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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN HEPARANASE IN COMPLEX WITH HEPMER M04S02A
 
Authors :  L. Wu, G. J. Davies
Date :  14 Oct 15  (Deposition) - 18 Nov 15  (Release) - 04 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glycoside Hydrolase, Ligand 2, 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
    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  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1BDP2Ligand/IonBETA-D-GLUCOPYRANURONIC ACID
2CL2Ligand/IonCHLORIDE ION
3GNS1Ligand/IonN-SULFO-ALPHA-D-GLUCOSAMINE
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NPO1Ligand/IonP-NITROPHENOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:334binding site for residue CL A 604
2AC2SOFTWAREGLY A:415 , THR A:416 , ASN A:439 , THR A:440binding site for residue CL A 605
3AC3SOFTWARETHR A:194 , ASN A:200 , SER A:202binding site for Mono-Saccharide NAG A 601 bound to ASN A 200
4AC4SOFTWAREASN A:238 , HOH A:706 , HOH A:795binding site for Mono-Saccharide NAG A 602 bound to ASN A 238
5AC5SOFTWAREASN A:459binding site for Mono-Saccharide NAG A 603 bound to ASN A 459
6AC6SOFTWAREASN A:224 , GLU A:225 , GLN A:270 , TYR A:298 , 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:707 , HOH A:715 , HOH A:753 , HOH A:837 , ASP B:62 , ASN B:64 , GLY B:96 , THR B:97binding site for Poly-Saccharide residues BDP A 606 through NPO A 609

(-) 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 5E98)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E98)

(-) Exons   (0, 0)

(no "Exon" information available for 5E98)

(-) 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.......eeeeee...hhhhhhhhhhhhhhhhhhh.eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....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
                 5e98 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
                 5e98 B  36 QDVVDLDFFTQEPLHLVSPSFLSVTIDANLATDPRFLILLGSPKLRTLARGLSPAYLRFGGTKTDFLIFDPKKE 109
                                    45        55        65        75        85        95       105
   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 5E98)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E98)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E98)

(-) 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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  5e98
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  HPSE_HUMAN | Q9Y251
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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 5e9b 5e9c 5l9y 5l9z 5la4 5la7

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5E98)