Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN HEPARANASE IN COMPLEX WITH HEPARIN TETRASACCHARIDE DP4
 
Authors :  L. Wu, G. J. Davies
Date :  15 Oct 15  (Deposition) - 18 Nov 15  (Release) - 04 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glycoside Hydrolase, Ligand 4, 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
    Fragment: RESIDUES 158-543
    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
    Fragment: RESIDUES 36-109
    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  (7, 9)

Asymmetric/Biological Unit (7, 9)
No.NameCountTypeFull Name
15KV1Ligand/Ion2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-BETA-D-GLUCOPYRANOSE
2CL1Ligand/IonCHLORIDE ION
3IDR1Ligand/IonL-IDURONIC ACID
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SGN1Ligand/IonN,O6-DISULFO-GLUCOSAMINE
6SO41Ligand/IonSULFATE ION
7UAP1Ligand/Ion4-DEOXY-2-O-SULFO-ALPHA-L-THREO-HEX-4-ENOPYRANURONICACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:399 , PRO A:400 , LYS A:501 , MET A:502 , HOH A:708 , HOH A:720 , HOH A:762 , HOH A:822 , LYS B:79binding site for residue SO4 A 605
2AC2SOFTWARETHR A:194 , ASN A:200 , SER A:202 , HOH A:839binding site for Mono-Saccharide NAG A 601 bound to ASN A 200
3AC3SOFTWAREASN A:238 , GLN A:241 , HOH A:704 , HOH A:711 , HOH A:803 , HOH A:846binding site for Mono-Saccharide NAG A 602 bound to ASN A 238
4AC4SOFTWAREASN A:459binding site for Mono-Saccharide NAG A 603 bound to ASN A 459
5AC5SOFTWARELYS A:159 , PHE A:160 , ASN A:224 , GLU A:225 , GLY A:269 , GLN A:270 , ARG A:272 , HIS A:296 , HIS A:297 , 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:702 , HOH A:703 , HOH A:706 , HOH A:808 , ASP B:62 , ASN B:64 , GLY B:96 , THR B:97binding site for Poly-Saccharide residues IDR A 606 through UAP 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 5E9C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E9C)

(-) Exons   (0, 0)

(no "Exon" information available for 5E9C)

(-) 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 ....eeehhhhhhhhhhhhhhh.eeeeeee............hhhhhhhhhhhhhhh...eeee..hhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......eeeeee...hhhhhhhhhhhhhhhhhhh.eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee.........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
                 5e9c 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
                 5e9c 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 5E9C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E9C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E9C)

(-) Gene Ontology  (31, 31)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    5KV  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IDR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SGN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UAP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  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 ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5e9c
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  HPSE_HUMAN | Q9Y251
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.166
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  HPSE_HUMAN | Q9Y251
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        HPSE_HUMAN | Q9Y251: 5e8m 5e97 5e98 5e9b 5l9y 5l9z 5la4 5la7

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5E9C)