Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  LECTIN (FOURTH ISOLATED FROM (GRIFFONIA SIMPLICIFOLIA)) COMPLEX WITH Y HUMAN BLOOD GROUP DETERMINANT
 
Authors :  L. T. J. Delbaere
Date :  15 Jun 96  (Deposition) - 23 Dec 96  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Glycoprotein, Lectin, Manganese (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 - GRIFFONIA SIMPLICIFOLIA LECTIN 4
    Chains: A
    Organ: SEEDS
    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  (8, 11)

Asymmetric Unit (8, 11)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA1Ligand/IonCALCIUM ION
3FUC3Ligand/IonALPHA-L-FUCOSE
4GAL1Ligand/IonBETA-D-GALACTOSE
5MAG1Ligand/IonBETA-METHYL-N-ACETYL-D-GLUCOSAMINE
6MN1Ligand/IonMANGANESE (II) ION
7NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
8PCA1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 1 (6, 18)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3FUC6Ligand/IonALPHA-L-FUCOSE
4GAL2Ligand/IonBETA-D-GALACTOSE
5MAG2Ligand/IonBETA-METHYL-N-ACETYL-D-GLUCOSAMINE
6MN-1Ligand/IonMANGANESE (II) ION
7NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
8PCA2Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:108 , HIS A:114 , ASN A:135 , ASP A:137 , TRP A:138 , GAL A:253 , FUC A:254 , MAG A:255 , HOH A:382 , HOH A:450 , HOH A:454BINDING SITE FOR RESIDUE FUC A 252
02AC2SOFTWAREASP A:89 , GLY A:107 , TRP A:133 , ASN A:135 , TYR A:223 , FUC A:252 , FUC A:254 , MAG A:255 , HOH A:463BINDING SITE FOR RESIDUE GAL A 253
03AC3SOFTWARESER A:65 , FUC A:252 , GAL A:253 , FUC A:254 , HOH A:463BINDING SITE FOR RESIDUE MAG A 255
04AC4SOFTWAREARG A:48 , SER A:49 , TYR A:105 , GLY A:222 , FUC A:252 , GAL A:253 , MAG A:255 , HOH A:457 , HOH A:463BINDING SITE FOR RESIDUE FUC A 254
05AC5SOFTWARESER A:101 , NAG A:257 , BMA A:258 , FUC A:262BINDING SITE FOR RESIDUE NAG A 256
06AC6SOFTWAREASN A:18 , PHE A:24 , NAG A:256 , FUC A:262BINDING SITE FOR RESIDUE NAG A 257
07AC7SOFTWARENAG A:256BINDING SITE FOR RESIDUE BMA A 258
08AC8SOFTWARELEU A:25 , GLY A:26 , NAG A:256 , NAG A:257BINDING SITE FOR RESIDUE FUC A 262
09AC9SOFTWAREGLU A:129 , ASP A:131 , ASP A:140 , HIS A:145 , HOH A:305 , HOH A:332BINDING SITE FOR RESIDUE MN A 250
10BC1SOFTWAREASP A:131 , TRP A:133 , ASN A:135 , ASP A:140 , HOH A:329 , HOH A:333BINDING SITE FOR RESIDUE CA A 251

(-) SS Bonds  (0, 0)

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

(-) 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 1GSL)

(-) 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 1GSL)

(-) 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 d1gsla_ A: Legume lectin                                                                                                                                                                                                                            SCOP domains
               CATH domains -1gslA00 A:2-243  [code=2.60.120.200, no name defined]                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.............eeeee..eee..eee.............eeeeeee..............eeeeeeeeeeee.......eeeeeeee........hhh...........hhh..eeeeeee....hhh......eeeeee......eeee..hhhh....eeeeeeeee....eeeeeeee....eeeeeee..hhhh....eeeeeeeee...eeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------LECTIN_----------------------------------------------------------------------------LECTIN_LEG------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gsl 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)
  - → 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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FUC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PCA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:85 - Pro A:86   [ RasMol ]  
    Ala A:88 - Asp A:89   [ RasMol ]  
    Val A:221 - Gly A:222   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1gsl
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  LEC4_GRISI | P24146
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  LEC4_GRISI | P24146
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LEC4_GRISI | P24146: 1lec 1led

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1GSL)