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(-) Description

Title :  CRYSTAL STRUCTURE OF GLUCOSIDASE II ALPHA SUBUNIT (ALPHA3-GLC2-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 :  2.40
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 Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 31-977
    Gene: CTHT_0064960
    Mutation: YES
    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, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GLC2Ligand/IonALPHA-D-GLUCOSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:303 , PHE A:305 , TRP A:415 , ASP A:443 , ILE A:444 , TRP A:517 , TRP A:554 , MET A:557 , ARG A:617 , TRP A:630 , ASP A:633 , PHE A:666 , HIS A:691 , HOH A:1148 , HOH A:1160binding site for Poly-Saccharide residues GLC A 1001 through GLC A 1002

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:39 -A:45

(-) 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 5DKZ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DKZ)

(-) 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:921
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhh......eee.hhhhee...eeeeeeeee......eeeeeeeeee.....eeeee.hhhhhh....hhhhh........hhhhhhh..........eeeee...eeeeeehhhh.eeeeee....eeeeee..eeeeee......ee.................eee..eee........eeeeeee....eeee.......................eee.....................eeeeee..eeeeeee.....eeeeeeee...............eeeeeeee....eeeeee...hhhhhhhhhhhhhh.....hhhhhh.ee......hhhhhhhhhhhhhhh.....eeeehhhhh..............hhhhhhhhhhh...eeeee...eee....hhhhhhhhhh.............eee..eeeee....hhhhhhhhhhhh...........eeeee.........hhhhh.....ee...eehhhhh.hhhhhhhhhhhhhhh...........eee.....hhhhh.ee.......hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhh.....ee.........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhh..hhhhh.....eee....eee.........eeeeee.....eee.....eee....eeeeee.......eeee..eeeee.......hhhhh...eeeeee......eeeeeee.....hhhhhh..eeeeeeee..eeeeee........hhhhhhhh..eeeeeeee..hhhhh...eeeeee..eeeeeeeeee........eeee....ee....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dkz A  33 EHDWKKCDQSGFCRRNRAYADHALSAISWESPYKIAPETGSFKDGQYQAIILKTINDHGETVRLPLTVSFLESGTARVTIDEEKRQKGEIELRHDSKARKERYNEAEQWVIVGGMTLDKGAKVDYEDKTQMTVKYGPSSKFEATIKFAPFSIDFKRDGASHIKFNDQGLLNIEHWRPKIDPPDDSTWWEESFGGNTDSKPRGPESVGLDISFVGYEHVFGIPSHASPLSLKQTRGGEGNYNEPYRMYNADVFEYILDSPMTLYGSIPFMQAHRKDSSVGIFWLNAAETWVDITKGKDSKNPLALGVKSKITTRTHWFSESGLLDVFVFLGPTPKDIISKYAELTGTTAMPQEFSLGYHQCRWNYVSDEDVKDVDRKMDKFNMPYDVIWLDIEYTDEKKYFTWDKHSFKDPIGMGKQLEAHGRKLVTIIDPHIKNTNNYPVVDELKSKDLAVKTKDGSIFEGWCWPGSSHWIDAFNPAAREWWKGLFKYDKFKGTMENTFIWNAMNEPSVFNGPEVTMPKDNLHHGNWEHRDVHNLNGMTFQNATYHALLSRKPGEHRRPFVLTRAFFAGSQRLGAMWTGDNTADWGYLKASIPMVLSQGIAGFPFAGADVGGFFGNPDKDLLTRWYQTGIFYPFFRAHAHIDARRREPYLTGEPYNTIIAAALRLRYSLLPSWYTAFRHAHLDGTPIIKPMFYTHPSEEAGLPIDDQFFIGNTGLLAKPVTDKDRTSVDIWIPDSEVYYDYFTYDIISAAKSKTATLDAPLEKIPLLMRGGHVFARRDIPRRSSALMKWDPYTLVVVLGNDRKAEGDLYVDDGDSFDYEKGQYIHRRFIFDANTLTSADYEGRDDKEGEWLKKMRTVNVEKIIVVGAPAAWKGKKTVTVESEGKTWAAAIEYNPAEKSRAAFAVVKKVGVRVGADFKIVFG 977
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212 ||    243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893    || 906       916       926       936       946       956       966       976 
                                                                                                                                                                                                               214|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   898|                                                                           
                                                                                                                                                                                                                236                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    902
   Legend:   → Mismatch (orange background)
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  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 5DKZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  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 ]  
 

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

5dkx 5dky 5dl0