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(-) Description

Title :  CRYSTAL STRUCTURE OF EDGP
 
Authors :  T. Yoshizawa, T. Shimizu, H. Hirano, M. Sato, H. Hashimoto
Date :  30 Nov 11  (Deposition) - 18 Apr 12  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Extracellular, Inhibitor, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Yoshizawa, T. Shimizu, H. Hirano, M. Sato, H. Hashimoto
Structural Basis For Inhibition Of Xyloglucan-Specific Endo-Beta-1, 4-Glucanase (Xeg) By Xeg-Protein Inhibitor
J. Biol. Chem. V. 287 18710 2012
PubMed-ID: 22496365  |  Reference-DOI: 10.1074/JBC.M112.350520

(-) Compounds

Molecule 1 - EDGP
    Chains: A
    Engineered: YES
    Expression System: DAUCUS CAROTA
    Expression System Cell: CARROT CALLUS CELL
    Expression System Common: CARROT
    Expression System Taxid: 562
    Gene: EDGP1
    Organism Common: CARROT
    Organism Scientific: DAUCUS CAROTA
    Organism Taxid: 4039

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:254 , SER A:256 , SER A:305 , HOH A:819BINDING SITE FOR RESIDUE NAG A 601
2AC2SOFTWAREASN A:299 , GLU A:337 , HOH A:655 , HOH A:885BINDING SITE FOR RESIDUE NAG A 701
3AC3SOFTWARESER A:124 , ASN A:410BINDING SITE FOR RESIDUE NAG A 801
4AC4SOFTWARECYS A:80 , ASN A:82 , PRO A:84 , ASN A:90 , HOH A:608BINDING SITE FOR RESIDUE NAG A 501

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:50 -A:138
2A:64 -A:77
3A:69 -A:93
4A:80 -A:88
5A:181 -A:406
6A:312 -A:358

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Thr A:30 -Pro A:31
2Asp A:197 -Pro A:198
3Leu A:202 -Pro A:203
4Ala A:307 -Pro A:308

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VLA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VLA)

(-) Exons   (0, 0)

(no "Exon" information available for 3VLA)

(-) 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:413
 aligned with Q05929_DAUCA | Q05929 from UniProtKB/TrEMBL  Length:433

    Alignment length:413
                                    30        40        50        60        70        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       390       400       410       420       430   
         Q05929_DAUCA    21 QPSFRPSALVVPVKKDASTLQYVTTINQRTPLVSENLVVDLGGRFLWVDCDQNYVSSTYRPVRCRTSQCSLSGSIACGDCFNGPRPGCNNNTCGVFPENPVINTATGGEVAEDVVSVESTDGSSSGRVVTVPRFIFSCAPTSLLQNLASGVVGMAGLGRTRIALPSQFASAFSFKRKFAMCLSGSTSSNSVIIFGNDPYTFLPNIIVSDKTLTYTPLLTNPVSTSATSTQGEPSVEYFIGVKSIKINSKIVALNTSLLSISSAGLGGTKISTINPYTVLETSIYKAVTEAFIKESAARNITRVASVAPFGACFSTDNILSTRLGPSVPSIDLVLQSESVVWTITGSNSMVYINDNVVCLGVVDGGSNLRTSIVIGGHQLEDNLVQFDLATSRVGFSGTLLGSRTTCANFNFTS 433
               SCOP domains d3vlaa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee......eeeeeee....eeeeeeee.....eeee..........ee....hhhhhhh...eee.............eeee..ee....ee..eeeeeeeeeeeee....eeeeeeeeeeeeeeehhhhhh.......eeee......hhhhhhhhhhh...eeeee........eeeeee...eee...eee.....eeee.....................ee...eeee..eee..hhhhh.........eee......eeeehhhhhhhhhhhhhhhhhh...ee........eee.....ee..ee....eeee......eeeehhhhheeeee..eeee.eeeee......eeehhhhhh.eeeeee....eeeeeee.hhhh.hhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vla A   1 xPSFRPSALVVPVKKDASTLQYVTTINQRTPLVSENLVVDLGGRFLWVDCDQNYVSSTYRPVRCRTSQCSLSGSIACGDCFNGPRPGCNNNTCGVFPENPVINTATGGEVAEDVVSVESTDGSSSGRVVTVPRFIFSCAPTSLLQNLASGVVGMAGLGRTRIALPSQFASAFSFKRKFAMCLSGSTSSNSVIIFGNDPYTFLPNIIVSDKTLTYTPLLTNPVSTSATSTQGEPSVEYFIGVKSIKINSKIVALNTSLLSISSAGLGGTKISTINPYTVLETSIYKAVTEAFIKESAARNITRVASVAPFGACFSTDNILSTRLGPSVPSIDLVLQSESVVWTITGSNSMVYINDNVVCLGVVDGGSNLRTSIVIGGHQLEDNLVQFDLATSRVGFSGTLLGSRTTCANFNFTS 413
                            |       10        20        30        40        50        60        70        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       390       400       410   
                            |                                                                                                                                                                                                                                                                                                                                                                                                                            
                            1-PCA
   Legend:   → Mismatch (orange background)
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VLA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VLA)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q05929_DAUCA | Q05929)
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.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

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

UniProtKB/TrEMBL
        Q05929_DAUCA | Q05929: 3vlb

(-) Related Entries Specified in the PDB File

3vl8 3vl9 3vlb