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 HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE, COMPLEX WITH GALACTOSE
 
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 :  1.91
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
    Chains: A, B
    EC Number: 3.2.1.49
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Plasmid: PIB/V5-HIS-TOPO TA
    Expression System Strain: HI-FIVE
    Expression System Taxid: 7111
    Expression System Vector Type: STABLE CELL LINE
    Gene: NAGA
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA-GALACTOSIDASE B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 25)

Asymmetric/Biological Unit (6, 25)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2CIT2Ligand/IonCITRIC ACID
3FUC2Ligand/IonALPHA-L-FUCOSE
4GLA4Ligand/IonALPHA D-GALACTOSE
5MAN4Ligand/IonALPHA-D-MANNOSE
6NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:124 , PHE A:159 , HOH A:531 , NAG A:625 , BMA A:626 , FUC A:627 , HOH A:629 , HOH A:753 , HOH A:851BINDING SITE FOR RESIDUE NAG A 624
02AC2SOFTWARENAG A:624 , BMA A:626 , HOH A:715BINDING SITE FOR RESIDUE NAG A 625
03AC3SOFTWAREPHE A:159 , NAG A:624 , NAG A:625BINDING SITE FOR RESIDUE BMA A 626
04AC4SOFTWARENAG A:624 , HOH A:788 , HOH A:816 , HOH A:851BINDING SITE FOR RESIDUE FUC A 627
05AC5SOFTWAREASP A:19 , ASN A:20 , ASN A:177 , GLY A:180 , ARG A:181 , HOH A:492 , HOH A:542 , NAG A:678 , HOH A:793 , HOH A:810 , HOH A:811BINDING SITE FOR RESIDUE NAG A 677
06AC6SOFTWAREASP A:19 , HOH A:532 , HOH A:569 , NAG A:677 , BMA A:679 , MAN A:681 , HOH A:849 , HOH A:869BINDING SITE FOR RESIDUE NAG A 678
07AC7SOFTWAREHOH A:483 , NAG A:678 , MAN A:680 , MAN A:681 , ARG B:61 , GLN B:64 , ASP B:65BINDING SITE FOR RESIDUE BMA A 679
08AC8SOFTWAREHOH A:559 , BMA A:679BINDING SITE FOR RESIDUE MAN A 680
09AC9SOFTWAREHOH A:589 , HOH A:595 , NAG A:678 , BMA A:679BINDING SITE FOR RESIDUE MAN A 681
10BC1SOFTWAREGLU A:383 , ASN A:385 , HOH A:541 , HOH A:735 , HOH A:908BINDING SITE FOR RESIDUE NAG A 885
11BC2SOFTWAREHOH 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 , ARG A:213 , ASP A:217 , HOH A:686 , HOH A:893 , HOH A:895 , GLA A:1500BINDING SITE FOR RESIDUE GLA A 1000
12BC3SOFTWAREALA A:191 , TYR A:192 , TYR A:215 , ASP A:217 , HOH A:686 , HOH A:733 , HOH A:791 , GLA A:1000BINDING SITE FOR RESIDUE GLA A 1500
13BC4SOFTWAREHIS A:110 , GLY A:113 , LEU A:114 , LYS A:115 , ASP A:151 , ARG A:181 , HOH A:425 , HOH A:444 , HOH A:580 , HOH A:685BINDING SITE FOR RESIDUE CIT A 1100
14BC5SOFTWAREASN B:124 , NAG B:625 , FUC B:627BINDING SITE FOR RESIDUE NAG B 624
15BC6SOFTWARENAG B:624 , FUC B:627 , HOH B:852BINDING SITE FOR RESIDUE NAG B 625
16BC7SOFTWARENAG B:624 , NAG B:625BINDING SITE FOR RESIDUE FUC B 627
17BC8SOFTWAREARG A:199 , ASP B:19 , ASN B:20 , ASN B:177 , GLY B:180 , HOH B:457 , HOH B:471 , HOH B:488 , HOH B:554 , NAG B:678 , HOH B:692 , HOH B:699BINDING SITE FOR RESIDUE NAG B 677
18BC9SOFTWAREASP B:19 , GLY B:21 , NAG B:677 , BMA B:679 , MAN B:681BINDING SITE FOR RESIDUE NAG B 678
19CC1SOFTWARENAG B:678 , MAN B:680 , MAN B:681BINDING SITE FOR RESIDUE BMA B 679
20CC2SOFTWAREBMA B:679 , HOH B:737 , HOH B:767 , HOH B:802BINDING SITE FOR RESIDUE MAN B 680
21CC3SOFTWAREHOH B:608 , NAG B:678 , BMA B:679BINDING SITE FOR RESIDUE MAN B 681
22CC4SOFTWAREGLU B:383 , ASN B:385 , HOH B:736 , HOH B:764 , HOH B:828BINDING SITE FOR RESIDUE NAG B 885
23CC5SOFTWARETRP B:33 , ASP B:78 , ASP B:79 , TYR B:119 , CYS B:127 , MET B:128 , LYS B:154 , ASP B:156 , ARG B:213 , ASP B:217 , HOH B:436 , HOH B:685 , HOH B:725 , HOH B:813 , GLA B:2500BINDING SITE FOR RESIDUE GLA B 2000
24CC6SOFTWARECYS B:127 , CYS B:158 , ALA B:191 , TYR B:192 , ASP B:217 , HOH B:612 , GLA B:2000BINDING SITE FOR RESIDUE GLA B 2500
25CC7SOFTWAREHIS B:110 , GLY B:113 , LEU B:114 , LYS B:115 , ASP B:151 , ARG B:181 , HOH B:552BINDING SITE FOR RESIDUE CIT B 2100

(-) 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 3H55)

(-) 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 d3h55a1 A:18-309 automated matches                                                                                                                                                                                                                                                                  d3h55a2 A:310-404 automated matches                                                             SCOP domains
               CATH domains 3h55A01 A:18-307 Aldolase class I                                                                                                                                                                                                                                                                 ------3h55A02 A:314-404 Golgi alpha-mannosidase II                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeehhhhhh.............hhhhhhhhhhhhhhh.hhhhh..eee.....eeee.....eee.......hhhhhhhhhhhh..eeeeeee............hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhh....eeee.hhhhhh......hhhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhh.......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
                 3h55 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 d3h55b1 B:18-309 automated matches                                                                                                                                                                                                                                                                  d3h55b2 B:310-404 automated matches                                                             SCOP domains
               CATH domains 3h55B01 B:18-307 Aldolase class I                                                                                                                                                                                                                                                                 ------3h55B02 B:314-404 Golgi alpha-mannosidase II                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeehhhhhh.............hhhhhhhhhhhhhhh.hhhhh..eee.....eeee.....eee.......hhhhhhhhhhhh..eeeeeee...............hhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhh....eeee.hhhhhh......hhhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhhhh....eee...........hhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhhh.......eeeee....eeeeeee.....eeeeeee......eeeee............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
                 3h55 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
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) 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 3H55)

(-) 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.

 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
    BMA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FUC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GLA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
    CC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:197 - Pro A:198   [ RasMol ]  
    Pro B:197 - Pro B:198   [ 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
  3h55
    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
  NAGAB_HUMAN | P17050
    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)
  3.2.1.49
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  609241
    Disease Information: OMIM
  609242
    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
  NAGAB_HUMAN | P17050
    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
        NAGAB_HUMAN | P17050: 3h53 3h54 3igu 4do4 4do5 4do6

(-) Related Entries Specified in the PDB File

3h53 CRYSTAL STRUCTURE OF HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE
3h54 CRYSTAL STRUCTURE OF HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE, COMPLEX WITH GALNAC