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(-) Description

Title :  CRYSTAL STRUCTURE OF ARTOCARPIN-MANNOPENTOSE COMPLEX
 
Authors :  A. A. Jeyaprakash, A. Srivastav, A. Surolia, M. Vijayan
Date :  28 Feb 04  (Deposition) - 15 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (3x)
Keywords :  Beta-Prism, Mannose-Specific, Lectin, Jacalin-Like, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Jeyaprakash, A. Srivastav, A. Surolia, M. Vijayan
Structural Basis For The Carbohydrate Specificities Of Artocarpin: Variation In The Length Of A Loop As A Strategy For Generating Ligand Specificity
J. Mol. Biol. V. 338 757 2004
PubMed-ID: 15099743  |  Reference-DOI: 10.1016/J.JMB.2004.03.040
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ARTOCARPIN
    Chains: A, B
    Organism Scientific: ARTOCARPUS INTEGER
    Organism Taxid: 3490
    Tissue: SEEDS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB
Biological Unit 2 (3x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1AYA2Mod. Amino AcidN-ACETYLALANINE
2MAN7Ligand/IonALPHA-D-MANNOSE
3SO45Ligand/IonSULFATE ION
Biological Unit 1 (3, 28)
No.NameCountTypeFull Name
1AYA4Mod. Amino AcidN-ACETYLALANINE
2MAN14Ligand/IonALPHA-D-MANNOSE
3SO410Ligand/IonSULFATE ION
Biological Unit 2 (3, 42)
No.NameCountTypeFull Name
1AYA6Mod. Amino AcidN-ACETYLALANINE
2MAN21Ligand/IonALPHA-D-MANNOSE
3SO415Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:15 , THR A:91 , THR A:93 , GLY A:137 , ASP A:138 , LEU A:139 , ASP A:141 , MAN A:406BINDING SITE FOR RESIDUE MAN A 405
02AC2SOFTWARELEU A:89 , ALA A:90 , THR A:91 , ASP A:138 , MAN A:405 , MAN A:407BINDING SITE FOR RESIDUE MAN A 406
03AC3SOFTWAREMAN A:406 , MAN A:408BINDING SITE FOR RESIDUE MAN A 407
04AC4SOFTWAREALA A:90 , MAN A:407BINDING SITE FOR RESIDUE MAN A 408
05AC5SOFTWAREGLY B:15 , THR B:91 , THR B:93 , GLY B:137 , ASP B:138 , LEU B:139 , ASP B:141 , MAN B:406BINDING SITE FOR RESIDUE MAN B 405
06AC6SOFTWARELEU B:89 , ALA B:90 , THR B:91 , ASP B:138 , MAN B:405 , MAN B:407BINDING SITE FOR RESIDUE MAN B 406
07AC7SOFTWAREMAN B:406 , HOH B:419BINDING SITE FOR RESIDUE MAN B 407
08AC8SOFTWAREGLY B:17 , ARG B:135BINDING SITE FOR RESIDUE SO4 B 500
09AC9SOFTWAREPHE B:86 , SER B:87 , ARG B:97BINDING SITE FOR RESIDUE SO4 B 501
10BC1SOFTWAREGLY A:17 , ARG A:135BINDING SITE FOR RESIDUE SO4 A 502
11BC2SOFTWAREGLN A:3 , GLN B:3BINDING SITE FOR RESIDUE SO4 A 503
12BC3SOFTWAREHOH B:419BINDING SITE FOR RESIDUE SO4 B 511

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VBP)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:71 -Pro A:72
2Gly A:110 -Pro A:111
3Phe B:71 -Pro B:72
4Gly B:110 -Pro B:111

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VBP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VBP)

(-) Exons   (0, 0)

(no "Exon" information available for 1VBP)

(-) 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:149
 aligned with Q7M1T4_ARTIN | Q7M1T4 from UniProtKB/TrEMBL  Length:149

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
         Q7M1T4_ARTIN     1 ASQTITVGPWGGPGGNGWDDGSYTGIRQIELSYKEAIGSFSVIYDLNGEPFSGPKHTSKLPYKNVKIELRFPDEFLESVSGYTAPFSALATPTPVVRSLTFKTNKGRTFGPYGDEEGTYFNLPIENGLIVGFKGRTGDLLDAIGVHMAL 149
               SCOP domains d1vbpa_ A: Artocarpin                                                                                                                                 SCOP domains
               CATH domains -1vbpA00 A:2-149  [code=2.100.10.30, no name defined]                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....eee.....eeeeeeeee...eeeeeeeeee..eeee..........eeeeee.......eeeeeeeeee........eee.eeeeee....eeeeee....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vbp A   1 aSQTITVGSWGGPGGNGWDDGSYTGIRQIELSYKEAIGSFSVIYDLNGDPFSGPKHTSKLPYKNVKIELKFPDEFLESVSGYTGPFSALATPTPVVRSLTFKTNKGRTFGPYGDEEGTYFNLPIENGLIVGFKGRTGDLLDAIGIHMSL 149
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140         
                            |                                                                                                                                                    
                            1-AYA                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:149
 aligned with Q7M1T4_ARTIN | Q7M1T4 from UniProtKB/TrEMBL  Length:149

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
         Q7M1T4_ARTIN     1 ASQTITVGPWGGPGGNGWDDGSYTGIRQIELSYKEAIGSFSVIYDLNGEPFSGPKHTSKLPYKNVKIELRFPDEFLESVSGYTAPFSALATPTPVVRSLTFKTNKGRTFGPYGDEEGTYFNLPIENGLIVGFKGRTGDLLDAIGVHMAL 149
               SCOP domains d1vbpb_ B: Artocarpin                                                                                                                                 SCOP domains
               CATH domains -1vbpB00 B:2-149  [code=2.100.10.30, no name defined]                                                                                                 CATH domains
           Pfam domains (1) --------------Jacalin-1vbpB01 B:15-147                                                                                                             -- Pfam domains (1)
           Pfam domains (2) --------------Jacalin-1vbpB02 B:15-147                                                                                                             -- Pfam domains (2)
         Sec.struct. author ....eeeeeee....eeee.....eeeeeeeee...eeeeeeeeee..eeee..........eeeeee.......eeeeeeeee..........eeeeeeeee....eeeeee....eeeeeeeee.eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vbp B   1 aSQTITVGSWGGPGGNGWDDGSYTGIRQIELSYKEAIGSFSVIYDLNGDPFSGPKHTSKLPYKNVKIELKFPDEFLESVSGYTGPFSALATPTPVVRSLTFKTNKGRTFGPYGDEEGTYFNLPIENGLIVGFKGRTGDLLDAIGIHMSL 149
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140         
                            1-AYA
   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, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Jacalin] (35)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1VBP)

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

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        Q7M1T4_ARTIN | Q7M1T4: 1j4s 1j4t 1j4u 1vbo 4akd

(-) Related Entries Specified in the PDB File

1j4s CRYSTAL STRUCTURE OF ARTOCARPIN FORM I
1j4t CRYSTAL STRUCTURE OF ARTOCARPIN FORM II
1j4u CRYSTAL STRUCTURE OF ARTOCARPIN-METHYL-ALPHA-MANNOSE COMPLEX
1vbo CRYSTAL STRUCTURE OF ARTOCARPIN-MANNOTRIOSE COMPLEX