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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PROHEPARANASE, 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 :  1.94
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
    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

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
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
2EDO6Ligand/Ion1,2-ETHANEDIOL
3FUC1Ligand/IonALPHA-L-FUCOSE
4NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:410 , VAL A:414 , GLY A:415 , THR A:416 , EDO A:608 , HOH A:731binding site for residue EDO A 607
02AC2SOFTWAREPRO A:54 , LYS A:411 , VAL A:414 , ASN A:439 , EDO A:607 , HOH A:716binding site for residue EDO A 608
03AC3SOFTWAREPRO A:509 , PRO A:510 , LEU A:511 , MET A:512 , HOH A:717binding site for residue EDO A 609
04AC4SOFTWARETYR A:174 , ASN A:178 , LEU A:182 , ASP A:183 , LEU A:184 , ASN A:217binding site for residue EDO A 610
05AC5SOFTWAREPHE A:327 , GLU A:331 , PRO A:335 , GLY A:336 , LYS A:337binding site for residue EDO A 611
06AC6SOFTWAREASP A:68 , GLN A:147 , ARG A:428binding site for residue EDO A 612
07AC7SOFTWAREASP A:62 , GLY A:96 , THR A:97 , HIS A:155 , ASN A:224 , GLU A:225 , TYR A:298 , GLU A:343 , TYR A:348 , GLY A:349 , GLY A:350 , GLN A:383 , TYR A:391 , HOH A:785binding site for residue 6S6 A 613
08AC8SOFTWAREPHE A:160 , ASN A:162 , LEU A:192binding site for Mono-Saccharide NAG A 601 bound to ASN A 162
09AC9SOFTWAREASN A:200 , SER A:202binding site for Mono-Saccharide NAG A 602 bound to ASN A 200
10AD1SOFTWAREASN A:238 , GLN A:241 , ARG A:254binding site for Mono-Saccharide NAG A 603 bound to ASN A 238
11AD2SOFTWAREVAL A:122 , ASN A:123 , LYS A:430 , HIS A:458 , ASN A:459 , LYS A:462 , HOH A:750 , HOH A:772binding site for Poly-Saccharide residues NAG A 604 through FUC A 606 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 5LA7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LA7)

(-) Exons   (0, 0)

(no "Exon" information available for 5LA7)

(-) 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.....eeeeehhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.eee......hhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhh.eeeeeee............hhhhhhhhhhhhhhh...eeee..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhhhhhhh....eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhheeeeee..................hhhhhhhhhhhhheeeee.eeee.......eeeeeeee...........eeeeeee.....eeee.........eeeeeeee...hhhhh..eee..ee..............eee.....eee...eeeeeee....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5la7 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)
  - → 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 5LA7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LA7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LA7)

(-) 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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  5la7
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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 5l9y 5l9z 5la4

(-) Related Entries Specified in the PDB File

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