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(-) Description

Title :  JACALIN-CARBOHYDRATE INTERACTIONS. DISTORTION OF THE LIGAND AS A DETERMINANT OF AFFINITY.
 
Authors :  K. V. Abhinav, K. Sharma, C. P. Swaminathan, A. Surolia, M. Vijayan
Date :  26 Aug 14  (Deposition) - 18 Feb 15  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.38
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D,E,F,G,H  (1x)
Biol. Unit 2:  A,B,C,D  (1x)
Biol. Unit 3:  E,F,G,H  (1x)
Keywords :  Galactose Specific Lectin, Beta-Prism I Fold, Post Translational Proteolysis, T-Antigen Binding Protein, Plant Lectins, Galactose And Sugar Binding Protein, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. V. Abhinav, K. Sharma, C. P. Swaminathan, A. Surolia, M. Vijayan
Jacalin-Carbohydrate Interactions: Distortion Of The Ligand Molecule As A Determinant Of Affinity.
Acta Crystallogr. , Sect. D V. 71 324 2015
PubMed-ID: 25664742  |  Reference-DOI: 10.1107/S139900471402553X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AGGLUTININ ALPHA CHAIN
    Chains: A, C, E, G
    Organism Common: CAMPEDAK,CHEMPEDAK
    Organism Scientific: ARTOCARPUS INTEGER
    Organism Taxid: 3490
    Synonym: JACALIN ALPHA CHAIN
 
Molecule 2 - AGGLUTININ BETA-3 CHAIN
    Chains: B, D, F, H
    Fragment: UNP RESIDUES 2-20
    Organism Common: CAMPEDAK,CHEMPEDAK
    Organism Scientific: ARTOCARPUS INTEGER
    Organism Taxid: 3490
    Synonym: JACALIN BETA-3 CHAIN

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCDEFGH
Biological Unit 2 (1x): ABCD    
Biological Unit 3 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
11473Ligand/Ion1-O-[P-NITROPHENYL]-BETA-D-GALACTOPYRANOSE
2EDO10Ligand/Ion1,2-ETHANEDIOL
3IPA1Ligand/IonISOPROPYL ALCOHOL
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
11473Ligand/Ion1-O-[P-NITROPHENYL]-BETA-D-GALACTOPYRANOSE
2EDO10Ligand/Ion1,2-ETHANEDIOL
3IPA1Ligand/IonISOPROPYL ALCOHOL
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
11471Ligand/Ion1-O-[P-NITROPHENYL]-BETA-D-GALACTOPYRANOSE
2EDO10Ligand/Ion1,2-ETHANEDIOL
3IPA1Ligand/IonISOPROPYL ALCOHOL
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
11472Ligand/Ion1-O-[P-NITROPHENYL]-BETA-D-GALACTOPYRANOSE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3IPA-1Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:1 , TYR A:78 , GLY A:121 , TYR A:122 , TRP A:123 , ASP A:125BINDING SITE FOR RESIDUE 147 A 201
02AC2SOFTWARELYS A:55 , HOH A:306BINDING SITE FOR RESIDUE EDO A 202
03AC3SOFTWARELEU A:34 , ASN A:35 , SER A:37 , ASP E:6 , PHE E:9 , TYR E:39BINDING SITE FOR RESIDUE EDO A 203
04AC4SOFTWARETHR A:23 , SER A:76 , HOH A:317BINDING SITE FOR RESIDUE EDO A 204
05AC5SOFTWAREPRO A:38 , VAL A:40 , EDO C:201BINDING SITE FOR RESIDUE EDO A 205
06AC6SOFTWAREPHE A:4 , ASP A:5 , GLN A:42 , HIS A:44BINDING SITE FOR RESIDUE EDO A 206
07AC7SOFTWAREASN A:74 , GLY A:101 , THR A:102 , HOH A:410BINDING SITE FOR RESIDUE IPA A 207
08AC8SOFTWAREEDO A:205 , TRP C:123BINDING SITE FOR RESIDUE EDO C 201
09AC9SOFTWARETYR C:19 , PRO C:95 , TYR C:96 , GLY C:97BINDING SITE FOR RESIDUE EDO C 202
10BC1SOFTWAREPHE C:51 , THR C:52 , PRO C:53 , HOH C:375BINDING SITE FOR RESIDUE EDO C 203
11BC2SOFTWARESER D:4 , TYR G:64 , ASN G:110 , GLY G:111BINDING SITE FOR RESIDUE EDO D 101
12BC3SOFTWAREGLY E:1 , SER E:76 , TYR E:78 , VAL E:80 , GLY E:121 , TYR E:122 , TRP E:123 , ASP E:125BINDING SITE FOR RESIDUE 147 E 201
13BC4SOFTWAREGLY C:1 , TYR C:78 , VAL C:79 , HOH C:322 , GLY G:1 , TYR G:78 , GLY G:121 , TYR G:122 , TRP G:123 , ASP G:125BINDING SITE FOR RESIDUE 147 G 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R6R)

(-) 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 4R6R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R6R)

(-) Exons   (0, 0)

(no "Exon" information available for 4R6R)

(-) 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
                 4r6r A   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHKSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   


Chain B from PDB  Type:PROTEIN  Length:17
                                                 
               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
                 4r6r B   2 EQSGISQTVIVGPWGAK  18
                                    11       


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
                 4r6r 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
                 4r6r D   4 SGISQTVIVGPWGA  17
                                    13    


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..eeee...........eeeeee.......eeeeeeeeeee..eeeeeeeeeee...eeeeee....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r6r 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
                 4r6r 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
                 4r6r 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
                 4r6r 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 4R6R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R6R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R6R)

(-) Gene Ontology  (4, 8)

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  4r6r
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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 5j4t 5j4x 5j50 5j51 5jm1
        LECB3_ARTIN | P18673: 1m26 1pxd 1toq 1tp8 1ugw 1ugx 1ugy 1uh0 1uh1 1ws4 1ws5 4r6n 4r6o 4r6p 4r6q 5j4t 5j4x 5j50 5j51 5jm1

(-) Related Entries Specified in the PDB File

1jac THE SAME PROTEIN COMPLEXED WITH ALPHA-METHYL-D-GALACTOSIDE.
1ku8 NATIVE JACALIN STRUCTURE.
1m26 JACALIN COMPLEXED WITH T-ANTIGEN.
1ugw THE SAME PROTEIN COMPLEXED WITH D-GALACTOSIDE.
1ugy JACALIN COMPLEXED WITH MELLIBIOSE.
1uh0 JACALIN COMPLEXED WITH ME-ALPHA-GALNAC.
4r6n
4r6o
4r6p
4r6q