3K85 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A D-GLYCERO-D-MANNO-HEPTOSE 1-PHOSPHATE KINASE FROM BACTERIODES THETAIOTAOMICRON

Authors :   K. Palani, D. Kumaran, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   13 Oct 09 (Deposition) - 08 Dec 09 (Release) - 08 Dec 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.28

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

Keywords :   Kinase, Bacteriodes Thetaiotaomicron, Protein Structure Initiative Ii(Psi Ii), Nysgxrc, 11277B, Structural Genomics, New York Sgx Research Center For Structural Genomics, Atp-Binding, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Palani, D. Kumaran, S. K. Burley, S. Swaminathan
Crystal Structure Of A D-Glycero-D-Manno-Heptose 1-Phosphate Kinase From Bacteriodes Thetaiotaomicron
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - D-GLYCERO-D-MANNO-HEPTOSE 1-PHOSPHATE KINASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	BC-PSGX3 (BC)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	BT-0704, BT_0474
	Organism Scientific	:	BACTEROIDES THETAIOTAOMICRON
	Organism Taxid	:	818

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 18)

No.	Name	Count	Type	Full Name
1	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 18)

No.	Name	Count	Type	Full Name
1	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 36)

No.	Name	Count	Type	Full Name
1	MSE	36	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3K85)

(no "SS Bond" information available for 3K85)

Asymmetric Unit

No.	Residues
1	Ser A:21	-	Pro A:22
2	Ser B:21	-	Pro B:22

(no "SAP(SNP)/Variant" information available for 3K85)

(no "PROSITE Motif" information available for 3K85)

(no "Exon" information available for 3K85)

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:306
 aligned with Q8AAJ0_BACTN | Q8AAJ0 from UniProtKB/TrEMBL  Length:348

    Alignment length:341
                                    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       301       311       321       331       341 
         Q8AAJ0_BACTN     2 IVRSKAPLRLGLAGGGSDVSPYSDIYGGLILNATINLYAYCTIEETNSGRIEINAYDAQCCKSYLSMSQLEIDGEASLIKGVYNRIIRDYRLEPKSFKITTYNDAPAGSGLGTSSTMVVCILKAFIEWLSLPLGDYETSRLAYEIERKDLGLSGGKQDQYAAAFGGFNYMEFLQNDLVIVNPLKMKRWIVDELESSMVLYFTGRSRSSAAIINEQKKNTSEGNQTAIEAMHKIKQSAIDTKLALLKGDVGEFARILGEGWENKKKMAGAITNPMIQEAFDVATGAGAMAGKVSGAGGGGFIMFVVEPTRKEEVVRALNNLNGFVMPFQFIDDGAHGWKIYS 342
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.......hhhhhh.eeeeeeeeeeeeeeeeee....eeeeee....eeeeee..........hhhhhhhhhhhhhhh......eeeeeee........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeeeee...eeeeeee..hhhhhhhhhhheeee..---------------------...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..-----------............eeee...---..eeee.hhhhhhhhhhhhhh...............eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k85 A   2 LVRSKAPLRLGLAGGGSDVSPYSDIYGGLILNATINLYAYCTIEETNSGRIEINAYDAQCCKSYLSmSQLEIDGEASLIKGVYNRIIRDYRLEPKSFKITTYNDAPAGSGLGTSSTmVVCILKAFIEWLSLPLGDYETSRLAYEIERKDLGLSGGKQDQYAAAFGGFNYmEFLQNDLVIVNPLKmKRWIVDELESSmVLYFT---------------------QTAIEAmHKIKQSAIDTKLALLKGDVGEFARILGEGWENKKK-----------EAFDVATGAGAmAGKVSGA---GFImFVVEPTRKEEVVRALNNLNGFVmPFQFIDDGAHGWKIYS 342
                                    11        21        31        41        51        61      | 71        81        91       101       111      |121       131       141       151       161       171       181    |  191      |201 |       -         -   |   231       241       251       261    |    -      |281       291    |  301 |     311       321    |  331       341 
                                                                                             68-MSE                                           118-MSE                                              171-MSE        186-MSE     198-MSE3                   225     |                                266         278        289-MSE296 300  |                    326-MSE            
                                                                                                                                                                                                                                                               231-MSE                                                                 303-MSE

Chain B from PDB  Type:PROTEIN  Length:306
 aligned with Q8AAJ0_BACTN | Q8AAJ0 from UniProtKB/TrEMBL  Length:348

    Alignment length:341
                                    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       301       311       321       331       341 
         Q8AAJ0_BACTN     2 IVRSKAPLRLGLAGGGSDVSPYSDIYGGLILNATINLYAYCTIEETNSGRIEINAYDAQCCKSYLSMSQLEIDGEASLIKGVYNRIIRDYRLEPKSFKITTYNDAPAGSGLGTSSTMVVCILKAFIEWLSLPLGDYETSRLAYEIERKDLGLSGGKQDQYAAAFGGFNYMEFLQNDLVIVNPLKMKRWIVDELESSMVLYFTGRSRSSAAIINEQKKNTSEGNQTAIEAMHKIKQSAIDTKLALLKGDVGEFARILGEGWENKKKMAGAITNPMIQEAFDVATGAGAMAGKVSGAGGGGFIMFVVEPTRKEEVVRALNNLNGFVMPFQFIDDGAHGWKIYS 342
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------GHMP_kinases_N-3k85B01 B:99-167                                      ------------------------------------                     ----------------GHMP_kinases_C-3k85B03 B:2           41-322                                       -------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------GHMP_kinases_N-3k85B02 B:99-167                                      ------------------------------------                     ----------------GHMP_kinases_C-3k85B04 B:2           41-322                                       -------------------- Pfam domains (2)
         Sec.struct. author .eeeeeeeeeeee.......hhhhhhheeeeeeeeeeeeeeeeee....eeeeee.hhheeeeee..........hhhhhhhhhhhhhhhh.....eeeeeee........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhhhh.eeeeeee...eeeeeee..hhhhhhhhhhheeeee.---------------------.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..-----------...hhhhhh...eeee...---..eeee.hhhhhhhhhhhhhhh..eee.........eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k85 B   2 LVRSKAPLRLGLAGGGSDVSPYSDIYGGLILNATINLYAYCTIEETNSGRIEINAYDAQCCKSYLSmSQLEIDGEASLIKGVYNRIIRDYRLEPKSFKITTYNDAPAGSGLGTSSTmVVCILKAFIEWLSLPLGDYETSRLAYEIERKDLGLSGGKQDQYAAAFGGFNYmEFLQNDLVIVNPLKmKRWIVDELESSmVLYFT---------------------QTAIEAmHKIKQSAIDTKLALLKGDVGEFARILGEGWENKKK-----------EAFDVATGAGAmAGKVSGA---GFImFVVEPTRKEEVVRALNNLNGFVmPFQFIDDGAHGWKIYS 342
                                    11        21        31        41        51        61      | 71        81        91       101       111      |121       131       141       151       161       171       181    |  191      |201 |       -         -   |   231       241       251       261    |    -      |281       291    |  301 |     311       321    |  331       341 
                                                                                             68-MSE                                           118-MSE                                              171-MSE        186-MSE     198-MSE3                   225     |                                266         278        289-MSE296 300  |                    326-MSE            
                                                                                                                                                                                                                                                               231-MSE                                                                 303-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 '\|'

(no "SCOP Domain" information available for 3K85)

(no "CATH Domain" information available for 3K85)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: S5 (103)

Family: GHMP_kinases_N (23)

Bacteroides thetaiotaomicron (1)

1a	GHMP_kinases_N-3k85B01	B:99-167
1b	GHMP_kinases_N-3k85B02	B:99-167

Clan: no clan defined [family: GHMP_kinases_C] (13)

Family: GHMP_kinases_C (13)

Bacteroides thetaiotaomicron (1)

2a	GHMP_kinases_C-3k85B03	B:241-322
2b	GHMP_kinases_C-3k85B04	B:241-322

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q8AAJ0_BACTN | Q8AAJ0)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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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	Sites
(no "Sites" information available for 3k85)

	Cis Peptide Bonds
		Ser A:21 - Pro A:22	[ RasMol ]
		Ser B:21 - Pro B:22	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Description

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Ligands, Modified Residues, Ions (1, 18)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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