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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN HEPARANASE, IN COMPLEX WITH GLUCURONIC ACID CONFIGURED AZIRIDINE PROBE JJB355
 
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 :  1.88
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Heparanase, Probe, Gh79, Hydrolase (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
    Chains: A
    EC Number: 3.2.1.166
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ENDO-GLUCORONIDASE,HEPARANASE-1,HPA1
 
Molecule 2 - HEPARANASE
    Chains: B
    EC Number: 3.2.1.166
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ENDO-GLUCORONIDASE,HEPARANASE-1,HPA1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
16S61Ligand/Ion(1~{S},2~{R},3~{S},4~{S},5~{S},6~{R})-2-(8-AZIDOOCTYLAMINO)-3,4,5,6-TETRAKIS(OXIDANYL)CYCLOHEXANE-1-CARBOXYLIC ACID
2EDO3Ligand/Ion1,2-ETHANEDIOL
3FUC1Ligand/IonALPHA-L-FUCOSE
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:414 , GLY A:415 , THR A:416 , HOH A:726 , HOH A:730binding site for residue EDO A 605
2AC2SOFTWAREASP A:317 , ARG A:428 , ARG A:429 , HOH A:799binding site for residue EDO A 606
3AC3SOFTWAREASP A:399 , PRO A:400 , LYS A:491 , SER A:492binding site for residue EDO A 607
4AC4SOFTWAREASN A:224 , GLU A:225 , ARG A:272 , TYR A:298 , GLU A:343 , TYR A:348 , GLY A:349 , GLY A:350 , TYR A:391 , THR A:440 , ASP A:441 , ASN A:442 , PRO A:443 , HOH A:776 , HOH A:819 , ASP B:62 , GLY B:96 , THR B:97binding site for residue 6S6 A 608
5AC5SOFTWARETHR A:194 , ASN A:200 , SER A:202 , HOH A:846 , HOH A:854binding site for Mono-Saccharide NAG A 601 bound to ASN A 200
6AC6SOFTWAREASN A:238 , HOH A:749 , HOH A:825binding site for Mono-Saccharide NAG A 602 bound to ASN A 238
7AC7SOFTWAREHIS A:458 , ASN A:459 , LYS A:462 , HOH A:736 , HOH A:797 , HOH A:816binding site for Poly-Saccharide residues NAG A 603 through FUC A 604 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:88 -Pro B:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L9Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L9Y)

(-) Exons   (0, 0)

(no "Exon" information available for 5L9Y)

(-) 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:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhhhhhh.eeeeeee............hhhhhhhhhhhhhhh...eeee..hhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......eeeeee...hhhhhhhhhhhhhhhh....eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeee.........hhhhhhhhhhhhhhhhhhh..eeee..................hhhhhhhhhhhhheeeee.eeee.......eeeeeeee...........eeeeeee.....eeee.........eeeeeeee...hhhhh..eee..ee..............ee......eee...eeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5l9y A 160 FKNSTYSRSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATREDFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGETSSAYGGGAPLLSDTFAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVYLHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGLPAFSYSFFVIRNAKVAACI 543
                                   169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539    


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.....eeeeehhhhhhh.hhhhhhhhhhhhhhhhhh..eeeee.hhhhh.eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 5l9y 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 5L9Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L9Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L9Y)

(-) 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 ]  
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  5l9y
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  3.2.1.166
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 Related Entries

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

UniProtKB/Swiss-Prot
        HPSE_HUMAN | Q9Y251: 5e8m 5e97 5e98 5e9b 5e9c 5l9z 5la4 5la7

(-) Related Entries Specified in the PDB File

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