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(-) Description

Title :  STRUCTURE OF THE BARLEY LIMIT DEXTRINASE-LIMIT DEXTRINASE INHIBITOR COMPLEX
 
Authors :  M. S. Moeller, M. B. Vester-Christensen, J. M. Jensen, M. Abou Hachem, A. Henriksen, B. Svensson
Date :  31 Mar 14  (Deposition) - 01 Apr 15  (Release) - 03 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.67
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Hydrolase-Hydrolase Inhibitor Complex, Starch Debranching Enzyme, Glycoside Hydrolase Family 13, Pullulanase, Cereal-Type Inhibitor, Cm-Protein, Endogenous Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Moller, M. B. Vester-Christensen, J. M. Jensen, M. Abou Hachem, A. Henriksen, B. Svensson
Crystal Structure Of Barley Limit Dextrinase:Limit Dextrinase Inhibitor (Ld:Ldi) Complex Reveals Insights Into Mechanism And Diversity Of Cereal-Type Inhibitors.
J. Biol. Chem. V. 290 12614 2015
PubMed-ID: 25792743  |  Reference-DOI: 10.1074/JBC.M115.642777

(-) Compounds

Molecule 1 - LIMIT DEXTRINASE
    Chains: A, B
    EC Number: 3.2.1.41
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Strain: GS115
    Expression System Taxid: 644223
    Expression System Vector: PPIC9K
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 22-904
    Mutation: YES
    Organism Common: BARLEY
    Organism Scientific: HORDEUM VULGARE
    Organism Taxid: 4513
 
Molecule 2 - LIMIT DEXTRINASE INHIBITOR
    Chains: C, D
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Strain: X33
    Expression System Taxid: 644223
    Expression System Vector: PPICZALPHAA
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 25-138
    Organism Common: BARLEY
    Organism Scientific: HORDEUM VULGARE
    Organism Taxid: 4513

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:348 , ASP A:351 , TYR A:353 , ASN A:701BINDING SITE FOR RESIDUE CA A1885
2AC2SOFTWARESER A:297 , LEU A:301 , GLY A:393BINDING SITE FOR RESIDUE CA A1886
3AC3SOFTWAREGLN B:348 , ASP B:351 , TYR B:353 , ASN B:701BINDING SITE FOR RESIDUE CA B1886
4AC4SOFTWARESER B:297 , LEU B:301 , GLY B:393BINDING SITE FOR RESIDUE CA B1887

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1C:9 -C:57
2C:23 -C:46
3C:32 -C:87
4C:47 -C:105
5D:9 -D:57
6D:23 -D:46
7D:32 -D:87
8D:47 -D:105

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly C:79 -Arg C:80
2Gly D:79 -Arg D:80

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CVW)

(-) 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:874
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee..eeee....hhhhh.eeeee.....ee...ee...eeee.eee....hhhhhh.hhhhh..eeee.....hhhhhh..eeeeee..eeeeeehhhhhhhhh......eeee...eeeeeee.....eeeeeee......eeeeee.eee..eeeeeee.hhh..eeeeeeeeee....eeeeeee........hhhhh.ee.....hhhhh..hhhhhhhhh....hhhhh.eeeehhhhhhhh..........hhhhhhh..hhhhhhhhhhhhhh..eeee...eee.....hhhhh.....hhhhhh....hhhhhhhhh............eeeeeee.hhhh.....hhhhhhhhhhhhhhhhh..eeeeee...............hhhhhh.........................hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhheeee....hhhhhhhh...............eeeehhhhhhhhh..........hhhhh...........hhhhhhhhhhhhhhhhhhhhh......eee.....eee................hhh.eee........hhhhhhhhhh....hhhhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhheee..........eeeeeee...............eeeeeeeee.....eeee.hhhh....eehhhhhh....hhhhheee....eeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cvw A   2 AFMPDARAYWVTSDLIAWNVGELEAQSVCLYASRAAAMSLSGGIQGYDSKVELQPESAGLPETVTQKFPFISSYRAFRVPSSVDVASLVKCQLVVASHVDVTGLQLPGVLDDMFAYTGPLGAVFSEDSVSLHLWAPTAQGVSVCFFDGPAGPALETVQLKESNGVWSVTGPREWENRYYLYEVDVYHPTKAQVLKCLAGDPYARSLSANGARTWLVDINNETLKPASWDELADEKPKLDSFSDITIYELHIRDFSAHDGTVDSDSRGGFRAFAYQASAGMEHLRKLSDAGLTHVHLLPSFHFAGVDDIKSNWKFVDECELATFPPGSDMQQAAVVAIQEEDPYNWGYNPVLWGVPKGSYASDPDGPSRIIEYRQMVQALNRIGLRVVMDVVYNHLDSSGPCGISSVLDKIVPGYYVRRDTNGQIENSAAMNNTASEHFMVDRLIVDDLLNWAVNYKVDGFRFDLMGHIMKRTMMRAKSALQSLTTDAHGVDGSKIYLYGEGWDFAEVARNQRGINGSQLNMSGTGIGSFNDRIRDAINGGNPFGNPLQQGFNTGLFLEPNGFYQGNEADTRRSLATYADQIQIGLAGNLRDYVLISHTGEAKKGSEIHTFDGLPVGYTASPIETINYVSAHDNETLFDVISVKTPMILSVDERCRINHLASSMMALSQGIPFFHAGDEILRSKSIDRDSYNSGDWFNKLDFTYETNNWGVGLPPSEKNEDNWPLMKPRLENPSFKPAKGHILAALDSFVDILKIRYSSPLFRLSTANDIKQRVRFHNTGPSLVPGVIVMGIEDARGESPEMAQLDTNFSYVVTVFNVCPHEVSMDIPALASMGFELHPVQVNSSDTLVRKSAYEAATGRFTVPGRTVSVFVEPR 884
                                    11        21        31        41||      54        64        74        84        94      |110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880    
                                                                   42|                                                    101|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                                                                    46                                                     108                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:871
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee..eeee..........eeeee.............eeee.ee.....hhhhhh.hhhhh..eeee.....hhhhhh..eeeeee..eeeeeehhhhhhhhhh.....eeee...eeeeeee.....eeeeeee......eeeeee.eee..eeeeeee.hhh..eeeeeeeeee....eeeeeee........hhhhh.ee.....hhhhh.....hhhhhh....hhhhh.eeeehhhhhhh...........hhhhhhh..hhhhhhhhhhhhhh..eeee...eee.....hhhhh...hhhhhh......hhhhhhhhhhh..........eeeeeee.hhhh.....hhhhhhhhhhhhhhhhh..eeeeee...............hhhhhh.........................hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhh........hhhhheeee....hhhhhhhh...............eeeehhhhhhhhh..........................hhhhhhhhhhhhhhhhhhhhh......eee.....eee..............hhh.eeee.......hhhhhhhhhh....hhhhhhhhhhhhhhhhhh...eeeee.hhhhh...........hhhhhh................hhhhhh.hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.hhhhh..hhhhhhhheee..........eeeeeee...............eeeeeeeee.....eeee.hhhh....eehhhhhh....hhhhheee....eeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cvw B   2 AFMPDARAYWVTSDLIAWNVGELEAQSVCLYASRAAAMSLGIQGYDSKVELQPESAGLPETVTQKFPFISSYRAFRVPSSVDVASLVKCQLVVASFVDVTGLQLPGVLDDMFAYTGPLGAVFSEDSVSLHLWAPTAQGVSVCFFDGPAGPALETVQLKESNGVWSVTGPREWENRYYLYEVDVYHPTKAQVLKCLAGDPYARSLSANGARTWLVDINNETLKPASWDELADEKPKLDSFSDITIYELHIRDFSAHDGTVDSDSRGGFRAFAYQASAGMEHLRKLSDAGLTHVHLLPSFHFAGVDDIKSNWKFVDECELATFPPGSDMQQAAVVAIQEEDPYNWGYNPVLWGVPKGSYASDPDGPSRIIEYRQMVQALNRIGLRVVMDVVYNHLDSSGPCGISSVLDKIVPGYYVRRDTNGQIENSAAMNNTASEHFMVDRLIVDDLLNWAVNYKVDGFRFDLMGHIMKRTMMRAKSALQSLTTDAHGVDGSKIYLYGEGWDFAEVARNQRGINGSQLNMSGTGIGSFNDRIRDAINGGNPFGNPLQQGFNTGLFLEPNGFYQGNEADTRRSLATYADQIQIGLAGNLRDYVLISHTGEAKKGSEIHDGLPVGYTASPIETINYVSAHDNETLFDVISVKTPMILSVDERCRINHLASSMMALSQGIPFFHAGDEILRSKSIDRDSYNSGDWFNKLDFTYETNNWGVGLPPSEKNEDNWPLMKPRLENPSFKPAKGHILAALDSFVDILKIRYSSPLFRLSTANDIKQRVRFHNTGPSLVPGVIVMGIEDARGESPEMAQLDTNFSYVVTVFNVCPHEVSMDIPALASMGFELHPVQVNSSDTLVRKSAYEAATGRFTVPGRTVSVFVEPRC 885
                                    11        21        31        41|       56        66        76        86        96     ||112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612     ||624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884 
                                                                  41|                                                    102|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          618|                                                                                                                                                                                                                                                                        
                                                                   47                                                     109                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           621                                                                                                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 4cvw C   8 ECQPGVDFPHNPLATCHTYVIKRVCGRGPSRPMLVKERCCRELAAVPDHCRCEALRILMDGVRTPEGRVVEGRLGDRRDCPREEQRAFAATLVTAAECNLS 108
                                    17        27        37        47        57        67        77        87        97       107 


Chain D from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhh....................hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4cvw D   6 KDECQPGVDFPHNPLATCHTYVIKRVCGRGPSRPMLVKERCCRELAAVPDHCRCEALRILMDGVRTPEGRVVEGRLGDRRDCPREEQRAFAATLVTAAECNL 107
                                    15        25        35        45        55        65        75        85        95       105
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4CVW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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 Related Entries

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(-) Related Entries Specified in the PDB File

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