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(-) Description

Title :  CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE ANALYSIS OF THE COMPLEX OF WHEAT GERM AGGLUTININ WITH A BIVALENT SIALOGLYCOPEPTIDE FROM GLYCOPHORIN A
 
Authors :  C. S. Wright
Date :  08 Jan 93  (Deposition) - 31 Jan 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,D,E
Keywords :  Lectin(Agglutinin) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. S. Wright, J. Jaeger
Crystallographic Refinement And Structure Analysis Of The Complex Of Wheat Germ Agglutinin With A Bivalent Sialoglycopeptide From Glycophorin A.
J. Mol. Biol. V. 232 620 1993
PubMed-ID: 8345526  |  Reference-DOI: 10.1006/JMBI.1993.1415
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AGGLUTININ ISOLECTIN 1 (WGA1)
    Chains: A, B
    Organism Common: BREAD WHEAT
    Organism Scientific: TRITICUM AESTIVUM
    Organism Taxid: 4565
 
Molecule 2 - T5 SIALOGLYCOPEPTIDE OF GLYCOPHORIN A
    Chains: D, E
    Engineered: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1GAL2Ligand/IonBETA-D-GALACTOSE
2NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
3PCA2Mod. Amino AcidPYROGLUTAMIC ACID
4SIA4Ligand/IonO-SIALIC ACID

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AUNKNOWNTYR B:21 , TYR B:23 , TYR B:30 , SER B:19NULL
02AC1SOFTWAREALA A:71 , GLU A:72 , SER B:105 , TRP B:107 , PHE B:109 , GLU B:115 , PHE B:116 , HOH B:526 , GAL D:2 , ALA D:9 , THR D:10 , HOH D:555 , HOH D:751BINDING SITE FOR RESIDUE SIA D 1
03AC2SOFTWAREASP B:86 , PHE B:109 , SIA D:1 , NDG D:3BINDING SITE FOR RESIDUE GAL D 2
04AC3SOFTWAREGAL D:2 , SIA D:4 , THR D:10 , ARG D:12 , HOH D:731BINDING SITE FOR RESIDUE NDG D 3
05AC4SOFTWARESER A:62 , TYR A:64 , TYR A:66 , GLU A:72 , TYR A:73 , HOH A:560 , SER B:114 , GLU B:115 , NDG D:3 , ASP D:5 , THR D:6 , THR D:10 , ARG D:12 , HOH D:731 , HOH D:873BINDING SITE FOR RESIDUE SIA D 4
06AC5SOFTWAREGAL B:173 , HOH B:789 , ALA E:5BINDING SITE FOR RESIDUE SIA B 172
07AC6SOFTWARESIA B:172 , NDG B:174 , SIA B:175 , HOH B:845 , ALA E:5BINDING SITE FOR RESIDUE GAL B 173
08AC7SOFTWAREARG B:2 , TYR B:23 , GAL B:173 , SIA B:175 , HOH B:732 , HOH B:861 , HOH B:866 , THR E:6BINDING SITE FOR RESIDUE NDG B 174
09AC8SOFTWARESER B:19 , TYR B:21 , TYR B:23 , ASP B:29 , TYR B:30 , GAL B:173 , NDG B:174 , HOH B:666 , HOH B:732 , HOH B:816 , HOH B:844 , THR E:6BINDING SITE FOR RESIDUE SIA B 175
10BUNKNOWNTYR A:64 , TYR A:66 , TYR A:73 , SER A:62 , GLU B:115 , SER B:114NULL
11CUNKNOWNTRP B:107 , PHE B:109 , PHE B:116 , SER B:105 , GLU A:72NULL

(-) 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 2CWG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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:129-171
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 2CWG)

(-) 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 d2cwga1 A:1-52 Wheat germ agglutinin (WGA)          d2cwga2 A:53-86                   d2cwga3 A:87-129                           d2cwga4 A:130-171                          SCOP domains
               CATH domains -2cwgA01 A:2-42                           2cwgA02 A:43-85                            2cwgA03 A:86-128                           2cwgA04 A:129-171                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................ee.....ee..................................ee.....ee.hhhhh............................ee.....ee.hhhhh............................ee.....ee.hhhhh........... 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
                 2cwg 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: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 d2cwgb1 B:1-52 Wheat germ agglutinin (WGA)          d2cwgb2 B:53-86                   d2cwgb3 B:87-129                           d2cwgb4 B:130-171                          SCOP domains
               CATH domains -2cwgB01 B:2-42                           2cwgB02 B:43-85                            2cwgB03 B:86-128                           2cwgB04 B:129-171                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhh......................................hhhhh......................................hhhhh......................................hhhhh........... 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:129-171               PROSITE (1)
                PROSITE (2) -----------CHIT_BIND_I_1       -----------------------CHIT_BIND_I_1       -----------------------CHIT_BIND_I_1       -----------------------CHIT_BIND_I_1       ----------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cwg B   1 xRCGEQGSNMECPNNLCCSQYGYCGMGGDYCGKGCQNGACWTSKRCGSQAGGATCTNNQCCSQYGYCGFGAEYCGAGCQGGPCRADIKCGSQAGGKLCPNNLCCSQWGFCGLGSEFCGGGCQSGACSTDKPCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGCDG 171
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 
                            1-PCA                                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 2cwg D   5 DTYAATPR  12


Chain E from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 2cwg E   5 ATP   7
   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  (1, 8)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CWG)

(-) 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.

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 Related Entries

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        AGI1_WHEAT | P10968: 1wgc 2uvo 2x3t 4aml 7wga

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