Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF SULFOLOBUS SOLFATARICUS 2-KETO-3-DEOXYGLUCONATE KINASE
 
Authors :  J. A. Potter, A. Theodossis, M. Kerou, H. J. Lamble, S. D. Bull, D. W. Houg M. J. Danson, G. L. Taylor
Date :  27 Jul 07  (Deposition) - 07 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Kinase, Transferase, Pfkb Family Carbohydrate Kinase, 2- Keto-3-Deoxygluconate Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Potter, M. Kerou, H. J. Lamble, S. D. Bull, D. W. Hough, M. J. Danson G. L. Taylor
The Structure Of Sulfolobus Solfataricus 2-Keto-3- Deoxygluconate Kinase.
Acta Crystallogr. , Sect. D V. 64 1283 2008
PubMed-ID: 19018105  |  Reference-DOI: 10.1107/S0907444908036111

(-) Compounds

Molecule 1 - FRUCTOKINASE
    Chains: A, B, C
    EC Number: 2.7.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Synonym: 2-KETO-3-DEOXYGLUCONATE KINASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2V78)

(-) Sites  (0, 0)

(no "Site" information available for 2V78)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V78)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Tyr A:96 -Pro A:97
2Tyr B:96 -Pro B:97
3Tyr C:96 -Pro C:97

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V78)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V78)

(-) Exons   (0, 0)

(no "Exon" information available for 2V78)

(-) Sequences/Alignments

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:311
 aligned with KDGK_SULSO | Q97U29 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:311
                                    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 
           KDGK_SULSO     2 VDVIALGEPLIQFNSFNPGPLRFVNYFEKHVAGSELNFCIAVVRNHLSCSLIARVGNDEFGKNIIEYSRAQGIDTSHIKVDNESFTGIYFIQRGYPIPMKSELVYYRKGSAGSRLSPEDINENYVRNSRLVHSTGITLAISDNAKEAVIKAFELAKSRSLDTNIRPKLWSSLEKAKETILSILKKYDIEVLITDPDDTKILLDVTDPDEAYRKYKELGVKVLLYKLGSKGAIAYKDNVKAFKDAYKVPVEDPTGAGDAMAGTFVSLYLQGKDIEYSLAHGIAASTLVITVRGDNELTPTLEDAERFLNEFK 312
               SCOP domains d2v78a_ A: automated matches                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeee....hhhhh.eeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh......eeee......eeeeee.......eeeeee....hhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh..eeee...hhhhh.hhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhh..hhhhhhhhhhhh.eeeeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v78 A   2 VDVIALGEPLIQFNSFNPGPLRFVNYFEKHVAGSELNFCIAVVRNHLSCSLIARVGNDEFGKNIIEYSRAQGIDTSHIKVDNESFTGIYFIQRGYPIPMKSELVYYRKGSAGSRLSPEDINENYVRNSRLVHSTGITLAISDNAKEAVIKAFELAKSRSLDTNIRPKLWSSLEKAKETILSILKKYDIEVLITDPDDTKILLDVTDPDEAYRKYKELGVKVLLYKLGSKGAIAYKDNVKAFKDAYKVPVEDPTGAGDAMAGTFVSLYLQGKDIEYSLAHGIAASTLVITVRGDNELTPTLEDAERFLNEFK 312
                                    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 


Chain B from PDB  Type:PROTEIN  Length:311
 aligned with KDGK_SULSO | Q97U29 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:311
                                    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 
           KDGK_SULSO     2 VDVIALGEPLIQFNSFNPGPLRFVNYFEKHVAGSELNFCIAVVRNHLSCSLIARVGNDEFGKNIIEYSRAQGIDTSHIKVDNESFTGIYFIQRGYPIPMKSELVYYRKGSAGSRLSPEDINENYVRNSRLVHSTGITLAISDNAKEAVIKAFELAKSRSLDTNIRPKLWSSLEKAKETILSILKKYDIEVLITDPDDTKILLDVTDPDEAYRKYKELGVKVLLYKLGSKGAIAYKDNVKAFKDAYKVPVEDPTGAGDAMAGTFVSLYLQGKDIEYSLAHGIAASTLVITVRGDNELTPTLEDAERFLNEFK 312
               SCOP domains d2v78b_ B: automated matches                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeee....hhhhh.eeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh......eeee......eeeeee.......eeeeee....hhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh..eeee...hhhhh.hhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhh..hhhhhhhhhhhh.eeeeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v78 B   2 VDVIALGEPLIQFNSFNPGPLRFVNYFEKHVAGSELNFCIAVVRNHLSCSLIARVGNDEFGKNIIEYSRAQGIDTSHIKVDNESFTGIYFIQRGYPIPMKSELVYYRKGSAGSRLSPEDINENYVRNSRLVHSTGITLAISDNAKEAVIKAFELAKSRSLDTNIRPKLWSSLEKAKETILSILKKYDIEVLITDPDDTKILLDVTDPDEAYRKYKELGVKVLLYKLGSKGAIAYKDNVKAFKDAYKVPVEDPTGAGDAMAGTFVSLYLQGKDIEYSLAHGIAASTLVITVRGDNELTPTLEDAERFLNEFK 312
                                    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 


Chain C from PDB  Type:PROTEIN  Length:311
 aligned with KDGK_SULSO | Q97U29 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:311
                                    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 
           KDGK_SULSO     2 VDVIALGEPLIQFNSFNPGPLRFVNYFEKHVAGSELNFCIAVVRNHLSCSLIARVGNDEFGKNIIEYSRAQGIDTSHIKVDNESFTGIYFIQRGYPIPMKSELVYYRKGSAGSRLSPEDINENYVRNSRLVHSTGITLAISDNAKEAVIKAFELAKSRSLDTNIRPKLWSSLEKAKETILSILKKYDIEVLITDPDDTKILLDVTDPDEAYRKYKELGVKVLLYKLGSKGAIAYKDNVKAFKDAYKVPVEDPTGAGDAMAGTFVSLYLQGKDIEYSLAHGIAASTLVITVRGDNELTPTLEDAERFLNEFK 312
               SCOP domains d2v78c_ C: automated matches                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeee....hhhhh..eeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh......eeee......eeeeee.......eeeeee...hhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh..eeee...hhhhh.hhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhh..hhhhhhhhhhhh.eeeeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v78 C   2 VDVIALGEPLIQFNSFNPGPLRFVNYFEKHVAGSELNFCIAVVRNHLSCSLIARVGNDEFGKNIIEYSRAQGIDTSHIKVDNESFTGIYFIQRGYPIPMKSELVYYRKGSAGSRLSPEDINENYVRNSRLVHSTGITLAISDNAKEAVIKAFELAKSRSLDTNIRPKLWSSLEKAKETILSILKKYDIEVLITDPDDTKILLDVTDPDEAYRKYKELGVKVLLYKLGSKGAIAYKDNVKAFKDAYKVPVEDPTGAGDAMAGTFVSLYLQGKDIEYSLAHGIAASTLVITVRGDNELTPTLEDAERFLNEFK 312
                                    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
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V78)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2V78)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (KDGK_SULSO | Q97U29)
molecular function
    GO:0008671    2-dehydro-3-deoxygalactonokinase activity    Catalysis of the reaction: 2-dehydro-3-deoxy-D-galactonate + ATP = 6-phospho-2-dehydro-3-deoxy-D-galactonate + ADP + 2 H(+).
    GO:0008673    2-dehydro-3-deoxygluconokinase activity    Catalysis of the reaction: 2-dehydro-3-deoxy-D-gluconate + ATP = 2-dehydro-3-deoxy-6-phospho-D-gluconate + ADP + 2 H(+).
    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: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:0046835    carbohydrate phosphorylation    The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y.
    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.

 Visualization

(-) Interactive Views

Asymmetric 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
(no "Ligands, Modified Residues, Ions" information available for 2v78)
 
  Sites
(no "Sites" information available for 2v78)
 
  Cis Peptide Bonds
    Tyr A:96 - Pro A:97   [ RasMol ]  
    Tyr B:96 - Pro B:97   [ RasMol ]  
    Tyr C:96 - Pro C:97   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2v78
    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
  KDGK_SULSO | Q97U29
    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)
  2.7.1.4
    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

(-) Analysis Tools

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
  KDGK_SULSO | Q97U29
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        KDGK_SULSO | Q97U29: 2var

(-) Related Entries Specified in the PDB File

2var CRYSTAL STRUCTURE OF SULFOLOBUS SOLFATARICUS 2 -KETO-3-DEOXYGLUCONATE KINASE COMPLEXED WITH 2-KETO-3-DEOXYGLUCONATE