Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  TENEBRIO MOLITOR ALPHA-AMYLASE-INHIBITOR COMPLEX
 
Authors :  V. Nahoum, M. P. Egloff, F. Payan
Date :  21 Jul 98  (Deposition) - 22 Jul 99  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Complex (Glycosidase-Inhibitor), Hydrolase, Lectin, Insect Alpha- Amylase, Inhibitors, Complex (Glycosidase-Inhibitor) Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Nahoum, F. Farisei, V. Le-Berre-Anton, M. P. Egloff, P. Rouge, E. Poerio, F. Payan
A Plant-Seed Inhibitor Of Two Classes Of Alpha-Amylases: X-Ray Analysis Of Tenebrio Molitor Larvae Alpha-Amylase In Complex With The Bean Phaseolus Vulgaris Inhibitor.
Acta Crystallogr. , Sect. D V. 55 360 1999
PubMed-ID: 10089450  |  Reference-DOI: 10.1107/S0907444998010701

(-) Compounds

Molecule 1 - ALPHA-AMYLASE
    ChainsA
    EC Number3.2.1.1
    Organism CommonYELLOW MEALWORM
    Organism ScientificTENEBRIO MOLITOR
    Organism Taxid7067
    Other DetailsLARVAE
 
Molecule 2 - ALPHA-AMYLASE-INHIBITOR
    ChainsB
    OrganSEED
    Organism ScientificPHASEOLUS VULGARIS
    Organism Taxid3885
    SynonymALPHA-AI

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PCA1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PCA2Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARENAG B:509BINDING SITE FOR RESIDUE NAG B 508
2AC2SOFTWAREASP B:63 , ASN B:65 , ARG B:136 , SER B:199 , SER B:201 , NAG B:508BINDING SITE FOR RESIDUE NAG B 509
3AC3SOFTWAREGLU B:170 , NAG B:511BINDING SITE FOR RESIDUE NAG B 510
4AC4SOFTWAREASN B:12 , LYS B:13 , SER B:26 , ASP B:173 , TRP B:174 , NAG B:510BINDING SITE FOR RESIDUE NAG B 511
5AC5SOFTWAREARG A:183 , LEU A:243 , ASN A:285 , ARG A:321BINDING SITE FOR RESIDUE CL A 498
6AC6SOFTWAREASN A:98 , ARG A:146 , ASP A:155 , HIS A:189BINDING SITE FOR RESIDUE CA A 500
7CICUNKNOWNASP A:185 , GLU A:222 , ASP A:287BINDING SITE

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:28 -A:84
2A:134 -A:148
3A:354 -A:360
4A:425 -A:437

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Val A:123 -Pro A:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VIW)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEA1_PHAVU121-127  1B:98-104
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEA1_PHAVU194-203  1B:171-180
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEA1_PHAVU121-127  2B:98-104
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEA1_PHAVU194-203  2B:171-180
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEA1_PHAVU121-127  1B:98-104
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEA1_PHAVU194-203  1B:171-180

(-) Exons   (0, 0)

(no "Exon" information available for 1VIW)

(-) 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:471
 aligned with AMY_TENMO | P56634 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:471
                                    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       420       430       440       450       460       470 
            AMY_TENMO     1 QKDANFASGRNSIVHLFEWKWNDIADECERFLQPQGFGGVQISPPNEYLVADGRPWWERYQPVSYIINTRSGDESAFTDMTRRCNDAGVRIYVDAVINHMTGMNGVGTSGSSADHDGMNYPAVPYGSGDFHSPCEVNNYQDADNVRNCELVGLRDLNQGSDYVRGVLIDYMNHMIDLGVAGFRVDAAKHMSPGDLSVIFSGLKNLNTDYGFADGARPFIYQEVIDLGGEAISKNEYTGFGCVLEFQFGVSLGNAFQGGNQLKNLANWGPEWGLLEGLDAVVFVDNHDNQRTGGSQILTYKNPKPYKMAIAFMLAHPYGTTRIMSSFDFTDNDQGPPQDGSGNLISPGINDDNTCSNGYVCEHRWRQVYGMVGFRNAVEGTQVENWWSNDDNQIAFSRGSQGFVAFTNGGDLNQNLNTGLPAGTYCDVISGELSGGSCTGKSVTVGDNGSADISLGSAEDDGVLAIHVNAKL 471
               SCOP domains d1viwa2 A:1-378 Animal alpha-amylase                                                                                                                                                                                                                                                                                                                                                      d1viwa1 A:379-471 Animal alpha-amylase                                                        SCOP domains
               CATH domains -1viwA01 A:2-379 Glycosidases                                                                                                                                                                                                                                                                                                                                                              1viwA02 A:380-471 Golgi alpha-mannosidase II                                                 CATH domains
               Pfam domains ------------------Alpha-amylase-1viwA02 A:19-324                                                                                                                                                                                                                                                                                    ------------------------------------------------------------Alpha-amylase_C-1viwA01 A:385-470                                                     - Pfam domains
         Sec.struct. author ....................hhhhhhhhhh..hhh...eeee.............hhhhh.............hhhhhhhhhhhhh...eeeeee...............................hhh............hhhh...............hhhhhhhhhhhhhhhh....eeee..hhh..hhhhhhhhhh.....hhh.......................hhhh........hhhhhhhhhhhh....hhhhhh..hhh....hhh....................hhhhhhhhhhhhhhhh..............................................hhh.hhhhhhhhhhhhh..............eeeeeehhheeeeee........................................................eeeehhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1viw A   1 xKDANFASGRNSIVHLFEWKWNDIADECERFLQPQGFGGVQISPPNEYLVADGRPWWERYQPVSYIINTRSGNESAFTDMTRRCNDAGVRIYVDAVINHMTGMNGVGTSGSSADHDGMNYPAVPYGSGDFHSPCEVNNYQDADNVRNCELVGLRDLNAGSDYVRGVLIDYMNHMIDLGVAGFRVDAAKHMSPGDLSVIFDGLKNLNTDYGFADGARPFIYQEVIDLGGEAISKNEYTGFGCVLEFQFGVSLGNAFQGGNQLKNLANWGPEWGLLEGLDAVVFVDNHDNQRTGGSQILTYKNPKPYKMAIAFMLAHPYGTTRIMSSFDFTDNDQGPPQDGSGNLISPGINDDNTCSNGYVCEHRWRQVYGMVGFRNAVEGTQVENWWSNDDNQIAFSRGSQGFVAFTNGGDLNQNLNTGLPAGTYCDVISGELSGGSCTGKSVTVGDNGSADISLGSAEDDGVLAIHVNAKL 471
                            |       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       420       430       440       450       460       470 
                            |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                            1-PCA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:198
 aligned with LEA1_PHAVU | P02873 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:205
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
           LEA1_PHAVU    24 ATETSFIIDAFNKTNLILQGDATVSSNGNLQLSYNSYDSMSRAFYSAPIQIRDSTTGNVASFDTNFTMNIRTHRQANSAVGLDFVLVPVQPESKGDTVTVEFDTFLSRISIDVNNNDIKSVPWDVHDYDGQNAEVRITYNSSTKVFSVSLSNPSTGKSNNVSTTVELEKEVYDWVSVGFSATSGAYQWSYETHDVLSWSFSSKFI 228
               SCOP domains d1viwb_ B: alpha-Amylase inhibitor                                                                                                                                                                            SCOP domains
               CATH domains 1viwB00 B:1-205  [code=2.60.120.200, no name defined]                                                                                                                                                         CATH domains
               Pfam domains -Lectin_legB-1viwB01 B:2-201                                                                                                                                                                             ---- Pfam domains
         Sec.struct. author ....eeee....hhheeee..eee.....eee.........eeee.................eeeeeeeee....--...eeeeeeee..-----.eeeeeee....eeee........eee..hhh.....eeeeee......eeeeeee......eeeeeee..........eeeee......hhhh..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------LECTIN_------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1viw B   1 ATETSFIIDAFNKTNLILQGDATVSSNGNLQLSYNSYDSMSRAFYSAPIQIRDSTTGNVASFDTNFTMNIRTHRQ--SAVGLDFVLVPVQ-----DTVTVEFDTFLSRISIDVNNNDIKSVPWDVHDYDGQNAEVRITYNSSTKVFSVSLSNPSTGKSNNVSTTVELEKEVYDWVSVGFSATSGAYQWSYETHDVLSWSFSSKFI 205
                                    10        20        30        40        50        60        70    |  |80        90     | 100       110       120       130       140       150       160       170       180       190       200     
                                                                                                     75 78          90    96                                                                                                             

   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  (3, 3)

Asymmetric Unit

(-) CATH Domains  (3, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: GHD (106)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (AMY_TENMO | P56634)
molecular function
    GO:0004556    alpha-amylase activity    Catalysis of the endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more alpha-(1->4)-linked D-glucose units.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0043169    cation binding    Interacting selectively and non-covalently with cations, charged atoms or groups of atoms with a net positive charge.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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.

Chain B   (LEA1_PHAVU | P02873)
molecular function
    GO:0015066    alpha-amylase inhibitor activity    Stops, prevents or reduces the activity of alpha-amylase.
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
biological process
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PCA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    CIC  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Val A:123 - Pro A:124   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1viw
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  AMY_TENMO | P56634
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  LEA1_PHAVU | P02873
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.1
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  AMY_TENMO | P56634
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  LEA1_PHAVU | P02873
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        AMY_TENMO | P566341clv 1jae 1tmq
        LEA1_PHAVU | P028731dhk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1VIW)