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 :  CRYSTAL STRUCTURE OF GLUCOSIDASE II ALPHA SUBUNIT (DNJ-BOUND FROM)
 
Authors :  T. Satoh, T. Toshimori, G. Yan, T. Yamaguchi, K. Kato
Date :  04 Sep 15  (Deposition) - 27 Jan 16  (Release) - 17 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Endoplasmic Reticulum, Glycoside Hydrolase, Glycosylation, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Satoh, T. Toshimori, G. Yan, T. Yamaguchi, K. Kato
Structural Basis For Two-Step Glucose Trimming By Glucosidase Ii Involved In Er Glycoprotein Quality Control.
Sci Rep V. 6 20575 2016
PubMed-ID: 26847925  |  Reference-DOI: 10.1038/SREP20575

(-) Compounds

Molecule 1 - ALPHA GLUCOSIDASE-LIKE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PCOLD-GST (MODIFIED)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 31-977
    Gene: CTHT_0064960
    Organism Scientific: CHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS 144.50 / IMI 039719)
    Organism Taxid: 759272
    Strain: DSM 1495 / CBS 144.50 / IMI 039719

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NOJ1Ligand/Ion1-DEOXYNOJIRIMYCIN

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:443 , ILE A:444 , TRP A:554 , ASP A:556 , ARG A:617 , TRP A:630 , ASP A:633 , PHE A:666 , HIS A:691 , HOH A:1123 , HOH A:1137 , HOH A:1629binding site for residue NOJ A 1000

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ala A:180 -Pro A:181
2Pro A:275 -Ser A:276
3Gly A:383 -Pro A:384
4Trp A:415 -Asn A:416
5Glu A:559 -Pro A:560
6Glu A:706 -Pro A:707

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DKY)

(-) 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:928
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhh......eee.hhhheee..eeeeeeeee......eeeeeeeeee.....eeeee.hhhhhh....hhhhh........hhhhhhh..........eeeee...eeeeeehhhhheeeeee....eeeeee..eeeeee......ee.................eee..eee........eeeeeee.....eee.......................eee.....................eeeeee..eeeeeee.....eeeeeeeee.............eeeeeeeee....eeeeee...hhhhhhhhhhhhhh.....hhhhhh.ee......hhhhhhhhhhhhhhh.....eeeehhhhh..............hhhhhhhhhhh...eeeee...eee....hhhhhhhhhh.............eee..eeeee....hhhhhhhhhhhh...........eeeee.........hhhhh.....ee...eehhhhh.hhhhhhhhhhhhhhh...........eee.....hhhhh.eee......hhhhhhhhhhhhhhhhhh....ee..........hhhhhhhhhhhhh.....ee.........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhh..hhhhh.....eee....eee.........eeeeee.....eee.....eee....eeeeee.......eeee..eeeee.......hhhhh...eeeeee......eeeeeee.....hhhhhh..eeeeeeee..eeeeee....hhhhh..hhhhhhhh..eeeeeeee..hhhhh...eeeeee..eeeeeeeeee........eeee....ee....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dky A  29 EFVKEHDWKKCDQSGFCRRNRAYADHALSAISWESPYKIAPETGSFKDGQYQAIILKTINDHGETVRLPLTVSFLESGTARVTIDEEKRQKGEIELRHDSKARKERYNEAEQWVIVGGMTLDKGAKVDYEDKTQMTVKYGPSSKFEATIKFAPFSIDFKRDGASHIKFNDQGLLNIEHWRPKIDPPDDSTWWEESFGGNTDSKPRGPESVGLDISFVGYEHVFGIPSHASPLSLKQTRGGEGNYNEPYRMYNADVFEYILDSPMTLYGSIPFMQAHRKDSSVGIFWLNAAETWVDITKGKDSKNPLALGVKSKITTRTHWFSESGLLDVFVFLGPTPKDIISKYAELTGTTAMPQEFSLGYHQCRWNYVSDEDVKDVDRKMDKFNMPYDVIWLDIEYTDEKKYFTWDKHSFKDPIGMGKQLEAHGRKLVTIIDPHIKNTNNYPVVDELKSKDLAVKTKDGSIFEGWCWPGSSHWIDAFNPAAREWWKGLFKYDKFKGTMENTFIWNDMNEPSVFNGPEVTMPKDNLHHGNWEHRDVHNLNGMTFQNATYHALLSRKPGEHRRPFVLTRAFFAGSQRLGAMWTGDNTADWGYLKASIPMVLSQGIAGFPFAGADVGGFFGNPDKDLLTRWYQTGIFYPFFRAHAHIDARRREPYLTGEPYNTIIAAALRLRYSLLPSWYTAFRHAHLDGTPIIKPMFYTHPSEEAGLPIDDQFFIGNTGLLAKPVTDKDRTSVDIWIPDSEVYYDYFTYDIISAAKSKTATLDAPLEKIPLLMRGGHVFARRDIPRRSSALMKWDPYTLVVVLGNDRKAEGDLYVDDGDSFDYEKGQYIHRRFIFDANTLTSADYEGRDDASIKEGEWLKKMRTVNVEKIIVVGAPAAWKGKKTVTVESEGKTWAAAIEYNPAEKSRAAFAVVKKVGVRVGADFKIVFG 977
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208     ||239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969        
                                                                                                                                                                                                                   214|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                                                                                                                                                                                                                    236
   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 5DKY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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
    NOJ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:180 - Pro A:181   [ RasMol ]  
    Glu A:559 - Pro A:560   [ RasMol ]  
    Glu A:706 - Pro A:707   [ RasMol ]  
    Gly A:383 - Pro A:384   [ RasMol ]  
    Pro A:275 - Ser A:276   [ RasMol ]  
    Trp A:415 - Asn A:416   [ 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
  5dky
    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
  G0SG42_CHATD | G0SG42
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  G0SG42_CHATD | G0SG42
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        G0SG42_CHATD | G0SG42: 5dkx 5dkz 5dl0 5jqp

(-) Related Entries Specified in the PDB File

5dkx 5dkz 5dl0