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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 :  1.60
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, 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  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2GLA4Ligand/IonALPHA D-GALACTOSE
3IPA3Ligand/IonISOPROPYL ALCOHOL
4NBZ4Ligand/IonNITROBENZENE
Biological Unit 1 (4, 16)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2GLA4Ligand/IonALPHA D-GALACTOSE
3IPA3Ligand/IonISOPROPYL ALCOHOL
4NBZ4Ligand/IonNITROBENZENE
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GLA2Ligand/IonALPHA D-GALACTOSE
3IPA1Ligand/IonISOPROPYL ALCOHOL
4NBZ2Ligand/IonNITROBENZENE
Biological Unit 3 (4, 9)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2GLA2Ligand/IonALPHA D-GALACTOSE
3IPA2Ligand/IonISOPROPYL ALCOHOL
4NBZ2Ligand/IonNITROBENZENE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:76 , TYR A:78 , TYR A:122 , TRP A:123 , GLA A:202 , HOH A:399BINDING SITE FOR RESIDUE NBZ A 201
02AC2SOFTWAREGLY A:1 , TYR A:78 , GLY A:121 , TYR A:122 , TRP A:123 , ASP A:125 , NBZ A:201 , HOH A:346BINDING SITE FOR RESIDUE GLA A 202
03AC3SOFTWAREGLN B:3 , SER B:4 , HOH B:210 , TYR E:64 , ASN E:110 , GLY E:111BINDING SITE FOR RESIDUE EDO B 101
04AC4SOFTWARESER C:76 , TYR C:78 , TYR C:122 , GLA C:202BINDING SITE FOR RESIDUE NBZ C 201
05AC5SOFTWAREGLY C:1 , PHE C:47 , TYR C:78 , GLY C:121 , TYR C:122 , TRP C:123 , ASP C:125 , NBZ C:201 , HOH C:342 , TYR G:122 , NBZ G:201BINDING SITE FOR RESIDUE GLA C 202
06AC6SOFTWAREASN C:16 , LEU C:17 , ASP C:27 , ASN C:43 , LYS C:45 , VAL E:40BINDING SITE FOR RESIDUE EDO C 203
07AC7SOFTWAREALA C:8 , LEU C:34 , HOH C:415 , ALA G:8 , LEU G:34BINDING SITE FOR RESIDUE IPA C 204
08AC8SOFTWARESER E:76 , TYR E:78 , TYR E:122 , GLA E:202 , HOH G:425BINDING SITE FOR RESIDUE NBZ E 201
09AC9SOFTWAREGLY E:1 , TYR E:78 , VAL E:80 , GLY E:121 , TYR E:122 , TRP E:123 , ASP E:125 , NBZ E:201 , HOH E:327 , HOH E:350 , HOH E:355BINDING SITE FOR RESIDUE GLA E 202
10BC1SOFTWAREALA A:8 , LEU A:34 , ALA E:8 , THR E:10BINDING SITE FOR RESIDUE IPA E 203
11BC2SOFTWAREPRO F:14 , GLY F:16 , ALA F:17 , LYS F:18BINDING SITE FOR RESIDUE EDO F 101
12BC3SOFTWAREGLY C:1 , GLA C:202 , TYR G:78 , TYR G:122 , GLA G:202BINDING SITE FOR RESIDUE NBZ G 201
13BC4SOFTWARETYR C:78 , VAL C:79 , HOH C:339 , GLY G:1 , TYR G:78 , GLY G:121 , TYR G:122 , TRP G:123 , ASP G:125 , NBZ G:201 , EDO G:204 , HOH G:322BINDING SITE FOR RESIDUE GLA G 202
14BC5SOFTWAREGLN D:3 , SER D:4 , TYR G:64 , ASN G:110 , GLY G:111BINDING SITE FOR RESIDUE EDO G 203
15BC6SOFTWAREASN C:74 , GLY G:1 , ASP G:125 , GLA G:202 , HOH G:344 , HOH G:404BINDING SITE FOR RESIDUE EDO G 204
16BC7SOFTWAREASN E:110 , TYR G:130 , GLN H:8 , THR H:9 , ILE H:11BINDING SITE FOR RESIDUE IPA H 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R6Q)

(-) 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 4R6Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R6Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4R6Q)

(-) 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
                 4r6q 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
                 4r6q 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
                 4r6q 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 .......eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 4r6q 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
                 4r6q E   1 GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHKSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   


Chain F 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
                 4r6q F   4 SGISQTVIVGPWGAK  18
                                    13     


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
                 4r6q 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
                 4r6q 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 4R6Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R6Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R6Q)

(-) Gene Ontology  (4, 8)

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