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(-) Description

Title :  CRYSTAL STRUCTURE OF APO HUMAN PROHEPARANASE
 
Authors :  L. Wu, Y. Jin, G. J. Davies
Date :  13 Jun 16  (Deposition) - 31 May 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Heparanase, Proenzyme, Gh79 (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Wu, J. Jiang, Y. Jin, W. W. Kallemeijn, C. L. Kuo, M. Artola, W. Dai, C. Van Elk, M. Van Eijk, G. A. Van Der Marel, J. D. C. Codee, B. I. Florea, J. M. F. G. Aerts, H. S. Overkleeft, G. J. Davies
Activity-Based Probes For Functional Interrogation Of Retaining Beta-Glucuronidases.
Nat. Chem. Biol. 2017
PubMed-ID: 28581485  |  Reference-DOI: 10.1038/NCHEMBIO.2395

(-) Compounds

Molecule 1 - HEPARANASE
    ChainsA
    EC Number3.2.1.166
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CommonCABBAGE LOOPER
    Expression System Taxid7111
    GeneHPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymENDO-GLUCORONIDASE,HEPARANASE-1,HPA1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2EDO5Ligand/Ion1,2-ETHANEDIOL
3FUC1Ligand/IonALPHA-L-FUCOSE
4NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:53 , PHE A:410 , VAL A:414 , GLY A:415 , THR A:416 , HOH A:781 , HOH A:814binding site for residue EDO A 608
2AC2SOFTWAREHIS A:155 , TYR A:298 , TYR A:348 , GLY A:349 , GLY A:350 , TYR A:391 , HOH A:724binding site for residue EDO A 609
3AC3SOFTWARETYR A:174 , ASN A:178 , LEU A:182 , ASP A:183 , LEU A:184 , ASN A:217binding site for residue EDO A 610
4AC4SOFTWARETYR A:264 , ASP A:291 , SER A:292 , LYS A:338 , GLU A:378 , HOH A:756binding site for residue EDO A 611
5AC5SOFTWAREILE A:318binding site for residue EDO A 612
6AC6SOFTWAREASN A:162binding site for Mono-Saccharide NAG A 601 bound to ASN A 162
7AC7SOFTWARETHR A:194 , ASN A:200 , SER A:202binding site for Mono-Saccharide NAG A 602 bound to ASN A 200
8AC8SOFTWAREASN A:238 , GLN A:241 , LYS A:251 , GLU A:288 , VAL A:289 , HOH A:701 , HOH A:824 , HOH A:850 , HOH A:873binding site for Poly-Saccharide residues NAG A 603 through BMA A 605 bound to ASN A 238
9AC9SOFTWAREVAL A:122 , ASN A:123 , LYS A:430 , HIS A:458 , ASN A:459 , LYS A:462 , HOH A:702 , HOH A:713binding site for Poly-Saccharide residues NAG A 606 through FUC A 607 bound to ASN A 459

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:127 -A:179
2A:437 -A:542

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:88 -Pro A:89
2Gly A:265 -Pro A:266
3Gln A:383 -Val A:384
4Tyr A:468 -Pro A:469

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LA4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LA4)

(-) Exons   (0, 0)

(no "Exon" information available for 5LA4)

(-) 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:508
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....ee.....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeehhhhh.eee......hhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhh.eeeeeee............hhhhhhhhhhhhhh....eeee..hhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......eeeeee...hhhhhhhhhhhhhhhh....eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhh...eee..................hhhhhhhhhhhhheeeee.eeee.......eeeeeeee...........eeeeeee.....eeee.........eeeeeeee...hhhhh..eee..ee..............ee......eee...eeeeeee....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5la4 A  36 QDVVDLDFFTQEPLHLVSPSFLSVTIDANLATDPRFLILLGSPKLRTLARGLSPAYLRFGGTKTDFLIFDPKKESTFEERSYWQSQVNQDICKYGSIPPDVEEKLRLEWPYQEQLLLREHYQKKFKNSTYSRSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATREDFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGETSSAYGGGAPLLSDTFAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVYLHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGLPAFSYSFFVIRNAKVAACI 543
                                    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       525       535        

   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 5LA4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LA4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LA4)

(-) 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 ]  
    Ser A:88 - Pro A: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 5e9b 5e9c 5l9y 5l9z 5la7

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LA4)