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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCEROL KINASE FROM CELLULOMONAS SP. NT3060
 
Authors :  K. Imada, T. Tamura, K. Namba, K. Inagaki
Date :  24 Oct 05  (Deposition) - 14 Nov 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha And Beta Protein, Ribonuclease H-Like Motif, Actin- Like Atpase Domain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Imada, T. Tamura, K. Inagaki
Structure Of Glycerol Kinase From Cellulomonas Sp. Nt3060
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCEROL KINASE
    Chains: A, B
    EC Number: 2.7.1.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: CELLULOMONAS SP.
    Organism Taxid: 40001
    Strain: NT3060

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:82 , GLU A:83 , ARG A:190 , ASP A:246 , GLN A:247 , PHE A:271 , HOH A:2128BINDING SITE FOR RESIDUE MPD A 1
2AC2SOFTWAREARG B:82 , GLU B:83 , TRP B:102 , ARG B:190 , ASP B:246 , PHE B:271 , GLU B:305 , HOH B:3167BINDING SITE FOR RESIDUE MPD B 1001
3AC3SOFTWAREVAL A:310 , TRP A:317 , PRO A:348 , ALA A:349 , HOH A:2105 , LEU B:369 , THR B:370BINDING SITE FOR RESIDUE MPD A 2001
4AC4SOFTWARELEU A:369 , ARG A:371 , VAL B:310 , LEU B:314 , TRP B:317 , PRO B:348 , ALA B:349 , HOH B:3051 , HOH B:3064BINDING SITE FOR RESIDUE MPD B 3001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D4W)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:355 -Pro A:356
2Ala B:355 -Pro B:356

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D4W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D4W)

(-) Exons   (0, 0)

(no "Exon" information available for 2D4W)

(-) Sequences/Alignments

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:503
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d2d4wa1 A:2-254 automated matches                                                                                                                                                                                                                            d2d4wa2 A:255-504 automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eeeeeee.....eeeeeeee...........eehhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeee.....eeee.........ee......hhhhhhhhhh..hhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhh.eeeehhhhhhhhhhh........eeehhhhh....ee....eehhhhhhhh..hhhhh.eee..eeeeee..........eeeeeeehhhhhhhhh......eeeeee...eeeeee............eeeeee.......eeeeeeee...hhhhhhhhhh.........hhhhhh........eee................eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhh....hhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d4w A   2 ADYVLAIDQGTTSSRAIVFDHSGEIYSTGQLEHDQIFPRAGWVEHNPEQIWNNVREVVGLALTRGNLTHEDIAAVGITNQRETAVVWDKTTGKPVYNAIVWQDTRTQKIVDELGGDEGAEKYKSIVGLPLATYFSGPKIKWILDNVEGAREKAEKGDLLFGNTDTWVLWNMTGGTEGGVHVTDVTNASRTMLMDLDTLSWREDIAADMGIPLSMLPDIRSSSEVYGHGRPRGLVPGVPIAGILGDQQAATFGQACFEVGQAKNTYGTGNFLLLNTGTEKVMSKNGLLTTVCYKIGDAPAVYALEGSIAVTGSLVQWLRDNLGMFEDAPDVEWLAGKVQDNGGAYFVPAFSGLFAPYWRPDARGALVGLTRYVNRNHIARAALEATAFQSREVVDAMNADSGVDLTELRVDGGMVANELLMQFQADQLGVDVVRPKVAETTALGAAYAAGIAVGFWKGEQDVIDNWAEDKRWSPSMESGERERLYRNWKKAVTKTMEWVDEDVE 504
                                    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       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501   


Chain B from PDB  Type:PROTEIN  Length:503
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d2d4wb1 B:2-254 automated matches                                                                                                                                                                                                                            d2d4wb2 B:255-504 automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eeeeeee.....eeeeeeee...........eehhhhhhhhhhhhhhhhhhhh......eeeeeeee.....eeee.........ee......hhhhhhhhh.......hhhhhh......hhhhhhhhhhhhh.hhhhhhhhh.eeeehhhhhhhhhhh........eeehhhhh....ee....eehhhhhhhh........eee..eeeeee..........eeeeeeehhhhhhhhh......eeeeee...eeeeeeee..........eeeeee.......eeeeeeee...hhhhhhhhhh.........hhhhhh........eee................eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhh....hhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d4w B   2 ADYVLAIDQGTTSSRAIVFDHSGEIYSTGQLEHDQIFPRAGWVEHNPEQIWNNVREVVGLALTRGNLTHEDIAAVGITNQRETAVVWDKTTGKPVYNAIVWQDTRTQKIVDELGGDEGAEKYKSIVGLPLATYFSGPKIKWILDNVEGAREKAEKGDLLFGNTDTWVLWNMTGGTEGGVHVTDVTNASRTMLMDLDTLSWREDIAADMGIPLSMLPDIRSSSEVYGHGRPRGLVPGVPIAGILGDQQAATFGQACFEVGQAKNTYGTGNFLLLNTGTEKVMSKNGLLTTVCYKIGDAPAVYALEGSIAVTGSLVQWLRDNLGMFEDAPDVEWLAGKVQDNGGAYFVPAFSGLFAPYWRPDARGALVGLTRYVNRNHIARAALEATAFQSREVVDAMNADSGVDLTELRVDGGMVANELLMQFQADQLGVDVVRPKVAETTALGAAYAAGIAVGFWKGEQDVIDNWAEDKRWSPSMESGERERLYRNWKKAVTKTMEWVDEDVE 504
                                    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       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D4W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D4W)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2D4W)

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