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(-) Description

Title :  STRUCTURE OF TETRAMERIC JACALIN COMPLEXED WITH GAL 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 :  1.65
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 And Sugar Binding Protein, Galactose Specific Lectin, Beta-Prism I Fold, Post Translational Proteolysis, T-Antigen Binding Protein, Reducing And Non-Reducing Sugars, Sugar Binding Protein (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
    Chains: A, C, E, G
    Organism Common: JACK FRUIT
    Organism Scientific: ARTOCARPUS INTEGER
    Organism Taxid: 3490
    Synonym: JACALIN ALPHA CHAIN
 
Molecule 2 - AGGLUTININ BETA-3 CHAIN
    Chains: B, D, F, H
    Organism Common: JACK FRUIT
    Organism Scientific: ARTOCARPUS INTEGER
    Organism Taxid: 3490
    Synonym: JACALIN 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, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
1EDO15Ligand/Ion1,2-ETHANEDIOL
2GAL1Ligand/IonBETA-D-GALACTOSE
3IPA1Ligand/IonISOPROPYL ALCOHOL
4MBG1Ligand/IonMETHYL-BETA-GALACTOSE
Biological Unit 1 (4, 11)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2GAL1Ligand/IonBETA-D-GALACTOSE
3IPA1Ligand/IonISOPROPYL ALCOHOL
4MBG1Ligand/IonMETHYL-BETA-GALACTOSE
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2GAL-1Ligand/IonBETA-D-GALACTOSE
3IPA-1Ligand/IonISOPROPYL ALCOHOL
4MBG-1Ligand/IonMETHYL-BETA-GALACTOSE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:35 , HOH A:366 , ASP E:5binding site for residue EDO A 201
02AC2SOFTWARETYR A:19 , LYS A:21 , HOH A:303 , HOH A:316 , LYS E:91 , THR E:92binding site for residue EDO A 202
03AC3SOFTWAREASN A:110 , GLY A:111 , LEU A:112 , SER F:4binding site for residue EDO A 203
04AC4SOFTWAREALA A:8 , PHE A:9 , THR A:10 , HOH A:370 , ALA E:8 , HOH E:317binding site for residue IPA A 204
05AC5SOFTWAREASP C:5 , GLY C:7 , HOH C:312 , ASN G:35binding site for residue EDO C 201
06AC6SOFTWAREASN C:16 , LEU C:17 , ASP C:27 , ASN C:43 , HOH C:346binding site for residue EDO C 202
07AC7SOFTWAREASP C:59binding site for residue EDO C 203
08AC8SOFTWARETRP C:123 , HOH C:389binding site for residue EDO C 204
09AC9SOFTWAREASN A:110 , GLN D:8 , THR D:9 , HOH D:207binding site for residue EDO D 101
10AD1SOFTWARELYS C:55 , HOH C:345 , HOH C:367 , GLU E:14 , LYS E:55binding site for residue EDO E 201
11AD2SOFTWAREASN E:16 , LEU E:17 , SER E:18 , ASP E:27 , ASN E:43 , HOH E:372binding site for residue EDO E 202
12AD3SOFTWARESER F:7 , GLN F:8 , THR F:9 , ASN G:110binding site for residue EDO F 101
13AD4SOFTWARETYR C:78 , HOH C:308 , HOH C:329 , PHE G:47 , TYR G:78 , HOH G:347 , HOH G:359binding site for residue EDO G 201
14AD5SOFTWAREPHE G:4 , ASP G:5 , ASP G:6 , GLN G:42 , HIS G:44 , HOH G:341binding site for residue EDO G 202
15AD6SOFTWAREALA C:8 , ALA G:8 , THR G:10 , HOH G:381binding site for residue EDO G 203
16AD7SOFTWARETYR G:126 , PRO H:14 , ALA H:17 , LYS H:18 , HOH H:202 , HOH H:206binding site for residue EDO H 101
17AD8SOFTWAREGLY A:1 , TYR A:78 , VAL A:80 , GLY A:121 , TYR A:122 , TRP A:123 , ASP A:125 , HOH A:305 , HOH A:326 , HOH A:335 , ALA B:17binding site for Poly-Saccharide residues GAL A 205 through MBG A 206

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J4X)

(-) 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 5J4X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J4X)

(-) Exons   (0, 0)

(no "Exon" information available for 5J4X)

(-) 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
                 5j4x 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
                 5j4x 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..eeee...........eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeee.....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j4x C   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHKSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   


Chain D from PDB  Type:PROTEIN  Length:15
                                               
               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
                 5j4x D   3 QSGISQTVIVGPWGA  17
                                    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
                 5j4x 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
                 5j4x 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
                 5j4x 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
                 5j4x 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 5J4X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J4X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J4X)

(-) Gene Ontology  (4, 8)

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  LECB3_ARTIN | P18673
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 Related Entries

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

UniProtKB/Swiss-Prot
        LECA_ARTIN | P18670: 1jac 1ku8 1kuj 1m26 1pxd 1toq 1tp8 1ugw 1ugx 1ugy 1uh0 1uh1 1ws4 1ws5 4ak4 4akb 4akc 4r6n 4r6o 4r6p 4r6q 4r6r 5j4t 5j50 5j51 5jm1
        LECB3_ARTIN | P18673: 1m26 1pxd 1toq 1tp8 1ugw 1ugx 1ugy 1uh0 1uh1 1ws4 1ws5 4r6n 4r6o 4r6p 4r6q 4r6r 5j4t 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 5j50 5j51 5j52