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(-) Description

Title :  MOUSE GALACTOCEREBROSIDASE COMPLEXED WITH 1-DEOXY-GALACTO-NOJIRIMYCIN DGJ
 
Authors :  C. H. Hill, A. H. Viuff, S. J. Spratley, S. Salamone, S. H. Christensen, R N. W. Moriarty, H. H. Jensen, J. E. Deane
Date :  17 Mar 15  (Deposition) - 01 Apr 15  (Release) - 10 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Complex, Lysosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. H. Hill, A. H. Viuff, S. J. Spratley, S. Salamone, S. H. Christensen, R. J. Read, N. W. Moriarty, H. H. Jensen, J. E. Deane
Azasugar Inhibitors As Pharmacological Chaperones For Krabbe Disease.
Chem. Sci. V. 6 3075 2015
PubMed-ID: 26029356  |  Reference-DOI: 10.1039/C5SC00754B

(-) Compounds

Molecule 1 - GALACTOCEREBROSIDASE
    Chains: A
    EC Number: 3.2.1.46
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293 T
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: GALCERASE, GALACTOCEREBROSIDE BETA-GALACTOSIDASE, GALACTOSYLCERAMIDASE, GALACTOSYLCERAMIDE BETA-GALACTOSIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2DGJ1Ligand/Ion(2R,3S,4R,5S)-2-(HYDROXYMETHYL)PIPERIDINE-3,4,5-TRIOL
3NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:48 , THR A:92 , THR A:93 , TRP A:135 , ASN A:181 , GLU A:182 , TYR A:238 , GLU A:258 , SER A:261 , TYR A:303 , ARG A:380BINDING SITE FOR RESIDUE DGJ A1001
2AC2SOFTWAREASP A:477 , ASN A:479 , PHE A:511 , ASP A:660 , HOH A:2168BINDING SITE FOR RESIDUE CA A3669
3AC3SOFTWAREARG A:37 , LYS A:248 , ILE A:281 , ASN A:284 , HOH A:2133BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1284 THROUGH NAG A2284 BOUND TO ASN A 284
4AC4SOFTWAREASP A:359 , LEU A:361 , ASN A:363 , LEU A:453BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1363 THROUGH NAG A2363 BOUND TO ASN A 363
5AC5SOFTWAREASN A:387BINDING SITE FOR MONO-SACCHARIDE NAG A1387 BOUND TO ASN A 387
6AC6SOFTWAREASN A:542 , LYS A:620 , TYR A:641 , ALA A:667 , ARG A:668BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1542 THROUGH NAG A2542 BOUND TO ASN A 542

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:271 -A:378

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Gly A:48 -Gly A:49
2Glu A:60 -Pro A:61
3Ala A:209 -Ser A:210
4Glu A:215 -Pro A:216
5Trp A:291 -Asn A:292
6Arg A:380 -Pro A:381
7Tyr A:641 -Pro A:642

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UFM)

(-) 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:640
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeee..eeeeee..............hhhhhhhhhhhh........eeeeee..........................hhhhhhhhhhhhh...eeeeee...hhhhhh.......hhhhhhhhhhhhhhhhhhhhh....ee........hhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhh.eeeee......hhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhhhhhh..eeeee..............................hhhhhhhhhhhh......eee...ee.....eeeeee.....eeeeee.....................eeeeeee.hhhh...eeeeeeee...eeeeeeeeee......eeeeee...eeeeee.....................eeee...............eeee..eeeee........eeeee................eeee......eeeeeeeeee......eeeeeeee..hhhhhhh.eeeeeeee...eeeeeee.....eeeeee.......eeeeeeeee..eeeeee..eeeeeeee.......eeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ufm A  25 GAYVLDDSDGLGREFDGIGAVSGGGATSRLLVNYPEPYRSEILDYLFKPNFGASLHILKVEIGGDGQTTDGTEPSHMHYELDENYFRGYEWWLMKEAKKRNPDIILMGLPWSFPGWLGKGFSWPYVNLQLTAYYVVRWILGAKHYHDLDIDYIGIWNERPFDANYIKELRKMLDYQGLQRVRIIASDNLWEPISSSLLLDQELWKVVDVIGAHYPGTYTVWNAKMSGKKLWSSEDFSTINSNVGAGCWSRILNQNYINGNMTSTIAWNLVASYYEELPYGRSGLMTAQEPWSGHYVVASPIWVSAHTTQFTQPGWYYLKTVGHLEKGGSYVALTDGLGNLTIIIETMSHQHSMCIRPYLPYYNVSHQLATFTLKGSLREIQELQVWYTKLGRLHFKQLDTLWLLDGSGSFTLELEEDEIFTLTTLTTGRKGSYPPPPSSKPFPTNYKDDFNVEYPLFSEAPNFADQTGVFEYYMNNEDREHRFTLRQVLNQRPITWAADASSTISVIGDHHWTNMTVQCDVYIETPRSGGVFIAGRVNKGGILIRSATGVFFWIFANGSYRVTADLGGWITYASGHADVTAKRWYTLTLGIKGYFAFGMLNGTILWKNVRVKYPGHGWAAIGTHTFEFAQFDNFRVEAAR 668
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414||     428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668
                                                                                                                                                                                                                                                                                                                                                                                                                                415|                                                                                                                                                                                                                                                        
                                                                                                                                                                                                                                                                                                                                                                                                                                 420
   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 4UFM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:209 - Ser A:210   [ RasMol ]  
    Arg A:380 - Pro A:381   [ RasMol ]  
    Glu A:215 - Pro A:216   [ RasMol ]  
    Glu A:60 - Pro A:61   [ RasMol ]  
    Gly A:48 - Gly A:49   [ RasMol ]  
    Trp A:291 - Asn A:292   [ RasMol ]  
    Tyr A:641 - Pro A:642   [ RasMol ]  
 

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  4ufm
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  GALC_MOUSE | P54818
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  3.2.1.46
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 Related Entries

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

UniProtKB/Swiss-Prot
        GALC_MOUSE | P54818: 3zr5 3zr6 4ccc 4ccd 4cce 4ufh 4ufi 4ufj 4ufk 4ufl 5n8k 5nxb

(-) Related Entries Specified in the PDB File

4ufh MOUSE GALACTOCEREBROSIDASE COMPLEXED WITH ISO-GALACTO- FAGOMINE IGF
4ufi MOUSE GALACTOCEREBROSIDASE COMPLEXED WITH AZA-GALACTO- FAGOMINE AGF
4ufj MOUSE GALACTOCEREBROSIDASE COMPLEXED WITH ISO-GALACTO- FAGOMINE LACTAM IGL
4ufk MOUSE GALACTOCEREBROSIDASE COMPLEXED WITH DIDEOXY-IMINO- LYXITOL DIL
4ufl MOUSE GALACTOCEREBROSIDASE COMPLEXED WITH DEOXY-GALACTO- NOEUROSTEGINE DGN