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(-) Description

Title :  STRUCTURE OF TETRAMERIC JACALIN COMPLEXED WITH GLCNAC BETA-(1,3) GAL-BETA-OME
 
Authors :  K. V. Abhinav, K. Sharma, A. Surolia, M. Vijayan
Date :  01 Apr 16  (Deposition) - 08 Feb 17  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Plant Lectins, Sugar Binding Protein, Galactose Specific Lectin, Beta-Prism I Fold, Post Translational Proteolysis, T-Antigen Binding Protein, Reducing And Non-Reducing Sugars (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. V. Abhinav, K. Sharma, A. Surolia, M. Vijayan
Distortion Of The Ligand Molecule As A Strategy For Modulating Binding Affinity: Further Studies Involving Complexes Of Jacalin With Beta-Substituted Disaccharides.
Iubmb Life V. 69 72 2017
PubMed-ID: 28111895  |  Reference-DOI: 10.1002/IUB.1593

(-) Compounds

Molecule 1 - AGGLUTININ ALPHA CHAIN
    ChainsA, C, E, G
    OrganSEED
    Organism CommonJACK FRUIT
    Organism ScientificARTOCARPUS INTEGER
    Organism Taxid3490
    SynonymJACALIN ALPHA CHAIN
 
Molecule 2 - AGGLUTININ BETA-3 CHAIN
    ChainsB, D, F, H
    OrganSEED
    Organism CommonJACK FRUIT
    Organism ScientificARTOCARPUS INTEGER
    Organism Taxid3490
    SynonymJACALIN BETA-3 CHAIN

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)ABCD    
Biological Unit 2 (1x)    EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2MBG2Ligand/IonMETHYL-BETA-GALACTOSE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2MBG1Ligand/IonMETHYL-BETA-GALACTOSE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2MBG1Ligand/IonMETHYL-BETA-GALACTOSE
3NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:53 , HOH A:304binding site for residue EDO A 201
02AC2SOFTWAREASN A:110 , GLY A:111 , LEU A:112 , GLN F:3 , SER F:4binding site for residue EDO A 202
03AC3SOFTWAREASP A:59 , SER A:62binding site for residue EDO A 203
04AC4SOFTWARETYR C:39 , VAL C:40 , SER E:18 , ASP E:27 , LYS E:45binding site for residue EDO E 201
05AC5SOFTWAREALA E:3 , PHE E:4 , ASP E:5 , LYS E:117 , GLY E:118 , TYR E:126binding site for residue PEG E 202
06AC6SOFTWARETHR E:102 , TRP F:15 , GLY F:16 , HOH F:202 , ASN G:105binding site for residue EDO F 101
07AC7SOFTWARETYR C:78 , VAL C:79 , GLY G:1 , TYR G:78 , GLY G:121 , TYR G:122 , TRP G:123 , ASP G:125 , HOH G:309binding site for residue MBG G 201
08AC8SOFTWAREALA G:3 , PHE G:4 , LYS G:117 , GLY G:118 , HOH G:301binding site for residue EDO G 202
09AC9SOFTWARESER G:46 , PHE G:47binding site for residue EDO G 203
10AD1SOFTWAREASN E:105 , THR G:72 , THR G:102 , TRP H:15 , GLY H:16 , HOH H:202 , HOH H:207binding site for residue EDO H 101
11AD2SOFTWAREGLY A:1 , PHE A:47 , TYR A:78 , GLY A:121 , TYR A:122 , TRP A:123 , ASP A:125 , HOH A:305 , HOH A:306 , HOH A:308 , HOH A:338binding site for Poly-Saccharide residues NAG A 204 through MBG A 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J4T)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Phe A:60 -Pro A:61
2Gly A:94 -Pro A:95
3Gly B:13 -Pro B:14
4Phe C:60 -Pro C:61
5Gly C:94 -Pro C:95
6Gly D:13 -Pro D:14
7Phe E:60 -Pro E:61
8Gly E:94 -Pro E:95
9Gly F:13 -Pro F:14
10Phe G:60 -Pro G:61
11Gly G:94 -Pro G:95
12Gly H:13 -Pro H:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J4T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J4T)

(-) Exons   (0, 0)

(no "Exon" information available for 5J4T)

(-) 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:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeeeeeee.....eeeeeeeeee..eeee...........eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j4t A   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHKSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   

Chain B from PDB  Type:PROTEIN  Length:16
                                                
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 5j4t B   3 QSGISQTVIVGPWGAK  18
                                    12      

Chain C from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeeeeeee.....eeeeeeeeee..eeeeeeee.......eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j4t C   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHKSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   

Chain D from PDB  Type:PROTEIN  Length:14
                                              
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 5j4t D   3 QSGISQTVIVGPWG  16
                                    12    

Chain E from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeeeeeee.....eeeeeeeeee..eeeeeeee.......eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j4t E   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHKSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   

Chain F from PDB  Type:PROTEIN  Length:16
                                                
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 5j4t F   3 QSGISQTVIVGPWGAK  18
                                    12      

Chain G from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeeeeeee.....eeeeeeeeee..eeee...........eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeee.....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j4t G   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHKSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   

Chain H from PDB  Type:PROTEIN  Length:15
                                               
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 5j4t H   4 SGISQTVIVGPWGAK  18
                                    13     

   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  (0, 0)

(no "SCOP Domain" information available for 5J4T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J4T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J4T)

(-) Gene Ontology  (4, 8)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        LECA_ARTIN | P186701jac 1ku8 1kuj 1m26 1pxd 1toq 1tp8 1ugw 1ugx 1ugy 1uh0 1uh1 1ws4 1ws5 4ak4 4akb 4akc 4r6n 4r6o 4r6p 4r6q 4r6r 5j4x 5j50 5j51 5jm1
        LECB3_ARTIN | P186731m26 1pxd 1toq 1tp8 1ugw 1ugx 1ugy 1uh0 1uh1 1ws4 1ws5 4r6n 4r6o 4r6p 4r6q 4r6r 5j4x 5j50 5j51 5jm1

(-) Related Entries Specified in the PDB File

1jac 1ku8 1kuj 1m26 1ugw 1ugx 1ugy 1uh0 1uh1 1ws4 1ws5 4r6n 4r6o 4r6p 4r6q 4r6r