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(-) Description

Title :  CRYSTAL STRUCTURE OF DROSOPHILA GRASS CLIP SERINE PROTEASE OF TOLL PATHWAY
 
Authors :  C. Kellenberger, P. Leone, L. Coquet, T. Jouenne, J. M. Reichhart, A. Ro
Date :  10 Nov 10  (Deposition) - 09 Feb 11  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Innate Immunity (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Kellenberger, P. Leone, L. Coquet, T. Jouenne, J. M. Reichhart, A. Roussel
Structure-Function Analysis Of Grass Clip Serine Protease Involved In Drosophila Toll Pathway Activation.
J. Biol. Chem. V. 286 12300 2011
PubMed-ID: 21310954  |  Reference-DOI: 10.1074/JBC.M110.182741

(-) Compounds

Molecule 1 - GRAM-POSITIVE SPECIFIC SERINE PROTEASE, ISOFORM B
    ChainsA, B
    EC Number3.4.21.4
    EngineeredYES
    Expression SystemDROSOPHILA MELANOGASTER
    Expression System Cell LineS2
    Expression System PlasmidPMT-DEST48
    Expression System Taxid7227
    Expression System Vector TypePLASMID
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2CA2Ligand/IonCALCIUM ION
3FUC3Ligand/IonALPHA-L-FUCOSE
4NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3FUC1Ligand/IonALPHA-L-FUCOSE
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3FUC2Ligand/IonALPHA-L-FUCOSE
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:269 , ASN A:270 , THR A:348 , HOH A:2386BINDING SITE FOR RESIDUE NAG A1385
2AC2SOFTWAREGLU A:179 , ARG A:181 , THR A:184 , ASP A:187 , HOH A:2189 , HOH A:2201BINDING SITE FOR RESIDUE CA A1386
3AC3SOFTWAREGLU B:179 , ARG B:181 , THR B:184 , ASP B:187 , HOH B:2191 , HOH B:2200BINDING SITE FOR RESIDUE CA B1389
4AC4SOFTWAREVAL A:119 , ASN A:121 , TYR A:123 , TYR A:173 , GLU A:174 , GLY A:205 , ILE A:206 , ASN A:230 , ARG A:231 , THR A:259 , ASN A:281 , HOH A:2138 , HOH A:2179 , HOH A:2184 , HOH A:2383 , HOH A:2384BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 230 RESIDUES 1381 TO 1384
5AC5SOFTWAREVAL B:119 , ASN B:121 , TYR B:123 , TYR B:173 , GLU B:174 , GLY B:205 , ILE B:206 , ASN B:230 , ARG B:231 , THR B:259 , ASN B:281 , HOH B:2141 , HOH B:2184 , HOH B:2389 , HOH B:2390 , HOH B:2391BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 230 RESIDUES 1381 TO 1384
6AC6SOFTWAREARG A:295 , ALA A:297 , HOH A:2309 , THR B:268 , GLU B:269 , ASN B:270 , VAL B:346 , VAL B:347 , THR B:348 , HOH B:2393BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 270 RESIDUES 1385 TO 1388

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:32 -A:88
2A:42 -A:78
3A:48 -A:89
4A:111 -A:243
5A:148 -A:164
6A:188 -A:197
7A:290 -A:304
8A:314 -A:349
9B:32 -B:88
10B:42 -B:78
11B:48 -B:89
12B:111 -B:243
13B:148 -B:164
14B:188 -B:197
15B:290 -B:304
16B:314 -B:349

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:115 -Ser A:116

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XXL)

(-) 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:354
 aligned with Q9VB68_DROME | Q9VB68 from UniProtKB/TrEMBL  Length:377

    Alignment length:354
                                                                                                                                                                                                                                                                                                                                                                                        377   
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376|   
         Q9VB68_DROME    27 DYADDCTTPDGDQGQCMPFSSCRTIEERLTEAQKAGQKVPADYASYLQKALCGEFNGVRHFCCPSANIQHNSKVMSLFKDENFDCGNFLSQRVSNGYEVKLSSRPWMALLRYQQFGESRFLCGGAMISERYILTAAHCVHGLQNDLYEIRLGEHRISTEEDCRQQGRKKKCAPPVVNVGIEKHLIHEKYDARHIMHDIALLKLNRSVPFQKHIKPICLPITDELKEKAEQISTYFVTGWGTTENGSSSDVLLQANVPLQPRSACSQAYRRAVPLSQLCVGGGDLQDSCKGDSGGPLQAPAQYLGEYAPKMVEFGIVSQGVVTCGQISLPGLYTNVGEYVQWITDTMASNGL---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee.....eeeeee...hhhhhhhhhhhhhh....hhhhhhhhhhheeeee..eeeeeee......hhhhhhhhh...........................eeeeeee....eeeeeeeeeee..eeeehhhhh......eeeeee..........eeee..eeee....eeeeeeeeee.............eeeee.................hhhhhhhh....eeeeee.............eeeeeeeehhhhhhhhhh......eeee......hhhhh....eeeeee........eeeeeeeeee...........eeeee...hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xxl A  27 DYADDCTTPDGDQGQCMPFSSCRTIEERLTEAQKAGQKVPADYASYLQKALCGEFNGVRHFCCPSANIQHNSKVMSLFKDENFDCGNFLSQRVSNGYEVKLSSRPWMALLRYQQFGESRFLCGGAMISERYILTAAHCVHGLQNDLYEIRLGEHRISTEEDCRQQGRKKKCAPPVVNVGIEKHLIHEKYDARHIMHDIALLKLNRSVPFQKHIKPICLPITDELKEKAEQISTYFVTGWGTTENGSSSDVLLQANVPLQPRSACSQAYRRAVPLSQLCVGGGDLQDSCKGDSGGPLQAPAQYLGEYAPKMVEFGIVSQGVVTCGQISLPGLYTNVGEYVQWITDTMASNGLLES 380
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376    

Chain B from PDB  Type:PROTEIN  Length:354
 aligned with Q9VB68_DROME | Q9VB68 from UniProtKB/TrEMBL  Length:377

    Alignment length:354
                                                                                                                                                                                                                                                                                                                                                                                        377   
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376|   
         Q9VB68_DROME    27 DYADDCTTPDGDQGQCMPFSSCRTIEERLTEAQKAGQKVPADYASYLQKALCGEFNGVRHFCCPSANIQHNSKVMSLFKDENFDCGNFLSQRVSNGYEVKLSSRPWMALLRYQQFGESRFLCGGAMISERYILTAAHCVHGLQNDLYEIRLGEHRISTEEDCRQQGRKKKCAPPVVNVGIEKHLIHEKYDARHIMHDIALLKLNRSVPFQKHIKPICLPITDELKEKAEQISTYFVTGWGTTENGSSSDVLLQANVPLQPRSACSQAYRRAVPLSQLCVGGGDLQDSCKGDSGGPLQAPAQYLGEYAPKMVEFGIVSQGVVTCGQISLPGLYTNVGEYVQWITDTMASNGL---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----CLIP-2xxlB03 B:32-89                                      -----------------------------Trypsin-2xxlB01 B:119-368                                                                                                                                                                                                                                 ------------ Pfam domains (1)
           Pfam domains (2) -----CLIP-2xxlB04 B:32-89                                      -----------------------------Trypsin-2xxlB02 B:119-368                                                                                                                                                                                                                                 ------------ Pfam domains (2)
         Sec.struct. author ....eee.....eeeeee...hhhhhhhhhhhhhh....hhhhhhhhhhheeeee..eeeeeee......hhhhhhhhh...........................eeeeeeee..eeeeeeeeeeee..eeeehhhhh......eeeeee..........eeee..eeee....eeeeeeeeee.............eeeee.................hhhhhhhh....eeeeee..ee..ee.....eeeeeeeehhhhhhhhhh......eeee......hhhhh....eeeeee........eeeeeeeeee...........eeeee...hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xxl B  27 DYADDCTTPDGDQGQCMPFSSCRTIEERLTEAQKAGQKVPADYASYLQKALCGEFNGVRHFCCPSANIQHNSKVMSLFKDENFDCGNFLSQRVSNGYEVKLSSRPWMALLRYQQFGESRFLCGGAMISERYILTAAHCVHGLQNDLYEIRLGEHRISTEEDCRQQGRKKKCAPPVVNVGIEKHLIHEKYDARHIMHDIALLKLNRSVPFQKHIKPICLPITDELKEKAEQISTYFVTGWGTTENGSSSDVLLQANVPLQPRSACSQAYRRAVPLSQLCVGGGDLQDSCKGDSGGPLQAPAQYLGEYAPKMVEFGIVSQGVVTCGQISLPGLYTNVGEYVQWITDTMASNGLLES 380
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376    

   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 2XXL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9VB68_DROME | Q9VB68)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0045752    positive regulation of Toll signaling pathway    Any process that activates or increases the frequency, rate or extent of the Tl signaling pathway.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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