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(-) Description

Title :  STRUCTURE OF A LECTIN FROM THE SEEDS OF VATAIREA MACROCARPA COMPLEXED WITH GALNAC
 
Authors :  B. L. Sousa, J. C. Silva-Filho, P. Kumar, A. Lyskowski, G. A. Bezerra, P. Delatorre, B. A. M. Rocha, C. S. Nagano, K. Gruber, B. S. Cavada
Date :  16 Jul 14  (Deposition) - 31 Dec 14  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Lectin, Legume, Dalbergieae, Galnac, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. L. Sousa, J. C. Silva Filho, P. Kumar, R. I. Pereira, A. Yskowski, B. A. Rocha, P. Delatorre, G. A. Bezerra, C. S. Nagano, K. Gruber, B. S. Cavada
High-Resolution Structure Of A New Tn Antigen-Binding Lecti From Vatairea Macrocarpa And A Comparative Analysis Of Tn-Binding Legume Lectins.
Int. J. Biochem. Cell Biol. V. 59C 103 2014
PubMed-ID: 25499445  |  Reference-DOI: 10.1016/J.BIOCEL.2014.12.002

(-) Compounds

Molecule 1 - SEED LECTIN
    Chains: A
    Organism Scientific: VATAIREA MACROCARPA
    Organism Taxid: 77050
    Synonym: VML

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 9)

Asymmetric Unit (6, 9)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2CA1Ligand/IonCALCIUM ION
3CIT1Ligand/IonCITRIC ACID
4GOL2Ligand/IonGLYCEROL
5MN1Ligand/IonMANGANESE (II) ION
6SO43Ligand/IonSULFATE ION
Biological Unit 1 (4, 28)
No.NameCountTypeFull Name
1A2G4Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2CA-1Ligand/IonCALCIUM ION
3CIT4Ligand/IonCITRIC ACID
4GOL8Ligand/IonGLYCEROL
5MN-1Ligand/IonMANGANESE (II) ION
6SO412Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:125 , PHE A:127 , ASN A:129 , ASP A:132 , HOH A:452 , HOH A:462binding site for residue CA A 301
2AC2SOFTWAREGLU A:123 , ASP A:125 , ASP A:132 , HIS A:137 , HOH A:454 , HOH A:540binding site for residue MN A 302
3AC3SOFTWAREASP A:87 , GLY A:105 , PHE A:127 , ASN A:129 , GLY A:212 , LEU A:213 , SER A:214 , HIS A:217 , HOH A:465 , HOH A:474 , HOH A:480 , HOH A:513binding site for residue A2G A 303
4AC4SOFTWARESER A:83 , LYS A:84 , THR A:85 , THR A:126 , PHE A:127 , SER A:128 , SER A:134 , ALA A:135 , ARG A:136 , HIS A:217 , SO4 A:307 , HOH A:483 , HOH A:515 , HOH A:518 , HOH A:525 , HOH A:528binding site for residue CIT A 304
5AC5SOFTWAREASN A:162 , TYR A:164 , SER A:166 , THR A:175 , SER A:177 , LEU A:178 , THR A:179 , HOH A:422 , HOH A:426 , HOH A:428binding site for residue GOL A 305
6AC6SOFTWARESER A:68 , GLU A:168 , ALA A:169 , SER A:170binding site for residue GOL A 306
7AC7SOFTWARELYS A:84 , HIS A:217 , CIT A:304 , HOH A:480 , HOH A:483binding site for residue SO4 A 307
8AC8SOFTWARELYS A:149 , ARG A:215 , HOH A:412 , HOH A:418binding site for residue SO4 A 308
9AC9SOFTWARETHR A:27 , LYS A:29 , LYS A:31 , HOH A:498 , HOH A:531binding site for residue SO4 A 309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U2A)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:86 -Asp A:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U2A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U2A)

(-) Exons   (0, 0)

(no "Exon" information available for 4U2A)

(-) 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:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..ee.....ee...ee..ee....eeeeee...ee.ee....ee.eeeeeeeee..........eeeeeeee........hhhhh........eeeeee...........eeeeee......eeee........eeeeeeeehhh.eeeeeeee....eeeeeeee.hhhhhh..eeeeeeeeee..........ee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u2a A   1 SEVVSFSFTKFNPNPKDIILQGDALVTSKGKLQLTKVKDGKPVDHSLGRALYAAPIHIWDDSTDRVASFATSFSFVVEAPDESKTADGIAFFLAPPDTQPQKDGGFLGLFNDIQTVAVEFDTFSNTWDPSARHIGINVNSIESMKYVKWGWENGKVANVYISYEASTKTLTASLTYPSNATSYIVSANVDLKSALPEWVRVGFSATSGLSRDHVETHDVLDWSFTSTLQ 233
                                    10        20        30        40        50        60        70        80        90       100       110 ||    124       134       144       154       164       174       184       194       204       214       224         
                                                                                                                                         112|                                                                                                                    
                                                                                                                                          117
   Legend:   → Mismatch (orange background)
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  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 4U2A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U2A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U2A)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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    Ala A:86 - Asp A:87   [ RasMol ]  
 
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        LECS_VATMA | P81371: 4u36 4wv8 4xtm 4xtp 4xxa

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