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(-) Description

Title :  CRYSTAL STRUCTURE OF IRIDOID SYNTHASE FROM CANTHARANTHUS ROSEUS IN COMPLEX WITH NAD+ AND 10-OXOGERANIAL
 
Authors :  Y. M. Hu, W. D. Liu, Y. Y. Zheng, Z. X. Xu, T. P. Ko, C. C. Chen, R. T. Guo
Date :  21 Aug 15  (Deposition) - 04 Nov 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Metal-Binding, Substrate Binding, Acidocalcisomal Pyrophosphatase, Inhibitor, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. M. Hu, W. D. Liu, S. R. Malwal, Y. Y. Zheng, X. X. Feng, T. P. Ko, C. C. Chen, Z. X. Xu, M. X. Liu, X. Han, J. Gao, E. Oldfield, R. T. Guo
Structures Of Iridoid Synthase From Cantharanthus Roseus With Bound Nad(+) , Nadph, Or Nad(+) /10-Oxogeranial: Reaction Mechanisms
Angew. Chem. Int. Ed. Engl. V. 54 15478 2015
PubMed-ID: 26768532  |  Reference-DOI: 10.1002/ANIE.201508310

(-) Compounds

Molecule 1 - IRIDOID SYNTHASE
    Chains: A, B
    EC Number: 1.3.1.99
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET32XA/LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 26-388
    Organism Common: MADAGASCAR PERIWINKLE
    Organism Scientific: CATHARANTHUS ROSEUS
    Organism Taxid: 4058

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2XOG2Ligand/Ion(2E,6E)-2,6-DIMETHYLOCTA-2,6-DIENEDIAL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2XOG2Ligand/Ion(2E,6E)-2,6-DIMETHYLOCTA-2,6-DIENEDIAL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2XOG2Ligand/Ion(2E,6E)-2,6-DIMETHYLOCTA-2,6-DIENEDIAL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:36 , THR A:38 , GLY A:39 , ILE A:40 , ALA A:65 , ARG A:66 , CYS A:83 , ASP A:84 , VAL A:85 , VAL A:107 , SER A:108 , TRP A:109 , MET A:121 , GLN A:142 , THR A:143 , TYR A:178 , PRO A:201 , ALA A:202 , VAL A:204 , SER A:211 , MET A:212 , MET A:213 , XOG A:402 , HOH A:523 , HOH A:530 , HOH A:540 , HOH A:541 , HOH A:555binding site for residue NAD A 401
2AC2SOFTWAREGLY A:144 , ILE A:145 , LYS A:146 , TYR A:178 , ILE A:345 , ALA A:346 , NAD A:401 , HOH A:561binding site for residue XOG A 402
3AC3SOFTWAREGLY B:36 , THR B:38 , GLY B:39 , ILE B:40 , ALA B:65 , ARG B:66 , CYS B:83 , ASP B:84 , VAL B:85 , VAL B:107 , SER B:108 , TRP B:109 , MET B:121 , GLN B:142 , THR B:143 , TYR B:178 , PRO B:201 , ALA B:202 , VAL B:204 , SER B:211 , MET B:212 , MET B:213 , XOG B:402 , HOH B:519 , HOH B:531 , HOH B:536 , HOH B:542 , HOH B:544binding site for residue NAD B 401
4AC4SOFTWAREGLY B:144 , ILE B:145 , LYS B:146 , TYR B:178 , ILE B:345 , NAD B:401binding site for residue XOG B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DBI)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:57 -Pro A:58
2Ser A:163 -Pro A:164
3Gly B:57 -Pro B:58
4Ser B:163 -Pro B:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DBI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DBI)

(-) Exons   (0, 0)

(no "Exon" information available for 5DBI)

(-) 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:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhh.........eeeeeee....hhhhhh...eeee....hhhhhhhhhh......eeee.......hhhhhhhhhhhhhhhhh.......eeeee..hhhhhh.....................hhhhhhhhhhhhhhhhh..eeeeeee.eee........hhhhhhhhhhhhhhhh...ee...hhhhhhh...eeehhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhh...ee.........hhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhh........hhhhhhh......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dbi A  26 KSYKSVALVVGVTGIVGSSLAEVLKLPDTPGGPWKVYGVARRPCPVWLAKKPVEYIQCDVSDNQETISKLSPLKDITHIFYVSWIGSEDCQTNATMFKNILNSVIPNASNLQHVCLQTGIKHYFGIFEEVPHDSPFTEDLPRLNVPNFYHDLEDILYEETGKNNLTWSVHRPALVFGFSPCSMMNIVSTLCVYATICKHENKALVYPGSKNSWNCYADAVDADLVAEHEIWAAVDPKAKNQVLNCNNGDVFKWKHIWKKLAEEFGIEMVGYVEGKEQVSLAELMKDKDQVWDEIVKKNNLVPTKLKEIAAFWFADIAFCSENLISSMNKSKELGFLGFRNSMKSFVSCIDKMRDYRFIPAS 390
                                    35        45        55        65        75        85        95       105       115       125       135       145       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389 
                                                                                                                                                          154|                                                                                                                                                                                                                                       
                                                                                                                                                           159                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:362
                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhh.........eeeeeee....hhhhhh...eeee....hhhhhhhhhh......eeee.......hhhhhhhhhhhhhhhhh.......eeeee..hhhhhh......................hhhhhhhhhhhhhhhhh..eeeeeee.eee........hhhhhhhhhhhhhhhh...ee...hhhhhhh...eeehhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhh...ee.........hhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhh........hhhhhhh......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dbi B  26 KSYKSVALVVGVTGIVGSSLAEVLKLPDTPGGPWKVYGVARRPCPVWLAKKPVEYIQCDVSDNQETISKLSPLKDITHIFYVSWIGSEDCQTNATMFKNILNSVIPNASNLQHVCLQTGIKHYFGIFEEVVPHDSPFTEDLPRLNVPNFYHDLEDILYEETGKNNLTWSVHRPALVFGFSPCSMMNIVSTLCVYATICKHENKALVYPGSKNSWNCYADAVDADLVAEHEIWAAVDPKAKNQVLNCNNGDVFKWKHIWKKLAEEFGIEMVGYVEGKEQVSLAELMKDKDQVWDEIVKKNNLVPTKLKEIAAFWFADIAFCSENLISSMNKSKELGFLGFRNSMKSFVSCIDKMRDYRFIPAS 390
                                    35        45        55        65        75        85        95       105       115       125       135       145       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388  
                                                                                                                                                          154|                                                                                                                                                                                                                                        
                                                                                                                                                           158
   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  (0, 0)

(no "SCOP Domain" information available for 5DBI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DBI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DBI)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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        IRIS_CATRO | K7WDL7: 5coa 5cob 5dbf 5dbg 5dcu 5dcw 5dcy 5df1 5emh

(-) Related Entries Specified in the PDB File

5dbf 5dbg