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(-) Description

Title :  STRUCTURES OF THE LECTIN IV OF GRIFFONIA SIMPLICIFOLIA AND ITS COMPLEX WITH THE LEWIS B HUMAN BLOOD GROUP DETERMINANT AT 2.0 ANGSTROMS RESOLUTION
 
Authors :  L. Delbaere, M. Vandonselaar, J. Quail
Date :  17 Dec 92  (Deposition) - 31 Jan 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Lectin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. T. Delbaere, M. Vandonselaar, L. Prasad, J. W. Quail, K. S. Wilson, Z. Dauter
Structures Of The Lectin Iv Of Griffonia Simplicifolia And Its Complex With The Lewis B Human Blood Group Determinant At 2. 0 A Resolution.
J. Mol. Biol. V. 230 950 1993
PubMed-ID: 8478943  |  Reference-DOI: 10.1006/JMBI.1993.1212
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - WEST-CENTRAL AFRICAN LEGUME LECTIN IV
    Chains: A
    Engineered: YES
    Organism Scientific: GRIFFONIA SIMPLICIFOLIA
    Organism Taxid: 3850

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 7)

Asymmetric Unit (6, 7)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2FUC1Ligand/IonALPHA-L-FUCOSE
3MN1Ligand/IonMANGANESE (II) ION
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PCA1Mod. Amino AcidPYROGLUTAMIC ACID
6SO41Ligand/IonSULFATE ION
Biological Unit 1 (4, 10)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FUC2Ligand/IonALPHA-L-FUCOSE
3MN-1Ligand/IonMANGANESE (II) ION
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PCA2Mod. Amino AcidPYROGLUTAMIC ACID
6SO42Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:101 , NAG A:257 , FUC A:262 , HOH A:365BINDING SITE FOR RESIDUE NAG A 256
2AC2SOFTWAREASN A:18 , PHE A:24 , LEU A:25 , NAG A:256 , FUC A:262BINDING SITE FOR RESIDUE NAG A 257
3AC3SOFTWARELEU A:25 , GLY A:26 , NAG A:256 , NAG A:257 , HOH A:386BINDING SITE FOR RESIDUE FUC A 262
4AC4SOFTWAREGLU A:129 , ASP A:131 , ASP A:140 , HIS A:145 , HOH A:305 , HOH A:332BINDING SITE FOR RESIDUE MN A 250
5AC5SOFTWAREASP A:131 , TRP A:133 , ASN A:135 , ASP A:140 , HOH A:329 , HOH A:333BINDING SITE FOR RESIDUE CA A 251
6AC6SOFTWARETYR A:8 , SER A:13 , LEU A:16 , GLU A:21 , ARG A:30BINDING SITE FOR RESIDUE SO4 A 500
7CAUNKNOWNASP A:131 , TRP A:133 , ASN A:135 , ASP A:140 , HOH A:329 , HOH A:333NULL
8CHOUNKNOWNARG A:48 , SER A:49 , ASP A:89 , TYR A:105 , GLY A:107 , PHE A:108 , HIS A:114 , TRP A:133 , ASN A:135 , TRP A:138 , GLY A:222 , TYR A:223NULL
9MNUNKNOWNGLU A:129 , ASP A:131 , ASP A:140 , HIS A:145 , HOH A:305 , HOH A:332NULL

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ala A:85 -Pro A:86
2Ala A:88 -Asp A:89
3Val A:221 -Gly A:222

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEC4_GRISI126-132  1A:126-132
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEC4_GRISI209-218  1A:209-218
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEC4_GRISI126-132  2A:126-132
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEC4_GRISI209-218  2A:209-218

(-) Exons   (0, 0)

(no "Exon" information available for 1LEC)

(-) 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:243
 aligned with LEC4_GRISI | P24146 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           LEC4_GRISI     1 QNTVNFTYPDFWSYSLKNGTEITFLGDATRIPGALQLTKTDANGNPVRSSAGQASYSEPVFLWDSTGKAASFYTSFTFLLKNYGAPTADGLAFFLAPVDSSVKDYGGFLGLFRHETAADPSKNQVVAVEFDTWINKDWNDPPYPHIGIDVNSIVSVATTRWENDDAYGSSIATAHITYDARSKILTVLLSYEHGRDYILSHVVDLAKVLPQKVRIGFSAGVGYDEVTYILSWHFFSTLDGTNK 243
               SCOP domains d1leca_ A: Legume lectin                                                                                                                                                                                                                            SCOP domains
               CATH domains -1lecA00 A:2-243  [code=2.60.120.200, no name defined]                                                                                                                                                                                              CATH domains
               Pfam domains -Lectin_legB-1lecA01 A:2-235                                                                                                                                                                                                               -------- Pfam domains
         Sec.struct. author ...eeeee..............eee...eee..eeee............eeeeeee..............eeeeeeeeeeeee......eeeeeee............................eeeeeee.............eeeeeee.....eee..hhhhhh....eeeeeeee...eeeeeeeee...eeeeeeeee.hhhhh....eeeeeeee..eeeeee..eeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------LECTIN_----------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lec A   1 xNTVNFTYPDFWSYSLKNGTEITFLGDATRIPGALQLTKTDANGNPVRSSAGQASYSEPVFLWDSTGKAASFYTSFTFLLKNYGAPTADGLAFFLAPVDSSVKDYGGFLGLFRHETAADPSKNQVVAVEFDTWINKDWNDPPYPHIGIDVNSIVSVATTRWENDDAYGSSIATAHITYDARSKILTVLLSYEHGRDYILSHVVDLAKVLPQKVRIGFSAGVGYDEVTYILSWHFFSTLDGTNK 243
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
                            |                                                                                                                                                                                                                                                  
                            1-PCA
   Legend:   → Mismatch (orange background)
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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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Concanavalin (293)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (LEC4_GRISI | P24146)
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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        LEC4_GRISI | P24146: 1gsl 1led

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