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(-) Description

Title :  STRUCTURE OF RIBB COMPLEXED WITH PO4 ION
 
Authors :  Z. Islam, A. Kumar, S. Singh, L. Salmon, S. Karthikeyan
Date :  24 Mar 14  (Deposition) - 25 Mar 15  (Release) - 13 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ribb, Riboflavin, Ligand, Complex, Crystal, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Islam, A. Kumar, S. Singh, L. Salmon, S. Karthikeyan
Structural Basis For Competitive Inhibition Of 3, 4-Dihydroxy-2-Butanone-4-Phosphate Synthase From Vibrio Cholerae.
J. Biol. Chem. V. 290 11293 2015
PubMed-ID: 25792735  |  Reference-DOI: 10.1074/JBC.M114.611830

(-) Compounds

Molecule 1 - 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 4.1.99.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RIBB, VC_A1060
    Organism Scientific: VIBRIO CHOLERAE SEROTYPE O1
    Organism Taxid: 243277
    Strain: ATCC 39315 / EL TOR INABA N16961
    Synonym: DHBP SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPO4 A:302 , HOH A:591binding site for residue EDO A 301
2AC2SOFTWAREARG A:151 , GLY A:153 , HIS A:154 , THR A:155 , EDO A:301 , HOH A:562binding site for residue PO4 A 302
3AC3SOFTWAREARG B:151 , GLY B:153 , HIS B:154 , THR B:155 , HOH B:771 , HOH B:801binding site for residue PO4 B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P6D)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:134 -Pro A:135
2Arg B:134 -Pro B:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P6D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P6D)

(-) Exons   (0, 0)

(no "Exon" information available for 4P6D)

(-) 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:201
                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh...eeee.........eeeee....hhhhhhhhhhhh....eeeehhhhhhhh.......eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeee...hhhhh..hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhh..eeehhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p6d A   5 SLLAEFGDPITRVENALQALREGRGVLLLDDEDRENEGDIIYAVESLTTAQMALMIRECSGIVCLCLTEAQADRLALPPTVSIEAKHGVTTGVSAQDRVTTIKTAANPQAKPEDLARPGHVFPLRARAGGVLARRGHTEGTVDLMQMAGLQPAGVLCELTNPDGSMAKTPEIIEFGKLHNMPVLTIEDMVQYRIQFDLKLA 218
                                    14        24        34        44        54        64        74        97       107       117       127       137       147       157       167       177       187       197       207       217 
                                                                                                         83|                                                                                                                         
                                                                                                          97                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh...eeee.........eeeee....hhhhhhhhhhhh....eeeehhhhhhhh..........eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeee...hhhhh..hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhh..eeehhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p6d B   6 LLAEFGDPITRVENALQALREGRGVLLLDDEDRENEGDIIYAVESLTTAQMALMIRECSGIVCLCLTEAQADRLALPPMAFTVSIEAKHGVTTGVSAQDRVTTIKTAANPQAKPEDLARPGHVFPLRARAGGVLARRGHTEGTVDLMQMAGLQPAGVLCELTNPDGSMAKTPEIIEFGKLHNMPVLTIEDMVQYRIQFDLKL 217
                                    15        25        35        45        55        65        75        95       105       115       125       135       145       155       165       175       185       195       205       215  
                                                                                                         84|                                                                                                                          
                                                                                                          95
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  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  (0, 0)

(no "SCOP Domain" information available for 4P6D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P6D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P6D)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        RIBB_VIBCH | Q9KKP2: 4p6c 4p6p 4p77 4p8e 4p8j

(-) Related Entries Specified in the PDB File

4p6c