Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN GALECTIN-4 N-TERMINAL CARBOHYDRATE RECOGNITION DOMAIN IN COMPLEX WITH LACTOSE-3'-SULFATE
 
Authors :  K. Bum-Erdene, H. Blanchard
Date :  21 Sep 15  (Deposition) - 17 Feb 16  (Release) - 17 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Galectin-4, Lectin, Sulfate, Sugar-Binding Protein, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Bum-Erdene, H. Leffler, U. J. Nilsson, H. Blanchard
Structural Characterisation Of Human Galectin-4 N-Terminal Carbohydrate Recognition Domain In Complex With Glycerol, Lactose, 3'-Sulfo-Lactose, And 2'-Fucosyllactose.
Sci Rep V. 6 20289 2016
PubMed-ID: 26828567  |  Reference-DOI: 10.1038/SREP20289

(-) Compounds

Molecule 1 - GALECTIN-4
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: N-TERMINAL CARBOHYDRATE RECOGNITION DOMAIN (UNP RESIDUES 1- 155)
    Gene: LGALS4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GAL-4,ANTIGEN NY-CO-27,L-36 LACTOSE-BINDING PROTEIN,L36LBP, LACTOSE-BINDING LECTIN 4

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
15GO4Ligand/Ion4-O-(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)-BETA-D-GLUCOPYRANOSE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15GO1Ligand/Ion4-O-(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)-BETA-D-GLUCOPYRANOSE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15GO1Ligand/Ion4-O-(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)-BETA-D-GLUCOPYRANOSE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
15GO1Ligand/Ion4-O-(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)-BETA-D-GLUCOPYRANOSE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
15GO1Ligand/Ion4-O-(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)-BETA-D-GLUCOPYRANOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:45 , HIS A:63 , ASN A:65 , ARG A:67 , ASN A:77 , TRP A:84 , GLU A:87 , HOH A:309 , HOH A:326 , HOH A:340 , HOH A:341 , HOH A:346 , HOH A:356 , HOH A:367 , HOH A:404 , HOH A:407 , GLY B:57 , LEU B:79 , GLY B:82 , TRP B:84 , 5GO B:201 , HOH B:301 , ASP C:55binding site for residue 5GO A 201
2AC2SOFTWARELYS A:83 , 5GO A:201 , HOH A:309 , HIS B:63 , ASN B:65 , ARG B:67 , ASN B:77 , TRP B:84 , GLU B:87 , HOH B:301 , HOH B:306 , HOH B:320 , HOH B:355 , HOH B:359 , GLN C:54 , GLN D:54 , ASP D:55 , HOH D:308binding site for residue 5GO B 201
3AC3SOFTWAREHIS C:63 , ASN C:65 , ARG C:67 , ASN C:77 , TRP C:84 , GLU C:87 , ARG C:89 , HOH C:327 , HOH C:340 , HOH C:348 , HOH C:375 , HOH C:382 , HOH C:392 , GLY D:82 , TRP D:84 , 5GO D:201 , HOH D:311 , HOH D:344binding site for residue 5GO C 201
4AC4SOFTWAREGLN A:54 , ASP A:55 , HOH A:364 , HOH A:387 , 5GO C:201 , HIS D:63 , ASN D:65 , ARG D:67 , ASN D:77 , TRP D:84 , GLU D:87 , ARG D:89 , HOH D:311 , HOH D:313 , HOH D:341 , HOH D:344 , HOH D:374 , HOH D:392 , HOH D:398binding site for residue 5GO D 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DUW)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:17 -Pro A:18
2Leu B:17 -Pro B:18
3Leu C:17 -Pro C:18
4Leu D:17 -Pro D:18

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DUW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DUW)

(-) Exons   (0, 0)

(no "Exon" information available for 5DUW)

(-) 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:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.........eeeeeeee......eeeeeee......eeeeeeeee.....eeeeeeee..ee...eee.........eeeeeeee...eeeeee..eeeeeee...hhhhh.eeeeee.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5duw A  15 PTLPYYQPIPGGLNVGMSVYIQGVASEHMKRFFVNFVVGQDPGSDVAFHFNPRFDGWDKVVFNTLQGGKWGSEERKRSMPFKKGAAFELVFIVLAEHYKVVVNGNPFYEYGHRLPLQMVTHLQVDGDLQLQSINFIGG 152
                                    24        34        44        54        64        74        84        94       104       114       124       134       144        


Chain B from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.........eeeeeeee......eeeeeee......eeeeeeeee.....eeeeeeee..ee...eee.........eeeeeeee...eeeeee..eeeeeee...hhhhh.eeeeee.eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5duw B  15 PTLPYYQPIPGGLNVGMSVYIQGVASEHMKRFFVNFVVGQDPGSDVAFHFNPRFDGWDKVVFNTLQGGKWGSEERKRSMPFKKGAAFELVFIVLAEHYKVVVNGNPFYEYGHRLPLQMVTHLQVDGDLQLQSINFIGGQ 153
                                    24        34        44        54        64        74        84        94       104       114       124       134       144         


Chain C from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.........eeeeeeee......eeeeee........eeeeeeee.....eeeeeeee..ee...eee.........eeeeeeee...eeeeee..eeeeeee...hhhhh.eeeeee.eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5duw C  15 PTLPYYQPIPGGLNVGMSVYIQGVASEHMKRFFVNFVVGQDPGSDVAFHFNPRFDGWDKVVFNTLQGGKWGSEERKRSMPFKKGAAFELVFIVLAEHYKVVVNGNPFYEYGHRLPLQMVTHLQVDGDLQLQSINFIG 151
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       


Chain D from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.........eeeeeeee......eeeeee........eeeeeeee.....eeeeeeee..ee...eee.........eeeeeeee...eeeeee..eeeeeee...hhhhh.eeeeee.eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5duw D  15 PTLPYYQPIPGGLNVGMSVYIQGVASEHMKRFFVNFVVGQDPGSDVAFHFNPRFDGWDKVVFNTLQGGKWGSEERKRSMPFKKGAAFELVFIVLAEHYKVVVNGNPFYEYGHRLPLQMVTHLQVDGDLQLQSINFIG 151
                                    24        34        44        54        64        74        84        94       104       114       124       134       144
   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 5DUW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DUW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DUW)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

 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
    5GO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:17 - Pro A:18   [ RasMol ]  
    Leu B:17 - Pro B:18   [ RasMol ]  
    Leu C:17 - Pro C:18   [ RasMol ]  
    Leu D:17 - Pro D:18   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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 | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 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
  5duw
    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
  LEG4_HUMAN | P56470
    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
  LEG4_HUMAN | P56470
    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
        LEG4_HUMAN | P56470: 1x50 4xzp 4ylz 4ym0 4ym1 4ym2 4ym3 5cbl 5duu 5duv 5dux

(-) Related Entries Specified in the PDB File

5duu 5duv 5dux