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(-) Description

Title :  CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA ACETOHYDROXYACID SYNTHASE IN COMPLEX WITH A SULFONYLUREA HERBICIDE, METSULFURON METHYL
 
Authors :  J. A. Mccourt, S. S. Pang, J. King-Scott, L. W. Guddat, R. G. Duggleby
Date :  10 Jan 05  (Deposition) - 17 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  A  (2x)
Keywords :  Acetohydroxyacid Synthase, Acetolactate Synthase, Herbicide, Sulfonylurea, Thiamin Diphosphate, Fad, Inhibitor, Cysteine-S- Dioxide, Ches, Metsulfuron Methyl, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. A. Mccourt, S. S. Pang, J. King-Scott, L. W. Guddat, R. G. Duggleby
Herbicide-Binding Sites Revealed In The Structure Of Plant Acetohydroxyacid Synthase
Proc. Natl. Acad. Sci. Usa V. 103 569 2006
PubMed-ID: 16407096  |  Reference-DOI: 10.1073/PNAS.0508701103

(-) Compounds

Molecule 1 - ACETOLACTATE SYNTHASE
    ChainsA
    EC Number2.2.1.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET30A(+)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 86-667
    GeneILVB
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymACETOHYDROXY-ACID SYNTHASE, ALS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 6)

Asymmetric Unit (6, 6)
No.NameCountTypeFull Name
11MM1Ligand/IonMETHYL 2-[({[(4-METHOXY-6-METHYL-1,3,5-TRIAZIN-2-YL)AMINO]CARBONYL}AMINO)SULFONYL]BENZOATE
2CSD1Mod. Amino Acid3-SULFINOALANINE
3FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4MG1Ligand/IonMAGNESIUM ION
5NHE1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
6P221Ligand/IonETHYL DIHYDROGEN DIPHOSPHATE
Biological Unit 1 (5, 20)
No.NameCountTypeFull Name
11MM4Ligand/IonMETHYL 2-[({[(4-METHOXY-6-METHYL-1,3,5-TRIAZIN-2-YL)AMINO]CARBONYL}AMINO)SULFONYL]BENZOATE
2CSD4Mod. Amino Acid3-SULFINOALANINE
3FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4MG-1Ligand/IonMAGNESIUM ION
5NHE4Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
6P224Ligand/IonETHYL DIHYDROGEN DIPHOSPHATE
Biological Unit 2 (5, 10)
No.NameCountTypeFull Name
11MM2Ligand/IonMETHYL 2-[({[(4-METHOXY-6-METHYL-1,3,5-TRIAZIN-2-YL)AMINO]CARBONYL}AMINO)SULFONYL]BENZOATE
2CSD2Mod. Amino Acid3-SULFINOALANINE
3FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4MG-1Ligand/IonMAGNESIUM ION
5NHE2Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
6P222Ligand/IonETHYL DIHYDROGEN DIPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:538 , ASN A:565 , HIS A:567 , P22 A:702 , HOH A:4063BINDING SITE FOR RESIDUE MG A 699
2AC2SOFTWAREGLY A:121 , ALA A:122 , VAL A:196 , PRO A:197 , PHE A:206 , GLN A:207 , LYS A:256 , ASP A:376 , ARG A:377 , TRP A:574 , SER A:653 , FAD A:701 , HOH A:4138BINDING SITE FOR RESIDUE 1MM A 695
3AC3SOFTWARELYS A:220 , HIS A:221 , MET A:226 , LEU A:273 , PRO A:274 , GLY A:275 , TYR A:276BINDING SITE FOR RESIDUE NHE A 696
4AC4SOFTWAREASP A:185 , PHE A:206 , ARG A:246 , GLY A:307 , GLY A:308 , GLY A:309 , THR A:331 , LEU A:332 , MET A:333 , LEU A:349 , GLY A:350 , MET A:351 , HIS A:352 , GLY A:371 , VAL A:372 , ARG A:373 , ASP A:375 , VAL A:378 , ASP A:395 , ILE A:396 , GLU A:400 , GLY A:413 , ASP A:414 , VAL A:415 , GLN A:489 , MET A:490 , SER A:507 , GLY A:508 , GLY A:509 , 1MM A:695 , HOH A:4147 , HOH A:4169 , HOH A:4177 , HOH A:4192 , HOH A:4253BINDING SITE FOR RESIDUE FAD A 701
5AC5SOFTWAREVAL A:485 , GLY A:486 , GLN A:487 , HIS A:488 , GLY A:537 , ASP A:538 , GLY A:539 , SER A:540 , ASN A:565 , HIS A:567 , LEU A:568 , GLY A:569 , MET A:570 , MG A:699 , HOH A:4131BINDING SITE FOR RESIDUE P22 A 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YHY)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:598 -Pro A:599
2Leu A:648 -Pro A:649

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPP_ENZYMESPS00187 Thiamine pyrophosphate enzymes signature.ILVB_ARATH521-540  1A:521-540
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPP_ENZYMESPS00187 Thiamine pyrophosphate enzymes signature.ILVB_ARATH521-540  4A:521-540
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPP_ENZYMESPS00187 Thiamine pyrophosphate enzymes signature.ILVB_ARATH521-540  2A:521-540

(-) Exons   (0, 0)

(no "Exon" information available for 1YHY)

(-) 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:582
 aligned with ILVB_ARATH | P17597 from UniProtKB/Swiss-Prot  Length:670

    Alignment length:582
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665  
           ILVB_ARATH    86 TFISRFAPDQPRKGADILVEALERQGVETVFAYPGGASMEIHQALTRSSSIRNVLPRHEQGGVFAAEGYARSSGKPGICIATSGPGATNLVSGLADALLDSVPLVAITGQVPRRMIGTDAFQETPIVEVTRSITKHNYLVMDVEDIPRIIEEAFFLATSGRPGPVLVDVPKDIQQQLAIPNWEQAMRLPGYMSRMPKPPEDSHLEQIVRLISESKKPVLYVGGGCLNSSDELGRFVELTGIPVASTLMGLGSYPCDDELSLHMLGMHGTVYANYAVEHSDLLLAFGVRFDDRVTGKLEAFASRAKIVHIDIDSAEIGKNKTPHVSVCGDVKLALQGMNKVLENRAEELKLDFGVWRNELNVQKQKFPLSFKTFGEAIPPQYAIKVLDELTDGKAIISTGVGQHQMWAAQFYNYKKPRQWLSSGGLGAMGFGLPAAIGASVANPDAIVVDIDGDGSFIMNVQELATIRVENLPVKVLLLNNQHLGMVMQWEDRFYKANRAHTFLGDPAQEDEIFPNMLLFAAACGIPAARVTKKADLREAIQTMLDTPGPYLLDVICPHQEHVLPMIPSGGTFNDVITEGDGR 667
               SCOP domains d1yhya2 A:86-280 Acetohydroxyacid synthase catalytic subunit                                                                                                                                       d1yhya1 A:281-459 Acetohydroxyacid synthase catalytic subunit                                                                                                                      d1yhya3 A:460-667 Acetohydroxyacid synthase catalytic subunit                                                                                                                                                    SCOP domains
               CATH domains 1yhyA01 A:86-280  [code=3.40.50.970, no name defined]                                                                                                                                              1yhyA02 A:281-453,A:648-667 TPP-binding domain                                                                                                                               1yhyA03 A:454-647  [code=3.40.50.970, no name defined]                                                                                                                                            1yhyA02              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eehhhhhhhhhhh....eeeee.hhhhhhhhhhhhhh...ee....hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh........hhhhhhh....eeee..hhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhee.........hhhhhh......hhhhhhhhhhhhhh...eeeee.hhhh.hhhhhhhhhhhhh..eee..............eeee.....hhhhhhhhhhh.eeeee....hhhhhh.........eeeeee.hhhhh.......eeee.hhhhhhhhhhhhhhh........hhhhhhhhhhhhh.............hhhhhhhhhhhhhh...eeee..hhhhhhhhhh........ee.........hhhhhhhhhhhhh....eeeeeehhhhhhh.hhhhhhhhhh...eeeeee...hhhhhhhhhhhh....................hhhhhhhhh...eeee....hhhhhhhhhhhh...eeeeee...............hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yhy A  86 TFISRFAPDQPRKGADILVEALERQGVETVFAYPGGASMEIHQALTRSSSIRNVLPRHEQGGVFAAEGYARSSGKPGICIATSGPGATNLVSGLADALLDSVPLVAITGQVPRRMIGTDAFQETPIVEVTRSITKHNYLVMDVEDIPRIIEEAFFLATSGRPGPVLVDVPKDIQQQLAIPNWEQAMRLPGYMSRMPKPPEDSHLEQIVRLISESKKPVLYVGGGCLNSSDELGRFVELTGIPVASTLMGLGSYPcDDELSLHMLGMHGTVYANYAVEHSDLLLAFGVRFDDRVTGKLEAFASRAKIVHIDIDSAEIGKNKTPHVSVCGDVKLALQGMNKVLENRAEELKLDFGVWRNELNVQKQKFPLSFKTFGEAIPPQYAIKVLDELTDGKAIISTGVGQHQMWAAQFYNYKKPRQWLSSGGLGAMGFGLPAAIGASVANPDAIVVDIDGDGSFIMNVQELATIRVENLPVKVLLLNNQHLGMVMQWEDRFYKANRAHTFLGDPAQEDEIFPNMLLFAAACGIPAARVTKKADLREAIQTMLDTPGPYLLDVICPHQEHVLPMIPSGGTFNDVITEGDGR 667
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335    |  345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665  
                                                                                                                                                                                                                                                                                        340-CSD                                                                                                                                                                                                                                                                                                                                   

   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  (2, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1YHY)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (ILVB_ARATH | P17597)
molecular function
    GO:0003984    acetolactate synthase activity    Catalysis of the reaction: 2 pyruvate = 2-acetolactate + CO2.
    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:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0030976    thiamine pyrophosphate binding    Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009082    branched-chain amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009097    isoleucine biosynthetic process    The chemical reactions and pathways resulting in the formation of isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid.
    GO:0009635    response to herbicide    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a herbicide stimulus. Herbicides are chemicals used to kill or control the growth of plants.
    GO:0009099    valine biosynthetic process    The chemical reactions and pathways resulting in the formation of valine, 2-amino-3-methylbutanoic acid.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009570    chloroplast stroma    The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ILVB_ARATH | P175971ybh 1yhz 1yi0 1yi1 1z8n 3e9y 3ea4 5k2o 5k3s 5k6q 5k6r 5k6t

(-) Related Entries Specified in the PDB File

1jsc CRYSTAL STRUCTURE OF YEAST ACETOHYDROXYACID SYNTHASE
1n0h CRYSTAL STRUCTURE OF YEAST ACETOHYDROXYACID SYNTHASE IN COMPLEX WITH A SULFONYLUREA HERBICIDE, CHLORIMURON ETHYL
1t9a CRYSTAL STRUCTURE OF YEAST ACETOHYDROXYACID SYNTHASE IN COMPLEX WITH A SULFONYLUREA HERBICIDE, TRIBENURON METHYL
1t9b CRYSTAL STRUCTURE OF YEAST ACETOHYDROXYACID SYNTHASE IN COMPLEX WITH A SULFONYLUREA HERBICIDE, CHLORSULFURON
1t9c CRYSTAL STRUCTURE OF YEAST ACETOHYDROXYACID SYNTHASE IN COMPLEX WITH A SULFONYLUREA HERBICIDE, SULFOMETURON METHYL
1t9d CRYSTAL STRUCTURE OF YEAST ACETOHYDROXYACID SYNTHASE IN COMPLEX WITH A SULFONYLUREA HERBICIDE, METSULFURON METHYL
1yhz THE SAME PROTEIN COMPLEX WITH A SULFONYLUREA HERBICIDE, CHLORSULFURON
1yi0 THE SAME PROTEIN COMPLEX WITH A SULFONYLUREA HERBICIDE, SULFOMETURON METHYL
1yi1 THE SAME PROTEIN COMPLEX WITH A SULFONYLUREA HERBICIDE, TRIBENURON METHYL