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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN HEPARANASE
 
Authors :  L. Wu, G. J. Davies
Date :  14 Oct 15  (Deposition) - 18 Nov 15  (Release) - 04 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glycoside Hydrolase, Apo, Protein, Sugar, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Wu, C. M. Viola, A. M. Brzozowski, G. J. Davies
Structural Characterization Of Human Heparanase Reveals Insights Into Substrate Recognition.
Nat. Struct. Mol. Biol. V. 22 1016 2015
PubMed-ID: 26575439  |  Reference-DOI: 10.1038/NSMB.3136

(-) Compounds

Molecule 1 - HEPARANASE
    ChainsA
    EC Number3.2.1.166
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System Taxid7111
    FragmentUNP RESIDUES 158-543
    GeneHPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymENDO-GLUCORONIDASE,HEPARANASE-1,HPA1, GLYCOSIDE HYDROLASE
 
Molecule 2 - HEPARANASE
    ChainsB
    EC Number3.2.1.166
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System Taxid7111
    FragmentUNP RESIDUES 36-109
    GeneHPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymENDO-GLUCORONIDASE,HEPARANASE-1,HPA1, GLYCOSIDE HYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 24)

Asymmetric/Biological Unit (4, 24)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2EDO15Ligand/Ion1,2-ETHANEDIOL
3FUC1Ligand/IonALPHA-L-FUCOSE
4NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:174 , ASN A:178 , LEU A:182 , ASP A:183 , LEU A:184 , ASN A:217 , HOH A:729 , HOH A:789binding site for residue EDO A 607
02AC2SOFTWAREASN A:224 , GLU A:225 , GLU A:343 , HOH A:741 , ASP B:27 , GLY B:61 , THR B:62binding site for residue EDO A 608
03AC3SOFTWAREVAL A:414 , GLY A:415 , THR A:416 , EDO A:612 , HOH A:704 , HOH A:711 , HOH B:228binding site for residue EDO A 609
04AC4SOFTWAREARG A:432 , VAL A:433 , TYR A:434 , HOH A:726 , HOH A:728 , HOH A:815 , HOH A:836binding site for residue EDO A 610
05AC5SOFTWAREARG A:374 , LEU B:14 , HOH B:204 , HOH B:222binding site for residue EDO A 611
06AC6SOFTWAREGLY A:415 , THR A:416 , ASN A:439 , THR A:440 , ASP A:441 , EDO A:609 , HOH A:826binding site for residue EDO A 612
07AC7SOFTWAREGLU A:225binding site for residue EDO A 613
08AC8SOFTWAREASP A:399 , PRO A:400 , LYS A:491 , HOH A:838binding site for residue EDO A 614
09AC9SOFTWAREGLU A:331 , PRO A:335 , HOH A:773binding site for residue EDO A 615
10AD1SOFTWARELYS A:251 , LYS A:255binding site for residue EDO A 616
11AD2SOFTWAREHOH A:866binding site for residue EDO A 617
12AD3SOFTWAREARG A:481 , ALA A:526 , HOH A:782binding site for residue EDO A 618
13AD4SOFTWARELYS A:427 , LYS A:462 , FUC A:606binding site for residue EDO A 619
14AD5SOFTWARESER A:212 , TYR A:216 , TRP A:220 , SER A:256binding site for residue EDO A 620
15AD6SOFTWAREGLN A:270binding site for residue CL A 621
16AD7SOFTWAREALA A:388 , HOH B:238 , HOH B:245binding site for residue CL A 622
17AD8SOFTWAREGLY A:239 , MET A:278binding site for residue CL A 623
18AD9SOFTWARECYS A:179 , PRO B:43 , ARG B:46 , ARG B:50 , HOH B:202binding site for residue EDO B 101
19AE1SOFTWAREASN A:162 , HOH A:731 , HOH A:774binding site for Mono-Saccharide NAG A 601 bound to ASN A 162
20AE2SOFTWAREASN A:200 , SER A:202 , HOH A:701 , HOH A:723 , HOH A:783binding site for Mono-Saccharide NAG A 602 bound to ASN A 200
21AE3SOFTWAREASN A:217 , HOH A:713 , HOH A:729binding site for Mono-Saccharide NAG A 603 bound to ASN A 217
22AE4SOFTWARELEU A:197 , ASN A:238 , GLN A:241 , HOH A:717 , HOH A:768 , HOH A:824binding site for Mono-Saccharide NAG A 604 bound to ASN A 238
23AE5SOFTWARELYS A:430 , HIS A:458 , ASN A:459 , LYS A:462 , EDO A:619 , HOH A:706 , HOH A:733 , HOH A:845binding site for Poly-Saccharide residues NAG A 605 through FUC A 606 bound to ASN A 459

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:437 -A:542

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gly A:265 -Pro A:266
2Gln A:383 -Val A:384
3Tyr A:468 -Pro A:469
4Gly A:484 -Pro A:485
5Ser B:53 -Pro B:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E8M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E8M)

(-) Exons   (0, 0)

(no "Exon" information available for 5E8M)

(-) 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:385
                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeehhhhhhhhhhhhhhh.eeeeeee............hhhhhhhhhhhhhh....eeee..hhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......eeeeee...hhhhhhhhhhhhhhhhhhh.eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhh..eeee..................hhhhhhhhhhhhheeeee.eeee.......eeeeeeee...........eeeeeee.....eeee.........eeeeeeee...hhhhh..eee..ee..............ee......eee...eeeeeee....hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e8m A 159 KFKNSTYSRSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATREDFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGETSSAYGGGAPLLSDTFAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVYLHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGLPAFSYSFFVIRNAKVAACI 543
                                   168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538     

Chain B from PDB  Type:PROTEIN  Length:74
                                                                                                          
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....ee.....eeeeee.hhhhh.hhhhhhhhhhhhhhhhhh..eeeeeehhhhh.eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 5e8m B   1 QDVVDLDFFTQEPLHLVSPSFLSVTIDANLATDPRFLILLGSPKLRTLARGLSPAYLRFGGTKTDFLIFDPKKE  74
                                    10        20        30        40        50        60        70    

   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 5E8M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E8M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E8M)

(-) Gene Ontology  (31, 31)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gln A:383 - Val A:384   [ RasMol ]  
    Gly A:265 - Pro A:266   [ RasMol ]  
    Gly A:484 - Pro A:485   [ RasMol ]  
    Ser B:53 - Pro B:54   [ RasMol ]  
    Tyr A:468 - Pro A:469   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        HPSE_HUMAN | Q9Y2515e97 5e98 5e9b 5e9c 5l9y 5l9z 5la4 5la7

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