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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  HOMOLOGY MODEL FOR HUMAN ALPHA-L-IDURONIDASE
 
Authors :  B. P. Rempel, L. A. Clarke, S. G. Withers
Date :  19 Nov 04  (Deposition) - 10 May 05  (Release) - 10 May 05  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Homology Model (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. P. Rempel, L. A. Clarke, S. G. Withers
A Homology Model For Human Alpha-L-Iduronidase: Insights Into Human Disease.
Mol. Genet. Metab. V. 85 28 2005
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-L-IDURONIDASE
    ChainsA
    EC Number3.2.1.76
    FragmentRESIDUES 36-522
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1Y24)

(-) Sites  (0, 0)

(no "Site" information available for 1Y24)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y24)

(-) Cis Peptide Bonds  (5, 5)

Theoretical Model
No.Residues
1Gln A:63 -Tyr A:64
2Ile A:85 -Lys A:86
3Leu A:216 -Arg A:217
4Gly A:220 -Pro A:221
5Thr A:337 -Thr A:338

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (52, 52)

Theoretical Model (52, 52)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_003351G51DIDUA_HUMANDisease (MPS1H)794726877AG51D
02UniProtVAR_003352A75TIDUA_HUMANDisease (MPS1H)758452450AA75T
03UniProtVAR_066215Y76CIDUA_HUMANDisease (MPS1S)780165694AY76C
04UniProtVAR_020975A79VIDUA_HUMANDisease (MPS1H/S)747981483AA79V
05UniProtVAR_003353H82PIDUA_HUMANDisease (MPS1H/S)794727239AH82P
06UniProtVAR_020976H82QIDUA_HUMANPolymorphism148775298AH82Q
07UniProtVAR_066216G84RIDUA_HUMANDisease (MPS1H/S)  ---AG84R
08UniProtVAR_003354R89QIDUA_HUMANDisease (MPS1S)121965029AR89Q
09UniProtVAR_003355R89WIDUA_HUMANDisease (MPS1S)754966840AR89W
10UniProtVAR_066217T103PIDUA_HUMANDisease (MPS1H)  ---AT103P
11UniProtVAR_003356R105QIDUA_HUMANPolymorphism3755955AR105Q
12UniProtVAR_003357G116RIDUA_HUMANPolymorphism148946496AG116R
13UniProtVAR_020977M133IIDUA_HUMANDisease (MPS1H)558683362AM133I
14UniProtVAR_066218E178KIDUA_HUMANDisease (MPS1H/S)  ---AE178K
15UniProtVAR_020978E182KIDUA_HUMANDisease (MPS1H)754154200AE182K
16UniProtVAR_066219F188LIDUA_HUMANDisease (MPS1H/S)  ---AF188L
17UniProtVAR_020979G208DIDUA_HUMANDisease (MPS1H)  ---AG208D
18UniProtVAR_003358L218PIDUA_HUMANDisease (MPS1H)869025584AL218P
19UniProtVAR_066220G219EIDUA_HUMANDisease (MPS1S)  ---AG219E
20UniProtVAR_020980L238QIDUA_HUMANDisease (MPS1H/S)148789453AL238Q
21UniProtVAR_020981S260FIDUA_HUMANDisease (MPS1H/S)  ---AS260F
22UniProtVAR_066221G265RIDUA_HUMANDisease (MPS1H/S)369090960AG265R
23UniProtVAR_066222E276KIDUA_HUMANDisease (MPS1S)  ---AE276K
24UniProtVAR_003359V279AIDUA_HUMANPolymorphism  ---AV279A
25UniProtVAR_017435A300TIDUA_HUMANPolymorphism121965030AA300T
26UniProtVAR_066223W306LIDUA_HUMANDisease (MPS1S)  ---AW306L
27UniProtVAR_003360D315YIDUA_HUMANDisease (MPS1H)  ---AD315Y
28UniProtVAR_003361A327PIDUA_HUMANDisease (MPS1H)199801029AA327P
29UniProtVAR_017436L346RIDUA_HUMANDisease (MPS1H/S)121965033AL346R
30UniProtVAR_066224N348KIDUA_HUMANDisease (MPS1S)746766617AN348K
31UniProtVAR_003362D349NIDUA_HUMANDisease (MPS1H)368454909AD349N
32UniProtVAR_020982D349YIDUA_HUMANDisease (MPS1H)  ---AD349Y
33UniProtVAR_020983N350IIDUA_HUMANDisease (MPS1S)  ---AN350I
34UniProtVAR_003364A361TIDUA_HUMANPolymorphism6831280AA361T
35UniProtVAR_020984R363CIDUA_HUMANDisease (MPS1H/S)750496798AR363C
36UniProtVAR_003365T366PIDUA_HUMANDisease (MPS1H)121965024AT366P
37UniProtVAR_003366Q380RIDUA_HUMANDisease (MPS1S)762903007AQ380R
38UniProtVAR_003367R383HIDUA_HUMANDisease (MPS1S)754949360AR383H
39UniProtVAR_066225P385RIDUA_HUMANDisease (MPS1H)  ---AP385R
40UniProtVAR_003368T388RIDUA_HUMANDisease (MPS1H)  ---AT388R
41UniProtVAR_066226L396PIDUA_HUMANDisease (MPS1H/S)  ---AL396P
42UniProtVAR_003370G409RIDUA_HUMANDisease (MPS1H)11934801AG409R
43UniProtVAR_020985S423RIDUA_HUMANDisease (MPS1S)  ---AS423R
44UniProtVAR_066227A436PIDUA_HUMANDisease (MPS1H/S)  ---AA436P
45UniProtVAR_066228H449NIDUA_HUMANPolymorphism532731688AH449N
46UniProtVAR_003372V454IIDUA_HUMANPolymorphism73066479AV454I
47UniProtVAR_003373R489PIDUA_HUMANDisease (MPS1H)4690226AR489P
48UniProtVAR_003374L490PIDUA_HUMANDisease (MPS1S)121965027AL490P
49UniProtVAR_003375R492PIDUA_HUMANDisease (MPS1S)121965026AR492P
50UniProtVAR_003376P496LIDUA_HUMANDisease (MPS1H/S)  ---AP496L
51UniProtVAR_066229P496RIDUA_HUMANDisease (MPS1H/S)772416503AP496R
52UniProtVAR_003377M504TIDUA_HUMANDisease (MPS1H/S)  ---AM504T

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

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F39PS01027 Glycosyl hydrolases family 39 active site.IDUA_HUMAN175-184  1A:175-184

(-) Exons   (11, 11)

Theoretical Model (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002479331aENSE00001295425chr4:980785-981030246IDUA_HUMAN1-53531A:36-5318
1.2bENST000002479332bENSE00000969312chr4:981597-981737141IDUA_HUMAN53-100481A:53-10048
1.6ENST000002479336ENSE00000969313chr4:994400-99448586IDUA_HUMAN100-129301A:100-12930
1.7aENST000002479337aENSE00000872490chr4:994670-994777108IDUA_HUMAN129-165371A:129-16537
1.8ENST000002479338ENSE00000872489chr4:995256-99535196IDUA_HUMAN165-197331A:165-19733
1.9cENST000002479339cENSE00000872488chr4:995467-995669203IDUA_HUMAN197-264681A:197-26468
1.9gENST000002479339gENSE00000969314chr4:995770-995949180IDUA_HUMAN265-324601A:265-32460
1.9hENST000002479339hENSE00001304368chr4:996057-996273217IDUA_HUMAN325-397731A:325-39773
1.10aENST0000024793310aENSE00000969318chr4:996520-996732213IDUA_HUMAN397-468721A:397-46872
1.11aENST0000024793311aENSE00001300133chr4:996824-996945122IDUA_HUMAN468-508411A:468-50841
1.11cENST0000024793311cENSE00000969321chr4:997133-997258126IDUA_HUMAN509-550421A:509-52214
1.12aENST0000024793312aENSE00001423282chr4:997337-99741377IDUA_HUMAN551-576260--
1.13ENST0000024793313ENSE00000969322chr4:997800-997900101IDUA_HUMAN576-610350--
1.14bENST0000024793314bENSE00001947294chr4:998048-998294247IDUA_HUMAN610-653440--

(-) Sequences/Alignments

Theoretical Model
   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:487
 aligned with IDUA_HUMAN | P35475 from UniProtKB/Swiss-Prot  Length:653

    Alignment length:487
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       
           IDUA_HUMAN    36 AARALWPLRRFWRSTGFCPPLPHSQADQYVLSWDQQLNLAYVGAVPHRGIKQVRTHWLLELVTTRGSTGRGLSYNFTHLDGYLDLLRENQLLPGFELMGSASGHFTDFEDKQQVFEWKDLVSSLARRYIGRYGLAHVSKWNFETWNEPDHHDFDNVSMTMQGFLNYYDACSEGLRAASPALRLGGPGDSFHTPPRSPLSWGLLRHCHDGTNFFTGEAGVRLDYISLHRKGARSSISILEQEKVVAQQIRQLFPKFADTPIYNDEADPLVGWSLPQPWRADVTYAAMVVKVIAQHQNLLLANTTSAFPYALLSNDNAFLSYHPHPFAQRTLTARFQVNNTRPPHVQLLRKPVLTAMGLLALLDEEQLWAEVSQAGTVLDSNHTVGVLASAHRPQGPADAWRAAVLIYASDDTRAHPNRSVAVTLRLRGVPPGPGLVYVTRYLDNGLCSPDGEWRRLGRPVFPTAEQFRRMRAAEDPVAAAPRPLPAGG 522
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee........................hhhhhhhhhhhhhh.........ee......hhhhh...........hhhhhhhhhhhhhh..ee..ee........ee....ee.......hhhhhhhhhhhhhhhhhhh..ee..........hhhhhhhhhhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhhh......eeeeee......ee..ee......hhhhhhhhhhhhhh.........eeeeeee............hhhhhhhhhhhhhhhhhh.eeee.......................ee...ee.hhhhhhhhhhhh..eeeeee..eeeee.....eeeeee...........eeeeeeee.....eeeeeee......hhhhhhh........hhhhhhhhhhhh..eeeee.......eeeeeeee....eeeeeeee................... Sec.struct. author
             SAPs(SNPs) (1) ---------------D-----------------------TC--V--P-R----Q-------------P-Q----------R----------------I--------------------------------------------K---K-----L-------------------D---------PE------------------Q---------------------F----R----------K--A--------------------T-----L--------Y-----------P------------------R-KNI----------T-C--P-------------R--H-R--R-------P------------R-------------R------------P------------N----I----------------------------------PP-P---L-------T------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------Q------W-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y--------------------------------------------------------------------------------------------------------------------------------------------------R-------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_H-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a         ----------------------------------------------Exon 1.6  PDB: A:100-129      -----------------------------------Exon 1.8  PDB: A:165-197         -------------------------------------------------------------------Exon 1.9g  PDB: A:265-324 UniProt: 265-324                  ------------------------------------------------------------------------Exon 1.10a  PDB: A:397-468 UniProt: 397-468                             ----------------------------------------Exon 1.11c     Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.2b  PDB: A:53-100 UniProt: 53-100        ----------------------------Exon 1.7a  PDB: A:129-165            -------------------------------Exon 1.9c  PDB: A:197-264 UniProt: 197-264                          ------------------------------------------------------------Exon 1.9h  PDB: A:325-397 UniProt: 325-397                               ----------------------------------------------------------------------Exon 1.11a  PDB: A:468-508               -------------- Transcript 1 (2)
                 1y24 A  36 AARALWPLRRFWRSTGFCPPLPHSQADQYVLSWDQQLNLAYVGAVPHRGIKQVRTHWLLELVTTRGSTGRGLSYNFTHLDGYLDLLRENQLLPGFELMGSASGHFTDFEDKQQVFEWKDLVSSLARRYIGRYGLAHVSKWNFETWNEPDHHDFDNVSMTMQGFLNYYDACSEGLRAASPALRLGGPGDSFHTPPRSPLSWGLLRHCHDGTNFFTGEAGVRLDYISLHRKGARSSISILEQEKVVAQQIRQLFPKFADTPIYNDEADPLVGWSLPQPWRADVTYAAMVVKVIAQHQNLLLANTTSAFPYALLSNDNAFLSYHPHPFAQRTLTARFQVNNTRPPHVQLLRKPVLTAMGLLALLDEEQLWAEVSQAGTVLDSNHTVGVLASAHRPQGPADAWRAAVLIYASDDTRAHPNRSVAVTLRLRGVPPGPGLVYVTRYLDNGLCSPDGEWRRLGRPVFPTAEQFRRMRAAEDPVAAAPRPLPAGG 522
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       

   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 1Y24)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Y24)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Y24)

(-) Gene Ontology  (15, 15)

Theoretical Model(hide GO term definitions)
Chain A   (IDUA_HUMAN | P35475)
molecular function
    GO:0003940    L-iduronidase activity    Catalysis of the hydrolysis of alpha-L-iduronosidic linkages in dermatan sulfate.
    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:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    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:0030207    chondroitin sulfate catabolic process    The chemical reactions and pathways resulting in the breakdown of chondroitin sulfate, any member of a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues, the repeat units of which consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate.
    GO:0030209    dermatan sulfate catabolic process    The chemical reactions and pathways resulting in the breakdown of dermatan sulfate, any of a group of glycosaminoglycans with repeats consisting of beta-(1,4)-linked L-iduronyl-beta-(1,3)-N-acetyl-D-galactosamine 4-sulfate units.
    GO:0005984    disaccharide metabolic process    The chemical reactions and pathways involving any disaccharide, sugars composed of two monosaccharide units.
    GO:0006027    glycosaminoglycan catabolic process    The chemical reactions and pathways resulting in the breakdown of glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars.
    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:0030135    coated vesicle    Small membrane-bounded organelle formed by pinching off of a coated region of membrane. Some coats are made of clathrin, whereas others are made from other proteins.
    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:0043202    lysosomal lumen    The volume enclosed within the lysosomal membrane.
    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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  Cis Peptide Bonds
    Gln A:63 - Tyr A:64   [ RasMol ]  
    Gly A:220 - Pro A:221   [ RasMol ]  
    Ile A:85 - Lys A:86   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        IDUA_HUMAN | P354753w81 3w82 4kgj 4kgl 4kh2 4mj2 4mj4 4obr 4obs

(-) Related Entries Specified in the PDB File

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