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

(-) Description

Title :  THE CRYSTAL STRUCTURE OF GALECTIN-8 C-CRD IN COMPLEX WITH NDP52
 
Authors :  S. Li, M. P. Wandel, F. Li, Z. Liu, C. He, J. Wu, Y. Shi, F. Randow
Date :  04 Sep 12  (Deposition) - 08 May 13  (Release) - 08 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Protein Interaction, Carbohydrate Recognition, Ndp52, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Li, M. P. Wandel, F. Li, Z. Liu, C. He, J. Wu, Y. Shi, F. Randow
Sterical Hindrance Promotes Selectivity Of The Autophagy Cargo Receptor Ndp52 For The Danger Receptor Galectin-8 In Antibacterial Autophagy
Sci. Signal. V. 6 Ra9 2013
PubMed-ID: 23386746  |  Reference-DOI: 10.1126/SCISIGNAL.2003730

(-) Compounds

Molecule 1 - GALECTIN-8
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 186-317
    Gene: LGALS8
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GAL-8, PO66 CARBOHYDRATE-BINDING PROTEIN, PO66-CBP, PROSTATE CARCINOMA TUMOR ANTIGEN 1, PCTA-1
 
Molecule 2 - PEPTIDE FROM CALCIUM-BINDING AND COILED-COIL DOMAIN- CONTAINING PROTEIN 2
    Chains: B
    Engineered: YES
    Fragment: UNP RESIDUES 368-381
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ANTIGEN NUCLEAR DOT 52 KDA PROTEIN, NUCLEAR DOMAIN 10 PROTEIN NDP52, NUCLEAR DOMAIN 10 PROTEIN 52, NUCLEAR DOT PROTEIN 52
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:226 , MET A:227 , ASN A:250 , ASN A:252 , GLY A:349 , ASP A:350 , ILE A:351BINDING SITE FOR RESIDUE GOL A 401
2AC2SOFTWAREHIS A:271 , ASN A:273 , ARG A:275 , ASN A:284 , TRP A:291 , GLU A:294 , HOH A:584BINDING SITE FOR RESIDUE GOL A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GXL)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Met A:227 -Pro A:228

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GXL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GXL)

(-) Exons   (0, 0)

(no "Exon" information available for 4GXL)

(-) Sequences/Alignments

Asymmetric/Biological 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:143
                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee.........eeeeeeee......eeeeeee....eeeeeeeee....eeeeeeee..ee................eeeeeeee...eeeeee..eeeeeee....hhhhh.eeeeee.eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gxl A 217 SSGENLYFQHMPFAARLNTPMGPGRTVVVKGEVNANAKSFNVDLLAGKSKDIALHLNPRLNIKAFVRNSFLQESWGEEERNITSFPFSPGMYFEMIIYCDVREFKVAVNGVHSLEYKHRFKELSSIDTLEINGDIHLLEVRSW 359
                                   226       236       246       256       266       276       286       296       306       316       326       336       346       356   


Chain B from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4gxl B 371 NPGLAYGNPYS 381
                                   380
   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 4GXL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GXL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GXL)

(-) Gene Ontology  (20, 24)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Met A:227 - Pro A:228   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  4gxl
    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
  CACO2_HUMAN | Q13137
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  LEG8_HUMAN | O00214
    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
  CACO2_HUMAN | Q13137
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  LEG8_HUMAN | O00214
    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
        CACO2_HUMAN | Q13137: 2mxp 3vvv 3vvw 4han 4xkl 5aaq
        LEG8_HUMAN | O00214: 2yro 2yv8 2yxs 3ap4 3ap5 3ap6 3ap7 3ap9 3apb 3ojb 3vkl 3vkm 3vkn 3vko 4bmb 4bme 4fqz 4han 5gzc 5gzd 5gze 5gzf 5gzg 5t7i 5t7s 5t7t 5t7u

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4GXL)