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(-) Description

Title :  FAVA BEAN LECTIN-GLUCOSE COMPLEX
 
Authors :  G. N. Reeke Jr. , J. W. Becker
Date :  05 Oct 05  (Deposition) - 18 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lectin-Glucose Complex, Plant Lectin, Glycoprotein, Carbohydrate Binding Protein, D-Glucose, Protein- Carbohydrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. N. Reeke Jr. , J. W. Becker
Three-Dimensional Structure Of Favin: Saccharide Binding-Cyclic Permutation In Leguminous Lectins
Science V. 234 1108 1986
PubMed-ID: 3775378
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FAVIN BETA CHAIN
    Chains: A, C
    Fragment: RESIDUES 1-182
    Organism Common: FAVA BEAN
    Organism Scientific: VICIA FABA
    Organism Taxid: 3906
    Other Details: EXTRACTED FROM SEEDS
    Synonym: LECTIN
 
Molecule 2 - FAVIN ALPHA CHAIN
    Chains: B, D
    Fragment: RESIDUES 183-233
    Organism Common: FAVA BEAN
    Organism Scientific: VICIA FABA
    Organism Taxid: 3906
    Other Details: EXTRACTED FROM SEEDS
    Synonym: LECTIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GLC2Ligand/IonALPHA-D-GLUCOSE
3MN2Ligand/IonMANGANESE (II) ION
4NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:81 , ASP A:82 , GLY A:99 , GLY A:100 , PHE A:124 , ASN A:126 , GLY B:211 , ALA B:212 , GLU B:213BINDING SITE FOR RESIDUE GLC A 801
2AC2SOFTWAREALA C:81 , ASP C:82 , GLY C:100 , PHE C:124 , ASN C:126 , GLY D:211 , ALA D:212 , GLU D:213BINDING SITE FOR RESIDUE GLC C 802
3AC3SOFTWAREASN A:168 , THR A:170BINDING SITE FOR RESIDUE NDG A 803
4AC4SOFTWAREASN C:168 , THR C:170 , THR C:171 , VAL C:173BINDING SITE FOR RESIDUE NDG C 804
5AC5SOFTWAREGLU A:120 , ASP A:122 , ASP A:130 , HIS A:137 , HOH A:702 , HOH A:707BINDING SITE FOR RESIDUE MN A 501
6AC6SOFTWAREASP A:122 , PHE A:124 , ASN A:126 , ASP A:130 , HOH A:701 , HOH A:703BINDING SITE FOR RESIDUE CA A 502
7AC7SOFTWAREGLU C:120 , ASP C:122 , ASP C:130 , HIS C:137 , HOH C:706 , HOH C:708BINDING SITE FOR RESIDUE MN C 601
8AC8SOFTWAREASP C:122 , PHE C:124 , ASN C:126 , ASP C:130 , HOH C:705 , HOH C:709BINDING SITE FOR RESIDUE CA C 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B7Y)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:81 -Asp A:82
2Ala C:81 -Asp C:82

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B7Y)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEC_VICFA117-123
 		  2A:117-123
C:117-123
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEC_VICFA198-207
 		  2B:198-207
D:198-207

(-) Exons   (0, 0)

(no "Exon" information available for 2B7Y)

(-) 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:181
 aligned with LEC_VICFA | P02871 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:181
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 
            LEC_VICFA     2 DEITSFSIPKFRPDQPNLIFQGGGYTTKEKLTLTKAVKNTVGRALYSLPIHIWDSETGNVADFTTTFIFVIDAPNGYNVADGFTFFIAPVDTKPQTGGGYLGVFNGKDYDKTAQTVAVEFDTFYNAAWDPSNGKRHIGIDVNTIKSISTKSWNLQNGEEAHVAISFNATTNVLSVTLLYPN 182
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2b7yA00 A:2-182  [code=2.60.120.200, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.........eeeee........eeee......eeeeee...ee..........eeeeeeeeeee.........eeeeeeee.......hhhhh..............eeeeee..............eeeeee......eeee........eeeeeeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------LECTIN_----------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b7y A   2 DEITSFSIPKFRPDQPNLIFQGGGYTTKEKLTLTKAVKNTVGRALYSLPIHIWDSETGNVADFTTTFIFVIDAPNGYNVADGFTFFIAPVDTKPQTGGGYLGVFNGKDYDKTAQTVAVEFDTFYNAAWDPSNGKRHIGIDVNTIKSISTKSWNLQNGEEAHVAISFNATTNVLSVTLLYPN 182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 


Chain B from PDB  Type:PROTEIN  Length:47
 aligned with LEC_VICFA | P02871 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:47
                                   192       202       212       222       
            LEC_VICFA   183 LTGYTLSEVVPLKDVVPEWVRIGFSATTGAEYATHEVLSWTFLSELT 229
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.hhhhh...eeeeeeeee......eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------LECTIN_LEG---------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                 2b7y B 183 LTGYTLSEVVPLKDVVPEWVRIGFSATTGAEYATHEVLSWTFLSELT 229
                                   192       202       212       222       


Chain C from PDB  Type:PROTEIN  Length:181
 aligned with LEC_VICFA | P02871 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:181
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 
            LEC_VICFA     2 DEITSFSIPKFRPDQPNLIFQGGGYTTKEKLTLTKAVKNTVGRALYSLPIHIWDSETGNVADFTTTFIFVIDAPNGYNVADGFTFFIAPVDTKPQTGGGYLGVFNGKDYDKTAQTVAVEFDTFYNAAWDPSNGKRHIGIDVNTIKSISTKSWNLQNGEEAHVAISFNATTNVLSVTLLYPN 182
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2b7yC00 C:2-182  [code=2.60.120.200, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeeee..ee....eeee.......eeeee...ee..........eeeeeeeeeee..........eeeeeee.......hhhhh..............eeeeee..............eeeeee......eeee........eeeeeee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------LECTIN_----------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b7y C   2 DEITSFSIPKFRPDQPNLIFQGGGYTTKEKLTLTKAVKNTVGRALYSLPIHIWDSETGNVADFTTTFIFVIDAPNGYNVADGFTFFIAPVDTKPQTGGGYLGVFNGKDYDKTAQTVAVEFDTFYNAAWDPSNGKRHIGIDVNTIKSISTKSWNLQNGEEAHVAISFNATTNVLSVTLLYPN 182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 


Chain D from PDB  Type:PROTEIN  Length:47
 aligned with LEC_VICFA | P02871 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:47
                                   192       202       212       222       
            LEC_VICFA   183 LTGYTLSEVVPLKDVVPEWVRIGFSATTGAEYATHEVLSWTFLSELT 229
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.hhhhhh..eeeeeeee.......eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------LECTIN_LEG---------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                 2b7y D 183 LTGYTLSEVVPLKDVVPEWVRIGFSATTGAEYATHEVLSWTFLSELT 229
                                   192       202       212       222
   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 2B7Y)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B7Y)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (LEC_VICFA | P02871)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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