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(-) Description

Title :  NATIVE DIOCLEA GUIANENSIS SEED LECTIN
 
Authors :  A. Romero, D. A. Wah, F. G. D. Sol, B. S. Cavada, M. V. Ramos, T. B. Grangeiro, A. H. Sampaio, J. J. Calvete
Date :  22 Mar 01  (Deposition) - 23 Mar 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lectin, Legume Lectin Oligomerisation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Wah, A. Romero, F. Gallego, B. S. Cavada, M. V. Ramos, T. B. Grangeiro, A. H. Sampaio, J. J. Calvete
Crystal Structure Of Native And Cd/Cd-Substituted Dioclea Guianensis Seed Lectin. A Novel Manganese- Binding Site And Structural Basis Of Dimer-Tetramer Association
J. Mol. Biol. V. 310 885 2001
PubMed-ID: 11453695  |  Reference-DOI: 10.1006/JMBI.2001.4814
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SEED LECTIN
    Chains: A, B
    Organism Common: DUKE
    Organism Scientific: DIOCLEA GUIANENSIS
    Organism Taxid: 99571
    Tissue: SEED
    Variant: LASIOPHYLLA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2MN7Ligand/IonMANGANESE (II) ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:8 , ASP A:10 , ASP A:19 , HIS A:24 , HOH A:2145 , HOH A:2146BINDING SITE FOR RESIDUE MN A 238
02AC2SOFTWAREASP A:10 , TYR A:12 , ASN A:14 , ASP A:19 , HOH A:2007 , HOH A:2138BINDING SITE FOR RESIDUE CA A 239
03AC3SOFTWARESER A:125 , HOH A:2147 , HOH A:2148 , HOH A:2149 , HIS B:127BINDING SITE FOR RESIDUE MN A 241
04AC4SOFTWAREHIS A:180 , HOH A:2150 , HOH A:2151BINDING SITE FOR RESIDUE MN A 242
05AC5SOFTWAREGLU B:8 , ASP B:10 , ASP B:19 , HIS B:24 , HOH B:2112BINDING SITE FOR RESIDUE MN B 238
06AC6SOFTWAREASP B:10 , TYR B:12 , ASN B:14 , ASP B:19 , HOH B:2004 , HOH B:2108BINDING SITE FOR RESIDUE CA B 239
07AC7SOFTWAREHIS A:127 , SER B:125 , HOH B:2113 , HOH B:2114BINDING SITE FOR RESIDUE MN B 241
08AC8SOFTWAREHIS B:180 , HOH B:2115 , HOH B:2116BINDING SITE FOR RESIDUE MN B 242
09AC9SOFTWAREGLU A:87 , GLU A:183 , GLU B:87 , GLU B:183BINDING SITE FOR RESIDUE CA B 243
10BC1SOFTWAREHIS B:51 , HOH B:2117 , HOH B:2118 , HOH B:2119BINDING SITE FOR RESIDUE MN B 244

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H9W)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:207 -Asp A:208
2Ala B:207 -Asp B:208

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H9W)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LECA_DIOGU5-11
 		  2A:5-11
B:5-11
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LECA_DIOGU85-94
 		  2A:85-94
B:85-94

(-) Exons   (0, 0)

(no "Exon" information available for 1H9W)

(-) Sequences/Alignments

Asymmetric/Biological 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:232
 aligned with LECA_DIOGU | P81637 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
           LECA_DIOGU     1 ADTIVAVELDSYPNTDIGDPSYPHIGIDIKSIRSKSTARWNMQTGKVGTAHISYNSVAKRLSAVVSYTGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADANSLHFSFNQFSQNPKDLILQSDATTDSDGNLELTKVSSSGDPQGSSVGRALFYAPVHIWEKSAVVAGFDATFTFLIKSPDRDPADGITFFIANTDTSIPSGSGGRLLGLFPDAN 237
               SCOP domains d1h9wa_ A: Legume lectin                                                                                                                                                                                                                      SCOP domains
               CATH domains 1h9wA00 A:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeeee.....eeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeee.-----.eeeeeee.........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h9w A   1 ADTIVAVELDSYPNTDIGDPSYPHIGIDIKSIRSKSTARWNMQTGKVGTAHISYNSVAKRLSAVVSYTGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKT-----ANSLHFSFNQFSQNPKDLILQGDATTDSDGNLELTKVSSSGDPQGSSVGRALFYAPVHIWEKSAVVASFDATFTFLIKSPDRDPADGITFFIANTDTSIPSGSGGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110      |  -  |    130       140       150       160       170       180       190       200       210       220       230       
                                                                                                                                              117   123                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:230
 aligned with LECA_DIOGU | P81637 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:236
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      
           LECA_DIOGU     1 ADTIVAVELDSYPNTDIGDPSYPHIGIDIKSIRSKSTARWNMQTGKVGTAHISYNSVAKRLSAVVSYTGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADANSLHFSFNQFSQNPKDLILQSDATTDSDGNLELTKVSSSGDPQGSSVGRALFYAPVHIWEKSAVVAGFDATFTFLIKSPDRDPADGITFFIANTDTSIPSGSGGRLLGLFPDA 236
               SCOP domains d1h9wb_ B: Legume lectin                                                                                                                                                                                                                     SCOP domains
               CATH domains 1h9wB00 B:1-236  [code=2.60.120.200, no name defined]                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee........................................hhhhhh..eeeeeeeee........eeeeeeeeeeee------.eeeeeee.........eeeee.........................eeeeee...ee............................eeeeeeee.........hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h9w B   1 ADTIVAVELDSYPNTDIGDPSYPHIGIDIKSIRSKSTARWNMQTGKVGTAHISYNSVAKRLSAVVSYTGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLK------ANSLHFSFNQFSQNPKDLILQGDATTDSDGNLELTKVSSSGDPQGSSVGRALFYAPVHIWEKSAVVASFDATFTFLIKSPDRDPADGITFFIANTDTSIPSGSGGRLLGLFPDA 236
                                    10        20        30        40        50        60        70        80        90       100       110     |   -  |    130       140       150       160       170       180       190       200       210       220       230      
                                                                                                                                             116    123
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H9W)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LECA_DIOGU | P81637)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0005537    mannose binding    Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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  Cis Peptide Bonds
    Ala A:207 - Asp A:208   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        LECA_DIOGU | P81637: 1h9p 2jdz 2je7

(-) Related Entries Specified in the PDB File

1h9p CRYSTAL STRUCTURE OF DIOCLEA GUIANENSIS SEED LECTIN