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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GALECTIN-7 IN COMPLEX WITH A GALACTOSE-BENZYLPHOSPHATE INHIBITOR
 
Authors :  G. Masuyer, C. T. Oberg, H. Leffler, U. J. Nilsson, K. R. Acharya
Date :  10 Aug 11  (Deposition) - 30 Nov 11  (Release) - 25 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Masuyer, T. Jabeen, C. T. Oberg, H. Leffler, U. J. Nilsson, K. R. Acharya
Inhibition Mechanism Of Human Galectin-7 By A Novel Galactose-Benzylphosphate Inhibitor.
Febs J. V. 279 193 2012
PubMed-ID: 22059385  |  Reference-DOI: 10.1111/J.1742-4658.2011.08414.X

(-) Compounds

Molecule 1 - GALECTIN-7
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentRESIDUES 4-136
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGAL-7, HKL-14, PI7, P53-INDUCED GENE 1 PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PGZ2Ligand/IonMETHYL 2-O-[(S)-(BENZYLOXY)(HYDROXY)PHOSPHORYL]-3-DEOXY-3-{[(4-METHYLPHENYL)CARBONYL]AMINO}-1-THIO-BETA-D-GALACTOPYRANOSIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PGZ1Ligand/IonMETHYL 2-O-[(S)-(BENZYLOXY)(HYDROXY)PHOSPHORYL]-3-DEOXY-3-{[(4-METHYLPHENYL)CARBONYL]AMINO}-1-THIO-BETA-D-GALACTOPYRANOSIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PGZ1Ligand/IonMETHYL 2-O-[(S)-(BENZYLOXY)(HYDROXY)PHOSPHORYL]-3-DEOXY-3-{[(4-METHYLPHENYL)CARBONYL]AMINO}-1-THIO-BETA-D-GALACTOPYRANOSIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:33 , HIS A:49 , ASN A:51 , ARG A:53 , ASN A:62 , TRP A:69 , GLU A:72 , PRO A:85 , GLU A:87 , ASP A:130 , HOH A:2001 , HOH A:2003 , HOH A:2004BINDING SITE FOR RESIDUE PGZ A 1
2AC2SOFTWAREARG B:31 , HIS B:49 , ASN B:51 , ARG B:53 , ASN B:62 , TRP B:69 , ARG B:71 , GLU B:72 , GLU B:73 , ARG B:74 , HIS B:107 , HOH B:2001 , HOH B:2002 , HOH B:2003 , HOH B:2004 , HOH B:2006 , HOH B:2007 , HOH B:2107BINDING SITE FOR RESIDUE PGZ B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZXE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZXE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZXE)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GALECTINPS51304 Galactoside-binding lectin (galectin) domain profile.LEG7_HUMAN6-136
 
  2A:5-135
B:5-135
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GALECTINPS51304 Galactoside-binding lectin (galectin) domain profile.LEG7_HUMAN6-136
 
  1A:5-135
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GALECTINPS51304 Galactoside-binding lectin (galectin) domain profile.LEG7_HUMAN6-136
 
  1-
B:5-135

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003786261ENSE00001687764chr19:39264157-3926412731LEG7_HUMAN1-220--
1.2ENST000003786262ENSE00001770113chr19:39263743-3926365589LEG7_HUMAN3-32302A:4-31
B:3-31
28
29
1.3ENST000003786263ENSE00001677371chr19:39262670-39262469202LEG7_HUMAN32-99682A:31-98
B:31-98
68
68
1.4ENST000003786264ENSE00001687329chr19:39261779-39261608172LEG7_HUMAN100-136372A:99-135
B:99-135
37
37

(-) 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:132
 aligned with LEG7_HUMAN | P47929 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:132
                                    14        24        34        44        54        64        74        84        94       104       114       124       134  
           LEG7_HUMAN     5 PHKSSLPEGIRPGTVLRIRGLVPPNASRFHVNLLCGEEQGSDAALHFNPRLDTSEVVFNSKEQGSWGREERGPGVPFQRGQPFEVLIIASDDGFKAVVGDAQYHHFRHRLPLARVRLVEVGGDVQLDSVRIF 136
               SCOP domains d3zxea_ A: Galectin-7                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.........eeeeeee.......eeeeee........eeeeeeee....eeeeeeee..ee...ee..........eeeeeeee...eeeeee..eeeeeee...hhhhh.eeeeee..eeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -GALECTIN  PDB: A:5-135 UniProt: 6-136                                                                                               PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:4-31       -------------------------------------------------------------------Exon 1.4  PDB: A:99-135               Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.3  PDB: A:31-98 UniProt: 32-99                               ------------------------------------- Transcript 1 (2)
                 3zxe A   4 PHKSSLPEGIRPGTVLRIRGLVPPNASRFHVNLLCGEEQGSDAALHFNPRLDTSEVVFNSKEQGSWGREERGPGVPFQRGQPFEVLIIASDDGFKAVVGDAQYHHFRHRLPLARVRLVEVGGDVQLDSVRIF 135
                                    13        23        33        43        53        63        73        83        93       103       113       123       133  

Chain B from PDB  Type:PROTEIN  Length:133
 aligned with LEG7_HUMAN | P47929 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:133
                                    13        23        33        43        53        63        73        83        93       103       113       123       133   
           LEG7_HUMAN     4 VPHKSSLPEGIRPGTVLRIRGLVPPNASRFHVNLLCGEEQGSDAALHFNPRLDTSEVVFNSKEQGSWGREERGPGVPFQRGQPFEVLIIASDDGFKAVVGDAQYHHFRHRLPLARVRLVEVGGDVQLDSVRIF 136
               SCOP domains d3zxeb_ B: Galectin-7                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........eeeeeeee.......eeeeee........eeeeeeee....eeeeeeee..ee...ee..........eeeeeeee...eeeeee..eeeeeee...hhhhh.eeeeee..eeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GALECTIN  PDB: B:5-135 UniProt: 6-136                                                                                               PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:3-31        -------------------------------------------------------------------Exon 1.4  PDB: B:99-135               Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.3  PDB: B:31-98 UniProt: 32-99                               ------------------------------------- Transcript 1 (2)
                 3zxe B   3 VPHKSSLPEGIRPGTVLRIRGLVPPNASRFHVNLLCGEEQGSDAALHFNPRLDTSEVVFNSKEQGSWGREERGPGVPFQRGQPFEVLIIASDDGFKAVVGDAQYHHFRHRLPLARVRLVEVGGDVQLDSVRIF 135
                                    12        22        32        42        52        62        72        82        92       102       112       122       132   

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZXE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZXE)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LEG7_HUMAN | P47929)
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.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0007157    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules    The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LEG7_HUMAN | P479291bkz 2gal 3gal 3zxf 4gal 4uw3 4uw4 4uw5 4uw6 4xbq 4y26 5gal 5h9q 5h9s

(-) Related Entries Specified in the PDB File

1bkz CRYSTAL STRUCTURE OF HUMAN GALECTIN-7
2gal CRYSTAL STRUCTURE OF HUMAN GALECTIN-7 IN COMPLEX WITH GALACTOSE
3gal CRYSTAL STRUCTURE OF HUMAN GALECTIN-7 IN COMPLEX WITH GALACTOSAMINE
3zxf HIGH RESOLUTION STRUCTURE OF HUMAN GALECTIN-7
4gal CRYSTAL STRUCTURE OF HUMAN GALECTIN-7 IN COMPLEX WITH LACTOSE
5gal CRYSTAL STRUCTURE OF HUMAN GALECTIN-7 IN COMPLEX WITH N-ACETYLLACTOSAMINE