1KO8 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF GLUCONATE KINASE

Authors :   L. Kraft, G. A. Sprenger, Y. Lindqvist

Date :   20 Dec 01 (Deposition) - 29 May 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Alfa/Beta, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Kraft, G. A. Sprenger, Y. Lindqvist
Conformational Changes During The Catalytic Cycle Of Gluconate Kinase As Revealed By X-Ray Crystallography.
J. Mol. Biol. V. 318 1057 2002
PubMed-ID: 12054802 | Reference-DOI: 10.1016/S0022-2836(02)00215-2
(for further references see the PDB file header)

Molecule 1 - GLUCONATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.1.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PJF119EH
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	GNTK
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	THERMORESISTANT GLUCONOKINASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	6PG	2	Ligand/Ion	6-PHOSPHOGLUCONIC ACID
2	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:17 , GLY A:18 , ASP A:40 , LEU A:121 , HIS A:127 , MG A:201 , HOH A:513 , HOH A:514 , HOH A:515 , HOH A:516 , HOH A:517	BINDING SITE FOR RESIDUE 6PG A 502
2	AC2	SOFTWARE	SER B:17 , GLY B:18 , LYS B:21 , HOH B:510 , HOH B:511 , HOH B:512 , HOH B:513	BINDING SITE FOR RESIDUE 6PG B 503
3	AC3	SOFTWARE	SER A:22 , 6PG A:502 , HOH A:512 , HOH A:513 , HOH A:515 , HOH A:516	BINDING SITE FOR RESIDUE MG A 201

(no "SS Bond" information available for 1KO8)

(no "Cis Peptide Bond" information available for 1KO8)

(no "SAP(SNP)/Variant" information available for 1KO8)

(no "PROSITE Motif" information available for 1KO8)

(no "Exon" information available for 1KO8)

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:172
 aligned with GNTK_ECOLI | P46859 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:172
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172  
           GNTK_ECOLI     3 TTNHDHHIYVLMGVSGSGKSAVASEVAHQLHAAFLDGDFLHPRRNIEKMASGEPLNDDDRKPWLQALNDAAFAMQRTNKVSLIVCSALKKHYRDLLREGNPNLSFIYLKGDFDVIESRLKARKGHFFKTQMLVTQFETLQEPGADETDVLVVDIDQPLEGVVASTIEVIKKG 174
               SCOP domains d1ko8a_ A: Gluconate kinase                                                                                                                                                  SCOP domains
               CATH domains 1ko8A00 A:3-174 P-loop containing nucleotide triphosphate hydrolases                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.....hhhhhhhhhhhh...eeee.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhh....eeeeeee.hhhhhhhhhh.......hhhhhhhhhhhh.........eeeee...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ko8 A   3 TTNHDHHIYVLMGVSGSGKSAVASEVAHQLHAAFLDGDFLHPRRNIEKMASGEPLNDDDRKPWLQALNDAAFAMQRTNKVSLIVCSALKKHYRDLLREGNPNLSFIYLKGDFDVIESRLKARKGHFFKTQMLVTQFETLQEPGADETDVLVVDIDQPLEGVVASTIEVIKKG 174
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain B from PDB  Type:PROTEIN  Length:168
 aligned with GNTK_ECOLI | P46859 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:172
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172  
           GNTK_ECOLI     3 TTNHDHHIYVLMGVSGSGKSAVASEVAHQLHAAFLDGDFLHPRRNIEKMASGEPLNDDDRKPWLQALNDAAFAMQRTNKVSLIVCSALKKHYRDLLREGNPNLSFIYLKGDFDVIESRLKARKGHFFKTQMLVTQFETLQEPGADETDVLVVDIDQPLEGVVASTIEVIKKG 174
               SCOP domains d1ko8b_ B: Gluconate kinase                                                                                                                                                  SCOP domains
               CATH domains 1ko8B00 B:3-174 P-loop containing nucleotide triphosphate hydrolases                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.....hhhhhhhhhhhh...eeee.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhh....eeeeeee.hhhhhhhhhh----...hhhhhhhhhhhh.........eeeee...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ko8 B   3 TTNHDHHIYVLMGVSGSGKSAVASEVAHQLHAAFLDGDFLHPRRNIEKMASGEPLNDDDRKPWLQALNDAAFAMQRTNKVSLIVCSALKKHYRDLLREGNPNLSFIYLKGDFDVIESRLK----HFFKTQMLVTQFETLQEPGADETDVLVVDIDQPLEGVVASTIEVIKKG 174
                                    12        22        32        42        52        62        72        82        92       102       112       122    |  132       142       152       162       172  
                                                                                                                                                 122  127

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Gluconate kinase (6)

Protein domain: Gluconate kinase (6)

Escherichia coli [TaxId: 562] (6)

1a	d1ko8a_	A:
1b	d1ko8b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Escherichia coli. Organism_taxid: 562. (54)

1a	1ko8A00	A:3-174
1b	1ko8B00	B:3-174

(no "Pfam Domain" information available for 1KO8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GNTK_ECOLI | P46859)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0046316	gluconokinase activity	Catalysis of the reaction: D-gluconate + ATP = 6-phospho-D-gluconate + 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.
biological process
	GO:0046177	D-gluconate catabolic process	The chemical reactions and pathways resulting in the breakdown of D-gluconate, the anion of D-gluconic acid, the aldonic acid derived from glucose.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	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/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		6PG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ko8)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1ko8
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	GNTK_ECOLI \| P46859
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.1.12
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	GNTK_ECOLI \| P46859
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	GNTK_ECOLI \| P46859	:	1knq 1ko1 1ko4 1ko5 1kof

1knq	1KNQ CONTAINS THE SAME PROTEIN, SPACE GROUP P212121.
1ko1	1KO1 CONTAINS THE SAME PROTEIN, SPACE GROUP C2.
1ko4	1KO4 CONTAINS THE SAME PROTEIN, SPACE GROUP P21212.
1ko5	1KO5 CONTAINS THE SAME PROTEIN COMPLEXED WITH ATP.
1kof	1KOF CONTAINS THE SAME PROTEIN COMPLEXED WITH AMPPCP.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File