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

(-) Description

Title :  CRYSTAL STRUCTURE OF WHEAT GERM AGGLUTININ ISOLECTIN 1 IN COMPLEX WITH GLYCOSYLURETHAN
 
Authors :  D. Schwefel, C. Maierhofer, J. G. Beck, S. Seeberger, K. Diederichs, H. M. Moeller, W. Welte, V. Wittmann
Date :  12 Mar 12  (Deposition) - 04 Apr 12  (Release) - 04 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sugar Binding Protein, Synthetic Carbohydrate Ligand, Protein Carbohydrate Interaction, Lectin, Chitin-Binding, Carbohydrate Binding Protein (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 1
    Chains: A, B
    Organism Common: BREAD WHEAT
    Organism Scientific: TRITICUM AESTIVUM
    Organism Taxid: 4565
    Synonym: ISOLECTIN A, WGA1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL; PROPANE-1,2,3-TRIOL
2GYU4Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-1-O-(PROPYLCARBAMOYL)-ALPHA-D-GLUCOPYRANOSE
3PCA2Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:21 , TYR A:23 , SER A:62 , TYR A:64 , TYR A:66 , GLU A:72 , TYR A:73 , HOH A:2063 , HOH A:2144 , HOH A:2145 , HOH A:2146 , SER B:114 , GLU B:115BINDING SITE FOR RESIDUE GYU A1172
2AC2SOFTWAREGLY A:51 , ALA A:53 , ASP A:86 , SER A:105 , TRP A:107 , PHE A:109 , PHE A:116 , HOH A:2103 , HOH A:2147 , ALA B:71 , GLU B:72BINDING SITE FOR RESIDUE GYU A1173
3AC3SOFTWAREGLY A:124 , ALA A:125 , CYS A:126 , THR A:128 , ASP A:129 , CYS A:153 , HOH A:2123 , HOH A:2129 , HOH A:2148 , MET B:26 , GLY B:27 , TRP B:41BINDING SITE FOR RESIDUE GOL A1174
4AC4SOFTWARESER A:114 , GLU A:115 , HOH A:2118 , SER B:62 , TYR B:66 , GLU B:72 , TYR B:73BINDING SITE FOR RESIDUE GYU B1171
5AC5SOFTWAREGLN A:20 , TYR A:21 , ALA A:71 , GLU A:72 , GLY A:138 , HOH A:2091 , ASP B:86 , SER B:105 , TRP B:107 , PHE B:109 , GLU B:115 , PHE B:116 , HOH B:2094 , HOH B:2095 , HOH B:2096 , HOH B:2097BINDING SITE FOR RESIDUE GYU B1172
6AC6SOFTWAREMET A:26 , GLY A:27 , TRP A:41 , HOH A:2037 , GLY B:124 , ALA B:125 , CYS B:126 , ASP B:129 , TYR B:145 , CYS B:153 , HOH B:2073 , HOH B:2077 , HOH B:2078BINDING SITE FOR RESIDUE GOL B1173

(-) 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 4AML)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AML)

(-) PROSITE Motifs  (2, 14)

Asymmetric/Biological Unit (2, 14)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHIT_BIND_I_2PS50941 Chitin-binding type-1 domain profile.AGI1_WHEAT26-68
69-111
 
112-154
 
155-197
 		  6-
A:43-85
B:43-85
A:86-128
B:86-128
A:129-171
B:129-170
2CHIT_BIND_I_1PS00026 Chitin recognition or binding domain signature.AGI1_WHEAT38-57
 
81-100
 
124-143
 
167-186
 		  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 4AML)

(-) 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 AGI1_WHEAT | P10968 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:171
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196 
           AGI1_WHEAT    27 QRCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG 197
               SCOP domains d4amla1 A:1-52 Wheat germ agglutinin (WGA)          d4amla2 A:53-86                   d4amla3 A:87-129                           d4amla4 A:130-171                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh....hhhhhee.....ee.hhhhhh.............hhhhhh........ee.....ee.hhhhhh.............hhhhhh...hhhhhee.....ee.hhhhhh......................hhhhhee.....ee.hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CHIT_BIND_I_2  PDB: - UniProt: 26-68      CHIT_BIND_I_2  PDB: A:43-85 UniProt: 69-111CHIT_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
                 4aml A   1 xRCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG 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 AGI1_WHEAT | P10968 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:170
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196
           AGI1_WHEAT    27 QRCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCD 196
               SCOP domains d4amlb1 B:1-52 Wheat germ agglutinin (WGA)          d4amlb2 B:53-86                   d4amlb3 B:87-129                           d4amlb4 B:130-170                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh...hhhhhee.....ee.hhhhhh.............hhhhhh........ee.....ee.hhhhhh.............hhhhhh...hhhhhee.....ee.hhhhhh..............hhhhh...hhhhhee.....ee.hhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CHIT_BIND_I_2  PDB: - UniProt: 26-68      CHIT_BIND_I_2  PDB: B:43-85 UniProt: 69-111CHIT_BIND_I_2  PDB: B:86-128               CHIT_BIND_I_2  PDB: B:129-170              PROSITE (1)
                PROSITE (2) -----------CHIT_BIND_I_1       -----------------------CHIT_BIND_I_1       -----------------------CHIT_BIND_I_1       -----------------------CHIT_BIND_I_1       ---------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aml B   1 xRCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCD 170
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
                            1-PCA
   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
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0 ; only for superseded entry 2UWG: 1,8)

(no "CATH Domain" information available for 4AML, only for superseded entry 2UWG replaced by 4AML)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AML)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AGI1_WHEAT | P10968)
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.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GYU  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4aml)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4aml
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  AGI1_WHEAT | P10968
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  AGI1_WHEAT | P10968
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        AGI1_WHEAT | P10968: 1wgc 2cwg 2uvo 2x3t 7wga

(-) Related Entries Specified in the PDB File

1wgc WHEAT GERM AGGLUTININ (ISOLECTIN 1) COMPLEX WITH N- ACETYLNEURAMINYLLACTOSE
2cwg WHEAT GERM AGGLUTININ ISOLECTIN 1 COMPLEX WITH T5 SIALOGLYCOPEPTIDE OF GLYCOPHORIN A
2uvo HIGH RESOLUTION CRYSTAL STRUCTURE OF WHEAT GERM AGGLUTININ IN COMPLEX WITH N-ACETYL-D-GLUCOSAMINE
2x3t GLUTARALDEHYDE-CROSSLINKED WHEAT GERM AGGLUTININ ISOLECTIN 1 CRYSTAL SOAKED WITH A SYNTHETIC GLYCOPEPTIDE
7wga WHEAT GERM AGGLUTININ (ISOLECTIN 1)