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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALPHA-L-IDURONIDASE COMPLEX WITH ALPHA-L-IDURONIC ACID
 
Authors :  H. Y. Bie, J. Yin, X. He, A. R. Kermode, M. N. G. James
Date :  07 Jan 14  (Deposition) - 14 Jan 15  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.46
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glycoside Hydrolase Family 39, Tim Barrel, Beta Sandwich, Fibronectin Iii Domain, Glycosaminoglycans, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Y. Bie, J. Yin, X. He, A. R. Kermode, M. N. G. James
Crystal Structure Of Human Alpha-L-Iduronidase Complex With Alpha-L-Iduronic Acid
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALPHA-L-IDURONIDASE
    ChainsA, B
    EC Number3.2.1.76
    EngineeredYES
    Expression SystemARABIDOPSIS THALIANA
    Expression System CommonTHALE CRESS
    Expression System PlasmidPARC5S3
    Expression System StrainCGL1 1
    Expression System Taxid3702
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 27-653
    GeneIDUA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 37)

Asymmetric Unit (8, 37)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CL2Ligand/IonCHLORIDE ION
3GOL9Ligand/IonGLYCEROL
4IDR2Ligand/IonL-IDURONIC ACID
5MAN8Ligand/IonALPHA-D-MANNOSE
6NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SO41Ligand/IonSULFATE ION
8TLA3Ligand/IonL(+)-TARTARIC ACID
Biological Unit 1 (7, 14)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CL-1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4IDR1Ligand/IonL-IDURONIC ACID
5MAN2Ligand/IonALPHA-D-MANNOSE
6NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SO41Ligand/IonSULFATE ION
8TLA1Ligand/IonL(+)-TARTARIC ACID
Biological Unit 2 (6, 21)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CL-1Ligand/IonCHLORIDE ION
3GOL6Ligand/IonGLYCEROL
4IDR1Ligand/IonL-IDURONIC ACID
5MAN6Ligand/IonALPHA-D-MANNOSE
6NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SO4-1Ligand/IonSULFATE ION
8TLA2Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (37, 37)

Asymmetric Unit (37, 37)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:110 , THR A:112 , HIS A:113BINDING SITE FOR RESIDUE NAG A 901
02AC2SOFTWAREGLU A:274 , ASN A:415 , NAG A:903BINDING SITE FOR RESIDUE NAG A 902
03AC3SOFTWARENAG A:902BINDING SITE FOR RESIDUE NAG A 903
04AC4SOFTWAREHIS A:356 , GLN A:370 , ASN A:372 , VAL A:494 , PHE A:495 , NAG A:905BINDING SITE FOR RESIDUE NAG A 904
05AC5SOFTWAREHIS A:356 , GLN A:370 , NAG A:904 , BMA A:906BINDING SITE FOR RESIDUE NAG A 905
06AC6SOFTWARETYR A:355 , NAG A:905 , MAN A:907 , MAN A:908BINDING SITE FOR RESIDUE BMA A 906
07AC7SOFTWAREPRO A:55 , BMA A:906BINDING SITE FOR RESIDUE MAN A 907
08AC8SOFTWAREBMA A:906BINDING SITE FOR RESIDUE MAN A 908
09AC9SOFTWARELYS A:324 , HIS A:416 , THR A:417 , ASP A:444 , ASP A:445 , ARG A:447BINDING SITE FOR RESIDUE GOL A 909
10BC1SOFTWAREHIS A:356 , ARG A:368 , PHE A:369 , GLN A:370 , VAL A:494BINDING SITE FOR RESIDUE GOL A 910
11BC2SOFTWARETRP A:41 , ALA A:335 , GLN A:400 , ALA A:403BINDING SITE FOR RESIDUE GOL A 911
12BC3SOFTWAREARG A:239 , GLY A:244 , THR A:245BINDING SITE FOR RESIDUE TLA A 912
13BC4SOFTWAREHIS A:91 , ASN A:181 , GLU A:182 , LYS A:264 , GLU A:299 , GLY A:305 , TRP A:306 , ASP A:349 , ARG A:363BINDING SITE FOR RESIDUE IDR A 913
14BC5SOFTWAREPRO A:302 , LEU A:303 , ARG A:313 , ARG A:363BINDING SITE FOR RESIDUE CL A 914
15BC6SOFTWAREARG A:48 , ARG A:83 , LYS A:86BINDING SITE FOR RESIDUE SO4 A 915
16BC7SOFTWAREARG B:100 , ASN B:110 , THR B:112 , GOL B:916BINDING SITE FOR RESIDUE NAG B 901
17BC8SOFTWAREGLU B:274 , ASN B:415 , NAG B:903BINDING SITE FOR RESIDUE NAG B 902
18BC9SOFTWARENAG B:902BINDING SITE FOR RESIDUE NAG B 903
19CC1SOFTWARELEU A:490 , GLY A:491 , VAL A:494 , PHE A:495 , GLN B:370 , ASN B:372 , VAL B:494 , PHE B:495 , NAG B:905 , GOL B:913BINDING SITE FOR RESIDUE NAG B 904
20CC2SOFTWAREGLY A:491 , ARG A:492 , TYR B:355 , HIS B:356 , GLN B:370 , NAG B:904 , BMA B:906 , HOH B:1033BINDING SITE FOR RESIDUE NAG B 905
21CC3SOFTWAREARG A:492 , TYR B:355 , NAG B:905 , MAN B:907 , MAN B:911BINDING SITE FOR RESIDUE BMA B 906
22CC4SOFTWAREBMA B:906 , MAN B:908 , MAN B:909BINDING SITE FOR RESIDUE MAN B 907
23CC5SOFTWAREARG A:492 , MAN B:907BINDING SITE FOR RESIDUE MAN B 908
24CC6SOFTWAREMAN B:907 , MAN B:910BINDING SITE FOR RESIDUE MAN B 909
25CC7SOFTWARECYS B:53 , TRP B:306 , SER B:307 , PHE B:352 , MAN B:909 , IDR B:921BINDING SITE FOR RESIDUE MAN B 910
26CC8SOFTWAREHIS A:356 , PRO A:357 , BMA B:906 , MAN B:912BINDING SITE FOR RESIDUE MAN B 911
27CC9SOFTWAREHIS B:358 , MAN B:911BINDING SITE FOR RESIDUE MAN B 912
28DC1SOFTWAREHIS B:356 , PRO B:359 , ARG B:368 , PHE B:369 , GLN B:370 , VAL B:494 , PHE B:495 , NAG B:904BINDING SITE FOR RESIDUE GOL B 913
29DC2SOFTWARETRP B:41 , ASN B:331 , ALA B:335 , TRP B:402 , ALA B:403BINDING SITE FOR RESIDUE GOL B 914
30DC3SOFTWAREPRO B:594 , PRO B:609BINDING SITE FOR RESIDUE GOL B 915
31DC4SOFTWAREARG B:100 , TYR B:109 , ASN B:110 , PHE B:111 , ARG B:162 , NAG B:901BINDING SITE FOR RESIDUE GOL B 916
32DC5SOFTWAREGLN B:71 , ALA B:75 , LEU B:120 , GLU B:123 , ASN B:124 , ARG B:555 , LEU B:557BINDING SITE FOR RESIDUE GOL B 917
33DC6SOFTWAREHIS B:185 , SER B:224 , HIS B:226BINDING SITE FOR RESIDUE GOL B 918
34DC7SOFTWAREARG B:44 , ARG B:45 , ARG B:48 , HOH B:1047BINDING SITE FOR RESIDUE TLA B 919
35DC8SOFTWAREARG B:45 , ARG B:48 , ARG B:83 , LYS B:86BINDING SITE FOR RESIDUE TLA B 920
36DC9SOFTWAREHIS B:91 , ASN B:181 , GLU B:182 , LYS B:264 , GLU B:299 , VAL B:304 , GLY B:305 , TRP B:306 , ASP B:349 , PHE B:352 , ARG B:363 , MAN B:910BINDING SITE FOR RESIDUE IDR B 921
37EC1SOFTWAREPRO B:302 , LEU B:303 , TRP B:312 , ARG B:313 , ARG B:363BINDING SITE FOR RESIDUE CL B 922

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:541 -A:577
2B:541 -B:577

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Gly A:220 -Pro A:221
2Pro A:228 -Pro A:229
3His A:356 -Pro A:357
4Arg A:375 -Pro A:376
5Leu A:532 -Pro A:533
6Gly B:220 -Pro B:221
7Pro B:228 -Pro B:229
8His B:356 -Pro B:357
9Arg B:375 -Pro B:376
10Leu B:532 -Pro B:533

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OBR)

(-) Sequences/Alignments

Asymmetric 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:595
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee......eeee......hhhhhhhhhhhhhhhhhh..eeee.hhhhh.......hhhhhhhhhhhhhh..eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhh.......hhhhhhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhh.............eeee.......hhhhhhhhhhhhhhhhhhhhhhh...eee............hhhhhhhhhhhhhhhhhhhhhhhhh........eeee...................eeeeee......eeeeeehhhhhhhhhhh....eeeeeeeee..eee.....eeeeeeee.........eeeeeeee......eeeeeeeeeeeee........eeeeeeee....hhhhhhhhh......hhhhhhhhhhh...ee...ee......eee..eeee.eeeeeeee..........eeeeeeeee..eeeeeee........eeeeeeeee...ee.........eeee........eeeeeeeee...........eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4obr A  28 APHLVQVDAARALWPLRRFWRSTGFCPPYVLSWDQQLNLAYVGAVPHRGIKQVRTHWLLELVTTLSYNFTHLDGYLDLLRENQLLPGFELMGSASGHFTDFEDKQQVFEWKDLVSSLARRYIGRYGLAHVSKWNFETWNEPDHHDFDNVSMTMQGFLNYYDACSEGLRAASPALRLGGPGDSFHTPPRSPLSWGLLRHCHDGTNFFTGEAGVRLDYISLHRKGARSSISILEQEKVVAQQIRQLFPKFADTPIYNDEADPLVGWSLPQPWRADVTYAAMVVKVIAQHQNLLLANTTSAFPYALLSNDNAFLSYHPHPFAQRTLTARFQVNNTRPPHVQLLRKPVLTAMGLLALLDEEQLWAEVSQAGTVLDSNHTVGVLASAHRPQGPADAWRAAVLIYASDDTRAHPNRSVAVTLRLRGVPPGPGLVYVTRYLDNGLCSPDGEWRRLGRPVFPTAEQFRRMRAAEDPVAAAPRPLPAGGRLTLRPALRLPSLLLVHVCARPEKPPGQVTRLRALPLTQGQLVLVWSDEHVGSKCLWTYEIQFSQDYTPVSRKPSTFNLFVFSPDTGAVSGSYRVRALDYWARPGPFSDPVPYLE 640
                                    37        47       |65        75        85        95   ||  112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582     ||595       605       615       625       635     
                                                      55|                                 99|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              588|                                                
                                                       64                                 107                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               592                                                

Chain B from PDB  Type:PROTEIN  Length:606
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee......eeee........hhhhhhhhhhhhh.......eeee.hhhhh.eee....eeehhhhhhhhhhhhhh..eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhh.......hhhhhhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhh.............eeee......hhhhhhhhhhhhhhhhhhhhhhhh...eee............hhhhhhhhhhhhhhhhhhhhhhhh.........eeee...................eeeeee......eeeeeehhhhhhhhhhh....eeeeeeeee..eee.....eeeeeeee.........eeeeeeee...........eeeeeeee........eeeeeeee....hhhhhhhhh......hhhhhhhhhh....eeeeeee......eee..ee...eeeeeeee..........eeeeeeeee..eeeeeee........eeeeeeeee......ee.........eeee........eeeeeeeee...........eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4obr B  28 APHLVQVDAARALWPLRRFWRSTGFCPPDPYVLSWDQQLNLAYVGAVPHRGIKQVRTHWLLELVTTRGSTLSYNFTHLDGYLDLLRENQLLPGFELMGSASGHFTDFEDKQQVFEWKDLVSSLARRYIGRYGLAHVSKWNFETWNEPDHHDFDNVSMTMQGFLNYYDACSEGLRAASPALRLGGPGDSFHTPPRSPLSWGLLRHCHDGTNFFTGEAGVRLDYISLHRKGARSSISILEQEKVVAQQIRQLFPKFADTPIYNDEADPLVGWSLPQPWRADVTYAAMVVKVIAQHQNLLLANTTSAFPYALLSNDNAFLSYHPHPFAQRTLTARFQVNNTRPPHVQLLRKPVLTAMGLLALLDEEQLWAEVSQAGTVLDSNHTVGVLASAHRPQGPADAWRAAVLIYASDDTRAHPNRSVAVTLRLRGVPPGPGLVYVTRYLDNGLCSPDGEWRRLGRPVFPTAEQFRRMRAAEDPVAAAPRPLPAGGRLTLRPALRLPSLLLVHVCARPEKPPGQVTRLRALPLTQGQLVLVWSDEHVGSKCLWTYEIQFSQDGKAYTPVSRKPSTFNLFVFSPDTGAVSGSYRVRALDYWARPGPFSDPVPYLEVP 642
                                    37        47       |63        73        83        93       103|      116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636      
                                                      55|                                      103|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
                                                       62                                       107                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       

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  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 4OBR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

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 Related Entries

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

UniProtKB/Swiss-Prot
        IDUA_HUMAN | P354751y24 3w81 3w82 4kgj 4kgl 4kh2 4mj2 4mj4 4obs

(-) Related Entries Specified in the PDB File

4kgj IDURONIDASE COMPLEX WITH 5-FLUORO-ALPHA-L- IDOPYRANOSYLURONIC ACID FLUORIDE
4kgl IDURONIDASE COMPLEX WITH [2R,3R,4R,5S]-2-CARBOXY-3,4,5- TRIHYDROXY-PIPERIDINE
4kh2 IDURONIDASE COMPLEX WITH 2-DEOXY-2-FLUORO-ALPHA-L- IDOPYRANOSYLURONIC ACID FLUORIDE
4mj2 R3 APO-IDURONIDASE STRUCTURE
4mj4 P21 APO-IDURONIDASE STRUCTURE
4obs