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(-) Description

Title :  CRYSTAL STRUCTURE OF WHEAT GERM AGGLUTININ ISOLECTIN 3 IN COMPLEX WITH A SYNTHETIC DIVALENT CARBOHYDRATE LIGAND
 
Authors :  D. Schwefel, C. Maierhofer, V. Wittmann, K. Diederichs, W. Welte
Date :  05 Feb 10  (Deposition) - 23 Feb 10  (Release) - 30 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chitin-Binding, Sugar Binding Protein, Protein-Carbohydrate Interaction (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Schwefel, C. Maierhofer, J. G. Beck, S. Seeberger, K. Diederichs, H. M. Moller, W. Welte, V. Wittmann
Structural Basis Of Multivalent Binding To Wheat Germ Agglutinin.
J. Am. Chem. Soc. V. 132 8704 2010
PubMed-ID: 20527753  |  Reference-DOI: 10.1021/JA101646K

(-) Compounds

Molecule 1 - AGGLUTININ ISOLECTIN 3
    ChainsA, B
    Organism CommonBREAD WHEAT
    Organism ScientificTRITICUM AESTIVUM
    Organism Taxid4565
    SynonymWHEAT GERM AGGLUTININ ISOLECTIN 3, WGA3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2GYT4Ligand/IonBIS-(2-ACETAMIDO-2-DEOXY-ALPHA-D-GLUCOPYRANOSYLOXYCARBONYL)-4,7,10-TRIOXA-1,13-TRIDECANEDIAMINE
3PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:2 , GLN A:6 , GLN A:20 , TYR A:21 , SER A:62 , TYR A:64 , HIS A:66 , ALA A:71 , GLU A:72 , TYR A:73 , ASP A:135 , ALA A:136 , GLY A:137 , ARG A:139 , GYT A:1173 , HOH A:2012 , HOH A:2035 , HOH A:2097 , HOH A:2098 , HOH A:2099 , HOH A:2100 , ASP B:86 , SER B:105 , TRP B:107 , TYR B:109 , SER B:114 , GLU B:115 , PHE B:116 , HOH B:2048BINDING SITE FOR RESIDUE GYT A1172
2AC2SOFTWARESER A:19 , TYR A:23 , GLY A:28 , ASP A:29 , TYR A:30 , GYT A:1172 , ASP B:129 , SER B:148 , TRP B:150 , SER B:152 , PRO B:157 , GLY B:158 , TYR B:159 , HOH B:2059BINDING SITE FOR RESIDUE GYT A1173
3AC3SOFTWAREASP A:86 , SER A:105 , TRP A:107 , TYR A:109 , SER A:114 , GLU A:115 , SER B:62 , TYR B:64 , HIS B:66 , ALA B:71 , GLU B:72 , TYR B:73 , GLY B:137 , HOH B:2018 , HOH B:2073 , HOH B:2074 , HOH B:2075BINDING SITE FOR RESIDUE GYT B1172
4AC4SOFTWAREASP A:129 , SER A:148 , TRP A:150 , SER A:152 , PRO A:157 , GLY A:158 , TYR A:159 , SER B:19 , TYR B:21 , TYR B:23 , GLY B:28 , ASP B:29 , TYR B:30 , LYS B:149 , ALA B:162 , GLY B:163 , HOH B:2069 , HOH B:2076 , HOH B:2077BINDING SITE FOR RESIDUE GYT B1173
5AC5SOFTWAREMET A:26 , GLY A:27 , ALA B:125 , CYS B:126 , ASP B:129 , TYR B:145 , CYS B:153BINDING SITE FOR RESIDUE GOL B1174

(-) SS Bonds  (32, 32)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:18
2A:12 -A:24
3A:17 -A:31
4A:35 -A:40
5A:46 -A:61
6A:55 -A:67
7A:60 -A:74
8A:78 -A:83
9A:89 -A:104
10A:98 -A:110
11A:103 -A:117
12A:121 -A:126
13A:132 -A:147
14A:141 -A:153
15A:146 -A:160
16A:164 -A:169
17B:3 -B:18
18B:12 -B:24
19B:17 -B:31
20B:35 -B:40
21B:46 -B:61
22B:55 -B:67
23B:60 -B:74
24B:78 -B:83
25B:89 -B:104
26B:98 -B:110
27B:103 -B:117
28B:121 -B:126
29B:132 -B:147
30B:141 -B:153
31B:146 -B:160
32B:164 -B:169

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X52)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X52)

(-) PROSITE Motifs  (2, 15)

Asymmetric/Biological Unit (2, 15)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHIT_BIND_I_2PS50941 Chitin-binding type-1 domain profile.AGI3_WHEAT1-42
43-85
 
86-128
 
129-171
 
  7A:2-42
A:43-85
B:43-85
A:86-128
B:86-128
A:129-171
B:129-171
2CHIT_BIND_I_1PS00026 Chitin recognition or binding domain signature.AGI3_WHEAT12-31
 
55-74
 
98-117
 
141-160
 
  8A:12-31
B:12-31
A:55-74
B:55-74
A:98-117
B:98-117
A:141-160
B:141-160

(-) Exons   (0, 0)

(no "Exon" information available for 2X52)

(-) 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:171
 aligned with AGI3_WHEAT | P10969 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 
           AGI3_WHEAT     1 QRCGEQGSGMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGKTCPNNHCCSQYGHCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGYCGLGSEFCGEGCQNGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG 171
               SCOP domains d2x52a1 A:1-52 automated matches                    d2x52a2 A:53-86 automated matches d2x52a3 A:87-129 automated matches         d2x52a4 A:130-171 automated matches        SCOP domains
               CATH domains -2x52A01 A:2-42                           2x52A02 A:43-85                            2x52A03 A:86-128                           2x52A04 A:129-171                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh....hhhhhee.....ee.hhhhhh..............hhhhh...hhhhhee.....ee.hhhhhh.............hhhhhh........ee.....ee.hhhhhh.............hhhhh....hhhhhee.....ee.hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CHIT_BIND_I_2  PDB: A:2-42 UniProt: 1-42  CHIT_BIND_I_2  PDB: A:43-85 UniProt: 43-85 CHIT_BIND_I_2  PDB: A:86-128               CHIT_BIND_I_2  PDB: A:129-171               PROSITE (1)
                PROSITE (2) -----------CHIT_BIND_I_1       -----------------------CHIT_BIND_I_1       -----------------------CHIT_BIND_I_1       -----------------------CHIT_BIND_I_1       ----------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x52 A   1 xRCGEQGSGMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGKTCPNNHCCSQYGHCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGYCGLGSEFCGEGCQNGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG 171
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 
                            |                                                                                                                                                                          
                            1-PCA                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:170
 aligned with AGI3_WHEAT | P10969 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
           AGI3_WHEAT     2 RCGEQGSGMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGKTCPNNHCCSQYGHCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGYCGLGSEFCGEGCQNGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG 171
               SCOP domains d2x52b1 B:2-52 automated matches                   d2x52b2 B:53-86 automated matches d2x52b3 B:87-129 automated matches         d2x52b4 B:130-171 automated matches        SCOP domains
               CATH domains 2x52B01 B:2-42                           2x52B02 B:43-85                            2x52B03 B:86-128                           2x52B04 B:129-171                           CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------Chitin_bind_1-2x52B01 B:129-169          -- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------Chitin_bind_1-2x52B02 B:129-169          -- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------Chitin_bind_1-2x52B03 B:129-169          -- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------Chitin_bind_1-2x52B04 B:129-169          -- Pfam domains (4)
           Pfam domains (5) -------------------------------------------------------------------------------------------------------------------------------Chitin_bind_1-2x52B05 B:129-169          -- Pfam domains (5)
           Pfam domains (6) -------------------------------------------------------------------------------------------------------------------------------Chitin_bind_1-2x52B06 B:129-169          -- Pfam domains (6)
           Pfam domains (7) -------------------------------------------------------------------------------------------------------------------------------Chitin_bind_1-2x52B07 B:129-169          -- Pfam domains (7)
           Pfam domains (8) -------------------------------------------------------------------------------------------------------------------------------Chitin_bind_1-2x52B08 B:129-169          -- Pfam domains (8)
         Sec.struct. author .hhhhhh...hhhhhee.....ee.hhhhhh.............hhhhhh...hhhhhee.....ee.hhhhhh..............hhhhh...hhhhhee.....ee.hhhhhh..............hhhhh...hhhhhee.....ee.hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CHIT_BIND_I_2  PDB: - UniProt: 1-42      CHIT_BIND_I_2  PDB: B:43-85 UniProt: 43-85 CHIT_BIND_I_2  PDB: B:86-128               CHIT_BIND_I_2  PDB: B:129-171               PROSITE (1)
                PROSITE (2) ----------CHIT_BIND_I_1       -----------------------CHIT_BIND_I_1       -----------------------CHIT_BIND_I_1       -----------------------CHIT_BIND_I_1       ----------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x52 B   2 RCGEQGSGMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGKTCPNNHCCSQYGHCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGYCGLGSEFCGEGCQNGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG 171
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

   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  (1, 8)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 8)

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

(-) Pfam Domains  (1, 8)

Asymmetric/Biological Unit

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AGI3_WHEAT | P10969)
molecular function
    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.
    GO:0008061    chitin binding    Interacting selectively and non-covalently with chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AGI3_WHEAT | P109691k7t 1k7u 1k7v 1wgt

(-) Related Entries Specified in the PDB File

1k7t CRYSTAL STRUCTURE ANALYSIS OF CROSSLINKED-WGA3 /GLCNACBETA1,6GAL COMPLEX
1k7u CRYSTAL STRUCTURE ANALYSIS OF CROSSLINKED-WGA3 /GLCNACBETA1,4GLCNAC COMPLEX
1k7v CRYSTAL STRUCTURE ANALYSIS OF CROSSLINKED-WGA3 /GLCNACBETA1,6GALBETA1,4GLC
1wgt WHEAT GERM AGGLUTININ (ISOLECTIN 3)
2x3t GLUTARALDEHYDE-CROSSLINKED WHEAT GERM AGGLUTININ ISOLECTIN 1 CRYSTAL SOAKED WITH A SYNTHETIC GLYCOPEPTIDE