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Title :   CRYSTAL STRUCTURE OF NUCLEOSIDE KINASE FROM CHLOROBIUM TEPIDUM IN COMPLEX WITH AMP

Authors :   L. Satyanarayana, S. K. Burley, S. Swaminathan, New York Sgx Resear For Structural Genomics (Nysgxrc)

Date :   22 Oct 09 (Deposition) - 03 Nov 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.88

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

Keywords :   Kinase, Pfkb, Nucleoside Kinase, Amp, Psi-Ii, Nysgxrc, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Satyanarayana, S. K. Burley, S. Swaminathan
Crystal Structure Of Nucleoside Kinase From Chlorobium Tepidum In Complex With Amp
To Be Published
PubMed: search

Molecule 1 - CARBOHYDRATE KINASE, PFKB FAMILY
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PSGX32 (BC)
	Expression System Strain	:	BL21 (DE3) CODON+RIL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CT0976
	Organism Scientific	:	CHLOROBACULUM TEPIDUM
	Organism Taxid	:	1097

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 16)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	GOL	2	Ligand/Ion	GLYCEROL
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 16)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	GOL	2	Ligand/Ion	GLYCEROL
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (3, 8)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	GOL	1	Ligand/Ion	GLYCEROL
3	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:8 , ASP A:12 , GLY A:27 , TYR A:31 , PHE A:81 , TRP A:83 , ARG A:94 , ASN A:125 , MSE A:149 , PHE A:151 , TRP A:152 , GLY A:234 , GLY A:236 , ASP A:237 , HOH A:330 , HOH A:336 , HOH A:400 , HOH A:435	BINDING SITE FOR RESIDUE AMP A 509
2	AC2	SOFTWARE	ASP A:147 , ILE A:171 , VAL A:172 , ASN A:173 , GLU A:176 , GLY A:236 , ASP A:237 , HOH A:313 , HOH A:318	BINDING SITE FOR RESIDUE GOL A 501
3	AC3	SOFTWARE	SER B:8 , ASP B:12 , GLY B:27 , TYR B:31 , PHE B:81 , TRP B:83 , ARG B:94 , ASN B:125 , MSE B:149 , PHE B:151 , TRP B:152 , GLY B:234 , ASP B:237 , HOH B:325 , HOH B:326 , HOH B:327	BINDING SITE FOR RESIDUE AMP B 509
4	AC4	SOFTWARE	ASP B:147 , ASN B:173 , GLU B:176 , GLY B:236 , ASP B:237 , HOH B:315 , HOH B:448	BINDING SITE FOR RESIDUE GOL B 501

(no "SS Bond" information available for 3KD6)

(no "Cis Peptide Bond" information available for 3KD6)

(no "SAP(SNP)/Variant" information available for 3KD6)

(no "PROSITE Motif" information available for 3KD6)

(no "Exon" information available for 3KD6)

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:300
 aligned with Q8KDR9_CHLTE | Q8KDR9 from UniProtKB/TrEMBL  Length:304

    Alignment length:300
                                    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
         Q8KDR9_CHLTE     1 MSLLVIGSLAFDDIETPFGRSDNTLGGSSTYIALSASYFTDEPIRMVGVVGSDFGKEHFDLLHAKNIDTRGIQVIEDGKTFRWAGRYHYDMNTRDTLDTQLNVFAEFDPHVPQYYRDSKFVCLGNIDPELQLKVLDQIDDPKLVVCDTMNFWIEGKPEELKKVLARVDVFIVNDSEARLLSGDPNLVKTARIIREMGPKTLIIKKGEHGALLFTDNGIFAAPAFPLESIYDPTGAGDTFAGGFIGHLARCGNTSEAEMRKAVLYGSAMASFCVEQFGPYRYNDLDLLEVDDRYQSFLELS 300
               SCOP domains d3kd6a_ A: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eeeeee....eeeeeeehhhhhhhhhhh......eeeeeeee...hhhhhhhhhhh.eeeeeeeee.....eeeeeee......eeeeeeehhhhh......hhhhh...eeee...hhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhh...eeeeehhhhhhhhh..hhhhhhhhhhh....eeeee.....eeeee..eeeee............hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kd6 A   1 LSLLVIGSLAFDDIETPFGRSDNTLGGSSTYIALSASYFTDEPIRmVGVVGSDFGKEHFDLLHAKNIDTRGIQVIEDGKTFRWAGRYHYDmNTRDTLDTQLNVFAEFDPHVPQYYRDSKFVCLGNIDPELQLKVLDQIDDPKLVVCDTmNFWIEGKPEELKKVLARVDVFIVNDSEARLLSGDPNLVKTARIIREmGPKTLIIKKGEHGALLFTDNGIFAAPAFPLESIYDPTGAGDTFAGGFIGHLARCGNTSEAEmRKAVLYGSAmASFCVEQFGPYRYNDLDLLEVDDRYQSFLELS 300
                                    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
                                                                        46-MSE                                       91-MSE                                                   149-MSE                                        196-MSE                                                       258-MSE   268-MSE

Chain B from PDB  Type:PROTEIN  Length:298
 aligned with Q8KDR9_CHLTE | Q8KDR9 from UniProtKB/TrEMBL  Length:304

    Alignment length:298
                                    11        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        
         Q8KDR9_CHLTE     2 SLLVIGSLAFDDIETPFGRSDNTLGGSSTYIALSASYFTDEPIRMVGVVGSDFGKEHFDLLHAKNIDTRGIQVIEDGKTFRWAGRYHYDMNTRDTLDTQLNVFAEFDPHVPQYYRDSKFVCLGNIDPELQLKVLDQIDDPKLVVCDTMNFWIEGKPEELKKVLARVDVFIVNDSEARLLSGDPNLVKTARIIREMGPKTLIIKKGEHGALLFTDNGIFAAPAFPLESIYDPTGAGDTFAGGFIGHLARCGNTSEAEMRKAVLYGSAMASFCVEQFGPYRYNDLDLLEVDDRYQSFLEL 299
               SCOP domains d3kd6b_ B: automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----PfkB-3kd6B01 B:7-283                                                                                                                                                                                                                                                                 ---------------- Pfam domains (1)
           Pfam domains (2) -----PfkB-3kd6B02 B:7-283                                                                                                                                                                                                                                                                 ---------------- Pfam domains (2)
         Sec.struct. author .eeee...eeeeee....eeeeeeehhhhhhhhhhh.......eeeeeee...hhhhhhhhhhh..eeeeeeee.....eeeeeee......eeeeeeehhhhh......hhhhh...eeee...hhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhh...eeeeehhhhhhhhh..hhhhhhhhhhh....eeeee.....eeeee..eeeee............hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kd6 B   2 SLLVIGSLAFDDIETPFGRSDNTLGGSSTYIALSASYFTDEPIRmVGVVGSDFGKEHFDLLHAKNIDTRGIQVIEDGKTFRWAGRYHYDmNTRDTLDTQLNVFAEFDPHVPQYYRDSKFVCLGNIDPELQLKVLDQIDDPKLVVCDTmNFWIEGKPEELKKVLARVDVFIVNDSEARLLSGDPNLVKTARIIREmGPKTLIIKKGEHGALLFTDNGIFAAPAFPLESIYDPTGAGDTFAGGFIGHLARCGNTSEAEmRKAVLYGSAmASFCVEQFGPYRYNDLDLLEVDDRYQSFLEL 299
                                    11        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        
                                                                       46-MSE                                       91-MSE                                                   149-MSE                                        196-MSE                                                       258-MSE   268-MSE

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Ribokinase-like (226)

Superfamily: Ribokinase-like (189)

Family: automated matches (88)

Protein domain: automated matches (88)

Chlorobaculum tepidum [TaxId: 1097] (1)

1a	d3kd6a_	A:
1b	d3kd6b_	B:

(no "CATH Domain" information available for 3KD6)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ribokinase (55)

Family: PfkB (39)

Chlorobium tepidum (1)

1a	PfkB-3kd6B01	B:7-283
1b	PfkB-3kd6B02	B:7-283

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q8KDR9_CHLTE | Q8KDR9)

molecular function
	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:0016773	phosphotransferase activity, alcohol group as acceptor	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
	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.
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.

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Biological Units
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Description

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Ligands, Modified Residues, Ions (3, 16)

Sites (4, 4)

SS Bonds (0, 0)

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