNKDFGDVNSFVNVDPEGKFVISTRVRCGRSMQGYPFNPCLTESQYKEMEAKVSSTLSSLEGELKGTYYPLTGMSKEVQQKLIDDHFLFKEGDRFLQAANAcRYWPAGRGIYHNDNKTFLVWVNEEDHLRIISMQMGGDLGQVFRRLTSAVNEIEKRIPFSHHDRLGFLTFCPTNLGTTVRASVHIKLPKLAANREKLEEVAGKYNLQVRGTRGEHTEAEGGIYDISNKRRMGLTEFQAVKEMQDGILELIKIEKEM 356
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200|      210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      
                                                                                                                                                                                                                                  201-CSO

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 4BG4)

(no "Pfam Domain" information available for 4BG4)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q004B5_LITVA | Q004B5)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004054	arginine kinase activity	Catalysis of the reaction: L-arginine + ATP = N(omega)-phospho-L-arginine + ADP + 2 H(+).
	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: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.

Asymmetric Unit
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	Cis Peptide Bonds
		Met B:1 - Ala B:2	[ RasMol ]
		Trp A:204 - Pro A:205	[ RasMol ]
		Trp B:204 - Pro B:205	[ RasMol ]

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	4bg4
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	2.7.3.3
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(no "Related Entries Specified in the PDB File" available for 4BG4)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 12)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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