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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF A PROTEASE-RESISTANT MUTANT FORM OF HUMAN GALECTIN-9
 
Authors :  H. Yoshida, S. Kamitori
Date :  16 May 14  (Deposition) - 20 May 15  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta Sandwich, Carbohydrate-Binding, Oligosaccharide, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Yoshida, M. Teraoka, N. Nishi, S. Kamitori
Crystal Structure Of A Protease-Resistant Mutant Form Of Human Galectin-9
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GALECTIN-9
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LGALS9
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GAL-9, ECALECTIN, TUMOR ANTIGEN HOM-HD-21

 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  (5, 20)

Asymmetric Unit (5, 20)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2EDO10Ligand/Ion1,2-ETHANEDIOL
3GAL4Ligand/IonBETA-D-GALACTOSE
4GLC2Ligand/IonALPHA-D-GLUCOSE
5ZN2Ligand/IonZINC ION
Biological Unit 1 (4, 9)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2EDO5Ligand/Ion1,2-ETHANEDIOL
3GAL2Ligand/IonBETA-D-GALACTOSE
4GLC1Ligand/IonALPHA-D-GLUCOSE
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (4, 9)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2EDO5Ligand/Ion1,2-ETHANEDIOL
3GAL2Ligand/IonBETA-D-GALACTOSE
4GLC1Ligand/IonALPHA-D-GLUCOSE
5ZN-1Ligand/IonZINC ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:100 , CYS A:102 , HIS A:188 , HIS A:320BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWAREASP A:100 , ASN A:115 , THR A:214 , SER A:273 , THR A:319 , EDO A:407 , HOH A:722 , HOH A:755BINDING SITE FOR RESIDUE EDO A 406
03AC3SOFTWAREASN A:34 , PHE A:99 , GLY A:213 , SER A:273 , PHE A:274 , EDO A:406 , HOH A:523BINDING SITE FOR RESIDUE EDO A 407
04AC4SOFTWARELYS A:265 , MET A:266 , VAL A:269 , HOH A:735BINDING SITE FOR RESIDUE EDO A 408
05AC5SOFTWAREGLN A:220 , SER A:221 , ASP A:315 , HOH A:533BINDING SITE FOR RESIDUE EDO A 409
06AC6SOFTWAREHIS A:129 , ARG A:130 , ASP A:132 , HOH A:720 , HOH A:745BINDING SITE FOR RESIDUE EDO A 410
07AC7SOFTWAREASP B:100 , CYS B:102 , HIS B:188 , HIS B:320BINDING SITE FOR RESIDUE ZN B 401
08AC8SOFTWAREASN B:34 , GLY B:35 , PRO B:98 , PHE B:99 , GLY B:213 , SER B:273 , PHE B:274 , SER B:275 , EDO B:407 , HOH B:518BINDING SITE FOR RESIDUE EDO B 406
09AC9SOFTWAREASP B:100 , ASN B:115 , SER B:273 , THR B:319 , EDO B:406 , HOH B:662 , HOH B:776BINDING SITE FOR RESIDUE EDO B 407
10BC1SOFTWARETHR A:319 , HOH A:508 , HOH A:544 , PRO B:217 , HOH B:501 , HOH B:726 , HOH B:731BINDING SITE FOR RESIDUE EDO B 408
11BC2SOFTWAREGLN A:94 , MET A:97 , PRO B:92 , VAL B:114 , ILE B:117 , PHE B:119 , HOH B:581 , HOH B:657BINDING SITE FOR RESIDUE EDO B 409
12BC3SOFTWAREGLU B:259 , ARG B:260 , SER B:261 , HOH B:530 , HOH B:536 , HOH B:674BINDING SITE FOR RESIDUE EDO B 410
13BC4SOFTWAREHIS A:61 , ASN A:63 , ARG A:65 , ASN A:75 , TRP A:82 , GLU A:85 , ARG A:87 , HOH A:574 , HOH A:607 , HOH A:624 , HOH A:725 , HOH A:753BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 402 TO 403
14BC5SOFTWAREHIS A:235 , ASN A:237 , ARG A:239 , ASN A:248 , GLU A:258 , ARG A:260 , HOH A:525 , HOH A:537 , HOH A:613 , HOH A:626 , HOH A:642 , HOH A:696 , GLU B:258 , HOH B:505 , HOH B:526 , HOH B:630BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 404 TO 405
15BC6SOFTWAREHIS B:61 , ASN B:63 , ARG B:65 , ASN B:75 , GLU B:85 , ARG B:87 , HOH B:531 , HOH B:664 , HOH B:704BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 402 TO 403
16BC7SOFTWAREGLU A:258 , HOH A:539 , HIS B:235 , ASN B:237 , ARG B:239 , ASN B:248 , GLU B:258 , ARG B:260 , HOH B:514 , HOH B:537 , HOH B:570 , HOH B:630 , HOH B:724 , HOH B:747 , HOH B:792 , HOH B:799BINDING SITE FOR DI-SACCHARIDE GAL B 404 AND GLC B 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WV6)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Val A:15 -Pro A:16
2Met A:193 -Pro A:194
3Val B:15 -Pro B:16
4Met B:193 -Pro B:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WV6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WV6)

(-) Exons   (0, 0)

(no "Exon" information available for 3WV6)

(-) 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:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....eeee........eeeeeeeee.......eeeeee.......eeeeeeee.....eeeeeeee..ee...eee.........eeeeeeee...eeeeee..eeeeeee...hhhhh.eeeeee.eeeeeeeeee..........eeee.........eeeeeeee......eeeeeee..eeeeeeeee....eeeeeeee..ee.................eeeeeeee...eeeeee..eeeeeee....hhhhh.eeeeee.eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wv6 A   5 GSQAPYLSPAVPFSGTIQGGLQDGLQITVNGTVLSSSGTRFAVNFQTGFSGNDIAFHFNPRFEDGGYVVCNTRQNGSWGPEERKTHMPFQKGMPFDLCFLVQSSDFKVMVNGILFVQYFHRVPFHRVDTISVNGSVQLSYISFQHMYPHPAYPMPFITTILGGLYPSKSILLSGTVLPSAQSFHINLCSGNHIAFHLNPRFDENAVVRNTQIDNSWGSEERSLPRKMPFVRGQSFSVWILCEAHCLKVAVDGQHLFEYYHRLRNLPTINRLEVGGDIQLTHVQT 323
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144     ||189       199       209       219       229       239       249       259       269       279       289       299       309       319    
                                                                                                                                                                           150|                                                                                                                                         
                                                                                                                                                                            186                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....eeee........eeeeeeeee.......eeeeee.......eeeeeeee.....eeeeeeee..ee...eee.........eeeeeeee...eeeeee..eeeeeee...hhhhh.eeeeee.eeeeeeeeee..........eeee.........eeeeeeee......eeeeeee..eeeeeeeee....eeeeeeee..ee.................eeeeeeee...eeeeee..eeeeeee....hhhhh.eeeeee.eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wv6 B   5 GSQAPYLSPAVPFSGTIQGGLQDGLQITVNGTVLSSSGTRFAVNFQTGFSGNDIAFHFNPRFEDGGYVVCNTRQNGSWGPEERKTHMPFQKGMPFDLCFLVQSSDFKVMVNGILFVQYFHRVPFHRVDTISVNGSVQLSYISFQHMYPHPAYPMPFITTILGGLYPSKSILLSGTVLPSAQSFHINLCSGNHIAFHLNPRFDENAVVRNTQIDNSWGSEERSLPRKMPFVRGQSFSVWILCEAHCLKVAVDGQHLFEYYHRLRNLPTINRLEVGGDIQLTHVQT 323
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144     ||189       199       209       219       229       239       249       259       269       279       289       299       309       319    
                                                                                                                                                                           150|                                                                                                                                         
                                                                                                                                                                            186
   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 3WV6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WV6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WV6)

(-) Gene Ontology  (62, 62)

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
    BGC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GLC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Met A:193 - Pro A:194   [ RasMol ]  
    Met B:193 - Pro B:194   [ RasMol ]  
    Val A:15 - Pro A:16   [ RasMol ]  
    Val B:15 - Pro B:16   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  3wv6
    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
  LEG9_HUMAN | O00182
    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
  LEG9_HUMAN | O00182
    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
        LEG9_HUMAN | O00182: 2eak 2eal 2yy1 2zhk 2zhl 2zhm 2zhn 3lsd 3lse 3nv1 3nv2 3nv3 3nv4 3wlu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3WV6)