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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TRITICUM XYLANSE INHIBITOR-I IN COMPLEX WITH BACILLUS SUBTILIS XYLANASE
 
Authors :  S. Sansen, M. Dewilde, C. J. De Ranter, K. Gebruers, K. Brijs, C. M. Cour J. A. Delcour, A. Rabijns
Date :  22 Sep 05  (Deposition) - 19 Sep 06  (Release) - 23 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Protein Complex; Two Beta-Barrel Domain; Beta-Jelly Roll; X- Ray Crystallography, Hydrolase Inhibitor-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Pollet, S. Sansen, G. Raedschelders, K. Gebruers, A. Rabijns, J. A. Delcour, C. M. Courtin
Identification Of Structural Determinants For Inhibition Strength And Specificity Of Wheat Xylanase Inhibitors Taxi-Ia And Taxi-Iia.
Febs J. V. 276 3916 2009
PubMed-ID: 19769747  |  Reference-DOI: 10.1111/J.1742-4658.2009.07105.X

(-) Compounds

Molecule 1 - XYLANASE INHIBITOR-I
    ChainsA
    Organism CommonBREAD WHEAT
    Organism ScientificTRITICUM AESTIVUM
    Organism Taxid4565
 
Molecule 2 - ENDO-1,4-BETA-XYLANASE A
    ChainsB
    EC Number3.2.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneXYNA
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    SynonymXYLANASE A;
1,4- BETA-D-XYLAN XYLANOHYDROLASE A

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2B42)

(-) Sites  (0, 0)

(no "Site" information available for 2B42)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:39 -A:124
2A:55 -A:80
3A:66 -A:92
4A:167 -A:378
5A:282 -A:327

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:277 -Pro A:278
2Ser B:74 -Pro B:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B42)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH11_1PS00776 Glycosyl hydrolases family 11 (GH11) active site signature 1.XYNA_BACSU103-113  1B:75-85
2GH11_2PS00777 Glycosyl hydrolases family 11 (GH11) active site signature 2.XYNA_BACSU197-208  1B:169-180

(-) Exons   (0, 0)

(no "Exon" information available for 2B42)

(-) 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:364
 aligned with Q8H0K8_WHEAT | Q8H0K8 from UniProtKB/TrEMBL  Length:402

    Alignment length:381
                                    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 
         Q8H0K8_WHEAT    22 LPVLAPVTKDPATSLYTIPFHDGASLVLDVAGPLVWSTCDGGQPPAEIPCSSPTCLLANAYPAPGCPAPSCGSDKHDKPCTAYPYNPVSGACAAGSLSHTRFVANTTDGSKPVSKVNVGVLAACAPSKLLASLPRGSTGVAGLANSGLALPAQVASAQKVANRFLLCLPTGGPGVAIFGGGPVPWPQFTQSMPYTPLVTKGGSPAHYISARSIVVGDTRVPVPEGALATGGVMLSTRLPYVLLRPDVYRPLMDAFTKALAAQHANGAPVARAVEAVAPFGVCYDTKTLGNNLGGYAVPNVQLGLDGGSDWTMTGKNSMVDVKQGTACVAFVEMKGVAAGDGRAPAVILGGAQMEDFVLDFDMEKKRLGFSRLPHFTGCGGL 402
               SCOP domains d2b42a1 A:1-381 Xylanase inhibitor TAXI-I                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2b42A01 A:1-180 Acid Proteases                                                                                                                                                      2b42A02 A:181-381 Acid Proteases                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......eeeeee..eeeeee.....eee....-----.....hhhhhhhh.........---------...ee............eeeeeeeeeeeee....eeeeeeeeeeeee.hhhhhh.....eeeeee......hhhhhhhhhhh...eeeee......eeeee......hhhhhh...eee..........ee.eeeeee..ee............eee......eeehhhhhhhhhhhhhhhhhh.---......ee........eee.hhh.ee..ee....eeeee...eeeeehhhhheeeee..eeee.eee.............eeehhhhhh.eeeeee....eeeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b42 A   1 LPVLAPVTKDPATSLYTIPFHDGASLVLDVAGPLVWSTCKG-----EIPCSSPTCLLANAYPAPGCPA---------KPCTAYPYNPVSGACAAGSLSHTRFVANTTDGSKPVSKVNVGVLAACAPSKLLASLPRGSTGVAGLANSGLALPAQVASAQKVANRFLLCLPTGGPGVAIFGGGPVPWPQFTQSMPYTPLVTKGGSPAHYISARSIVVGDTRVPVPEGALATGGVMLSTRLPYVLLRPDVYRPLMDAFTKALAAQ---GAPVARAVVAVAPFGVCYDTKTLGNNLGGYAVPNVQLGLDGGSDWTMTGKNSMVDVKQGTACVAFVEMKGVAAGDGRAPAVILGGAQMEDFVLDFDMEKKRLGFSRLPHFTGCGGL 381
                                    10        20        30        40|     | 50        60       | -       |80        90       100       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 
                                                                   41    47                   68        78                                                                                                                                                                                     262 266                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:184
 aligned with XYNA_BACSU | P18429 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:184
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209    
           XYNA_BACSU    30 STDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDRTTFTQYWSVRQSKRPTGSNATITFSNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVW 213
               SCOP domains d2b42b_ B: Xylanase II                                                                                                                                                                   SCOP domains
               CATH domains 2b42B00 B:2-185  [code=2.60.120.180, no name defined]                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eeeeee....eeeeeee...eeeeeeee.......eeeeeeeeeeeeeeeeeeeeeeee...eeeeeeeee.......eeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeeeeee.........eeeehhhhhhhhhhh......eeeeeeeeeeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------GH11_1     -----------------------------------------------------------------------------------GH11_2      ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b42 B   2 STDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDRTTFTQYWSVRQSKRPTGSNATITFTNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVW 185
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181    

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B42)

(-) Gene Ontology  (10, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8H0K8_WHEAT | Q8H0K8)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0045493    xylan catabolic process    The chemical reactions and pathways resulting in the breakdown of xylan, a polymer containing a beta-1,4-linked D-xylose backbone.

Chain B   (XYNA_BACSU | P18429)
molecular function
    GO:0031176    endo-1,4-beta-xylanase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    GO:0045493    xylan catabolic process    The chemical reactions and pathways resulting in the breakdown of xylan, a polymer containing a beta-1,4-linked D-xylose backbone.

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    Ala A:277 - Pro A:278   [ RasMol ]  
    Ser B:74 - Pro B:75   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        XYNA_BACSU | P184291axk 1xxn 2b45 2b46 2dcy 2dcz 2qz3 2z79 3exu 3hd8 5k9y
UniProtKB/TrEMBL
        Q8H0K8_WHEAT | Q8H0K81t6e 1t6g

(-) Related Entries Specified in the PDB File

1t6e STRUCTURE OF TRITICUM AESTIVUM XYLANASE INHIBITOR-I
1t6g STRUCTURE OF TRITICUM AESTIVUM XYLANASE INHIBITOR-I IN COMPLEX WITH ASPERGILLUS NIGER XYLANASE-I
2b45 STRUCTURE OF AN ENGINEERED UNINHIBITED BACILLUS SUBTILIS XYLANASE IN FREE STATE
2b46 STRUCTURE OF AN ENGINEERED UNINHIBITED BACILLUS SUBTILIS XYLANASE WITH XYLOBIOSE