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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE,COMPLEX WITH GALNAC
 
Authors :  N. E. Clark, S. C. Garman
Date :  21 Apr 09  (Deposition) - 20 Oct 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glycoprotein, Carbohydrate-Binding Protein, Glycosidase, Lysosomal Enzyme, (Beta/Alpha)8 Barrel, Protein-Ligand Complex, Disease Mutation, Disulfide Bond, Hydrolase, Lysosome (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. E. Clark, S. C. Garman
The 1. 9 A Structure Of Human Alpha-N-Acetylgalactosaminidase: The Molecular Basis Of Schindler And Kanzaki Diseases
J. Mol. Biol. V. 393 435 2009
PubMed-ID: 19683538  |  Reference-DOI: 10.1016/J.JMB.2009.08.021

(-) Compounds

Molecule 1 - ALPHA-N-ACETYLGALACTOSAMINIDASE
    ChainsA, B
    EC Number3.2.1.49
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System PlasmidPIB/V5-HIS-TOPO TA
    Expression System StrainHI-FIVE
    Expression System Taxid7111
    Expression System Vector TypeSTABLE CELL LINE
    GeneNAGA
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymALPHA-GALACTOSIDASE B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 36)

Asymmetric/Biological Unit (6, 36)
No.NameCountTypeFull Name
1A2G2Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2BMA3Ligand/IonBETA-D-MANNOSE
3FUC2Ligand/IonALPHA-L-FUCOSE
4GOL15Ligand/IonGLYCEROL
5MAN4Ligand/IonALPHA-D-MANNOSE
6NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (36, 36)

Asymmetric Unit (36, 36)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:40 , ASN A:41 , CYS A:42 , ASP A:43 , ARG A:97 , HOH A:509 , HOH A:676BINDING SITE FOR RESIDUE GOL A 1024
02AC2SOFTWAREMET A:56 , GLU A:57 , ASP A:60 , TYR A:108 , HOH A:723BINDING SITE FOR RESIDUE GOL A 1039
03AC3SOFTWAREPHE A:125 , GLY A:129 , PHE A:159BINDING SITE FOR RESIDUE GOL A 1108
04AC4SOFTWAREGLY A:129BINDING SITE FOR RESIDUE GOL A 1113
05AC5SOFTWARETHR A:25 , PRO A:26 , PRO A:27 , MET A:28 , GLY A:71 , THR A:73 , TYR A:74 , HOH A:804BINDING SITE FOR RESIDUE GOL A 1165
06AC6SOFTWARETYR A:192 , ASP A:216 , ASP A:217 , HOH A:708 , A2G A:1000BINDING SITE FOR RESIDUE GOL A 1200
07AC7SOFTWARETRP A:33 , CYS A:127 , MET A:128 , ASP A:217 , HOH A:709 , A2G A:1000BINDING SITE FOR RESIDUE GOL A 1201
08AC8SOFTWAREARG A:344 , THR A:345 , ASP A:346 , GLN B:219BINDING SITE FOR RESIDUE GOL A 1328
09AC9SOFTWAREASN A:48 , ASP A:285 , ARG A:287 , THR A:288BINDING SITE FOR RESIDUE GOL A 1030
10BC1SOFTWARELEU A:226 , ASN A:230 , VAL A:233 , GLU A:325 , TYR A:327BINDING SITE FOR RESIDUE GOL A 1210
11BC2SOFTWAREASN A:124 , PHE A:159 , NAG A:625 , FUC A:627 , HOH A:657 , HOH A:660 , HOH A:707BINDING SITE FOR RESIDUE NAG A 624
12BC3SOFTWAREHOH A:578 , NAG A:624 , BMA A:626 , HOH A:657BINDING SITE FOR RESIDUE NAG A 625
13BC4SOFTWAREPHE A:159 , HOH A:578 , NAG A:625BINDING SITE FOR RESIDUE BMA A 626
14BC5SOFTWARENAG A:624BINDING SITE FOR RESIDUE FUC A 627
15BC6SOFTWAREASP A:19 , ASN A:177 , GLY A:180 , ARG A:181 , HOH A:481 , HOH A:587 , NAG A:678 , HOH A:760 , HOH A:761 , HOH A:803BINDING SITE FOR RESIDUE NAG A 677
16BC7SOFTWAREASP A:19 , GLY A:21 , HOH A:426 , NAG A:677 , BMA A:679 , MAN A:681 , HOH A:790BINDING SITE FOR RESIDUE NAG A 678
17BC8SOFTWAREHOH A:569 , NAG A:678 , MAN A:680 , MAN A:681 , HOH A:701 , ARG B:61 , GLN B:64 , ASP B:65BINDING SITE FOR RESIDUE BMA A 679
18BC9SOFTWAREBMA A:679 , HOH A:719 , HOH A:730BINDING SITE FOR RESIDUE MAN A 680
19CC1SOFTWARENAG A:678 , BMA A:679BINDING SITE FOR RESIDUE MAN A 681
20CC2SOFTWAREGLU A:383 , ASN A:385 , HOH A:451 , HOH A:516 , HOH A:609 , HOH A:724BINDING SITE FOR RESIDUE NAG A 885
21CC3SOFTWAREHOH A:12 , TRP A:33 , ASP A:78 , ASP A:79 , TYR A:119 , CYS A:127 , MET A:128 , LYS A:154 , ASP A:156 , SER A:188 , ALA A:191 , ARG A:213 , ASP A:217 , HOH A:708 , GOL A:1200 , GOL A:1201BINDING SITE FOR RESIDUE A2G A 1000
22CC4SOFTWAREILE B:40 , ASN B:41 , ASP B:43BINDING SITE FOR RESIDUE GOL B 1024
23CC5SOFTWAREGLY B:129BINDING SITE FOR RESIDUE GOL B 1108
24CC6SOFTWAREMET B:128 , TYR B:130BINDING SITE FOR RESIDUE GOL B 1113
25CC7SOFTWAREALA B:191 , TYR B:192 , ASP B:216 , ASP B:217 , A2G B:2000BINDING SITE FOR RESIDUE GOL B 1200
26CC8SOFTWAREARG A:37 , GLN A:219 , ARG B:344 , THR B:345 , ASP B:346BINDING SITE FOR RESIDUE GOL B 1328
27CC9SOFTWAREASN B:124 , HOH B:525 , NAG B:625 , FUC B:627 , HOH B:629BINDING SITE FOR RESIDUE NAG B 624
28DC1SOFTWAREHOH B:565 , NAG B:624 , FUC B:627BINDING SITE FOR RESIDUE NAG B 625
29DC2SOFTWAREHOH B:531 , NAG B:624 , NAG B:625BINDING SITE FOR RESIDUE FUC B 627
30DC3SOFTWAREARG A:199 , ASP B:19 , ASN B:20 , ASN B:177 , GLY B:180 , ARG B:181 , HOH B:463 , HOH B:478 , HOH B:530 , HOH B:538 , HOH B:648 , NAG B:678BINDING SITE FOR RESIDUE NAG B 677
31DC4SOFTWAREASP B:19 , GLY B:21 , NAG B:677 , BMA B:679 , MAN B:681BINDING SITE FOR RESIDUE NAG B 678
32DC5SOFTWARENAG B:678 , MAN B:680 , MAN B:681BINDING SITE FOR RESIDUE BMA B 679
33DC6SOFTWAREBMA B:679 , HOH B:697BINDING SITE FOR RESIDUE MAN B 680
34DC7SOFTWARENAG B:678 , BMA B:679 , HOH B:728BINDING SITE FOR RESIDUE MAN B 681
35DC8SOFTWAREGLU B:383 , ASN B:385BINDING SITE FOR RESIDUE NAG B 885
36DC9SOFTWARETRP B:33 , ASP B:78 , ASP B:79 , TYR B:119 , CYS B:127 , MET B:128 , LYS B:154 , ASP B:156 , SER B:188 , ARG B:213 , ASP B:217 , HOH B:435 , HOH B:457 , GOL B:1200BINDING SITE FOR RESIDUE A2G B 2000

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:38 -A:80
2A:42 -A:49
3A:127 -A:158
4A:187 -A:209
5B:38 -B:80
6B:42 -B:49
7B:127 -B:158
8B:187 -B:209

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:197 -Pro A:198
2Pro B:197 -Pro B:198

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 8)

Asymmetric/Biological Unit (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_000496S160CNAGAB_HUMANDisease (SCHIND)121434532A/BS160C
2UniProtVAR_000497E325KNAGAB_HUMANDisease (SCHIND)121434529A/BE325K
3UniProtVAR_022525R329QNAGAB_HUMANDisease (KANZD)121434533A/BR329Q
4UniProtVAR_000498R329WNAGAB_HUMANDisease (KANZD)121434530A/BR329W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALPHA_GALACTOSIDASEPS00512 Alpha-galactosidase signature.NAGAB_HUMAN71-86
 
  2A:71-86
B:71-86

(-) Exons   (0, 0)

(no "Exon" information available for 3H54)

(-) 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:387
 aligned with NAGAB_HUMAN | P17050 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:387
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       
          NAGAB_HUMAN    18 LDNGLLQTPPMGWLAWERFRCNINCDEDPKNCISEQLFMEMADRMAQDGWRDMGYTYLNIDDCWIGGRDASGRLMPDPKRFPHGIPFLADYVHSLGLKLGIYADMGNFTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQGYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVNYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIK 404
               SCOP domains d3h54a1 A:18-309 automated matches                                                                                                                                                                                                                                                                  d3h54a2 A:310-404 automated matches                                                             SCOP domains
               CATH domains 3h54A01 A:18-307 Aldolase class I                                                                                                                                                                                                                                                                 ------3h54A02 A:314-404 Golgi alpha-mannosidase II                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeehhhhhh.............hhhhhhhhhhhhhhhhhhhhh..eee.....eeee.....eee......hhhhhhhhhhhhh..eeeeeee............hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhh....eeeehhhhhh.......hhhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhhhh....eee...........hhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhhh.......eeeee....eeeeeee.....eeeeeee......eeeeee.hhhh......eeeee.....eeeee....eeeeee....eeeeeeee.. Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------------------------------------------------------------------------------------------------------------C--------------------------------------------------------------------------------------------------------------------------------------------------------------------K---Q--------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W--------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -----------------------------------------------------ALPHA_GALACTOSID------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h54 A  18 LDNGLLQTPPMGWLAWERFRCNINCDEDPKNCISEQLFMEMADRMAQDGWRDMGYTYLNIDDCWIGGRDASGRLMPDPKRFPHGIPFLADYVHSLGLKLGIYADMGNFTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQGYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVQYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIK 404
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       

Chain B from PDB  Type:PROTEIN  Length:387
 aligned with NAGAB_HUMAN | P17050 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:387
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       
          NAGAB_HUMAN    18 LDNGLLQTPPMGWLAWERFRCNINCDEDPKNCISEQLFMEMADRMAQDGWRDMGYTYLNIDDCWIGGRDASGRLMPDPKRFPHGIPFLADYVHSLGLKLGIYADMGNFTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQGYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVNYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIK 404
               SCOP domains d3h54b1 B:18-309 automated matches                                                                                                                                                                                                                                                                  d3h54b2 B:310-404 automated matches                                                             SCOP domains
               CATH domains 3h54B01 B:18-307 Aldolase class I                                                                                                                                                                                                                                                                 ------3h54B02 B:314-404 Golgi alpha-mannosidase II                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeehhhhhh.............hhhhhhhhhhhhhhhhhhhhh..eee.....eeee.....eee.......hhhhhhhhhhhh..eeeeeee...............hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhh....eeee.hhhhhh......hhhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhhhh....eee...........hhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhhh.......eeeee....eeeeeee.....eeeeeee......eeeee.hhhhh......eeeee.....eeeee.....eeeee....eeeeeeee.. Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------------------------------------------------------------------------------------------------------------C--------------------------------------------------------------------------------------------------------------------------------------------------------------------K---Q--------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W--------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -----------------------------------------------------ALPHA_GALACTOSID------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h54 B  18 LDNGLLQTPPMGWLAWERFRCNINCDEDPKNCISEQLFMEMADRMAQDGWRDMGYTYLNIDDCWIGGRDASGRLMPDPKRFPHGIPFLADYVHSLGLKLGIYADMGNFTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQGYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVQYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIK 404
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       

   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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H54)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NAGAB_HUMAN | P17050)
molecular function
    GO:0008456    alpha-N-acetylgalactosaminidase activity    Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-galactosamine residues in N-acetyl-alpha-D-galactosaminides.
    GO:0004557    alpha-galactosidase activity    Catalysis of the hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactohydrolase.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0016052    carbohydrate catabolic process    The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0019377    glycolipid catabolic process    The chemical reactions and pathways resulting in the breakdown of glycolipid, a class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide).
    GO:0016139    glycoside catabolic process    The chemical reactions and pathways resulting in the breakdown of glycosides, compounds in which a glycosyl group is substituted into a hydroxyl, thiol or selenol group in another compound.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.

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 Related Entries

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        NAGAB_HUMAN | P170503h53 3h55 3igu 4do4 4do5 4do6

(-) Related Entries Specified in the PDB File

3h53 CRYSTAL STRUCTURE OF HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE
3h55 CRYSTAL STRUCTURE OF HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE, COMPLEX WITH GALACTOSE