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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN HEPARANASE IN COMPLEX WITH HEPMER M09S05A
 
Authors :  L. Wu, G. J. Davies
Date :  14 Oct 15  (Deposition) - 18 Nov 15  (Release) - 04 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glycoside Hydrolase, Ligand 3, 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
    FragmentRESIDUES 158-543
    GeneHPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymENDO-GLUCORONIDASE,HEPARANASE-1,HPA1
 
Molecule 2 - HEPARANASE
    ChainsB
    EC Number3.2.1.166
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System Taxid7111
    FragmentRESIDUES 36-109
    GeneHPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymENDO-GLUCORONIDASE,HEPARANASE-1,HPA1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1BDP2Ligand/IonBETA-D-GLUCOPYRANURONIC ACID
2CL1Ligand/IonCHLORIDE ION
3GNS1Ligand/IonN-SULFO-ALPHA-D-GLUCOSAMINE
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SGN1Ligand/IonN,O6-DISULFO-GLUCOSAMINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:415 , THR A:416 , ASN A:439binding site for residue CL A 604
2AC2SOFTWAREASN A:200 , SER A:202 , HOH A:832binding site for Mono-Saccharide NAG A 601 bound to ASN A 200
3AC3SOFTWAREASN A:238 , HOH A:701 , HOH A:719 , HOH A:791binding site for Mono-Saccharide NAG A 602 bound to ASN A 238
4AC4SOFTWAREASN A:459 , HOH A:711 , HOH A:785binding site for Mono-Saccharide NAG A 603 bound to ASN A 459
5AC5SOFTWAREPHE A:160 , ASN A:224 , GLU A:225 , ARG A:303 , GLU A:343 , TYR A:348 , GLY A:349 , GLY A:350 , GLN A:383 , VAL A:384 , ALA A:388 , GLY A:389 , TYR A:391 , HOH A:703 , HOH A:738 , ASP B:62 , ASN B:64 , GLY B:96 , THR B:97binding site for Poly-Saccharide residues BDP A 605 through GNS A 608

(-) 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:88 -Pro B:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E9B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E9B)

(-) Exons   (0, 0)

(no "Exon" information available for 5E9B)

(-) 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 ....eeehhhhhhhhhhhhhhhheeeeeee............hhhhhhhhhhhhhh....eeee..hhhhhhhhhh...hhhhhhhhhhhhhhhhhh........eeeee...hhhhhhhhhhhhhhhh....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
                 5e9b 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
                 5e9b B  36 QDVVDLDFFTQEPLHLVSPSFLSVTIDANLATDPRFLILLGSPKLRTLARGLSPAYLRFGGTKTDFLIFDPKKE 109
                                    45        55        65        75        85        95       105    

   Legend:   → Mismatch (orange background)
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  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 5E9B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E9B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E9B)

(-) 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:88 - Pro B:89   [ 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 | Q9Y2515e8m 5e97 5e98 5e9c 5l9y 5l9z 5la4 5la7

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5E9B)