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(-) Description

Title :  HEPARINASEII H202A/Y257A DOUBLE MUTANT COMPLEXED WITH A HEPARAN SULFATE TETRASACCHARIDE SUBSTRATE
 
Authors :  D. Shaya, M. Cygler
Date :  18 Aug 08  (Deposition) - 30 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha And Beta Lyase, Alpha6/Alpha6 Incomplete Toroid, Sugar Binding Protein, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Shaya, W. Zhao, M. L. Garron, Z. Xiao, Q. Cui, Z. Zhang, T. Sulea, R. J. Linhardt, M. Cygler
Catalytic Mechanism Of Heparinase Ii Investigated By Site-Directed Mutagenesis And The Crystal Structure With It Substrate.
J. Biol. Chem. V. 285 20051 2010
PubMed-ID: 20404324  |  Reference-DOI: 10.1074/JBC.M110.101071

(-) Compounds

Molecule 1 - HEPARINASE II PROTEIN
    ChainsA, B
    FragmentUNP RESIDUES 24-772
    MutationYES
    Organism ScientificPEDOBACTER HEPARINUS
    Organism Taxid984

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2GCD2Ligand/Ion4,5-DEHYDRO-D-GLUCURONIC ACID
3GCU2Ligand/IonD-GLUCURONIC ACID
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
5ZN2Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:408 , ASP A:425 , HIS A:451 , HOH A:780 , HOH A:1162 , HOH A:1189BINDING SITE FOR RESIDUE ZN A 1
02AC2SOFTWARETRP A:84 , PHE A:97 , TYR A:98 , LYS A:102BINDING SITE FOR RESIDUE ACT A 773
03AC3SOFTWAREPRO A:658 , LYS A:659 , LYS A:660 , ALA A:661 , HOH A:1161BINDING SITE FOR RESIDUE ACT A 3
04AC4SOFTWARELYS A:508BINDING SITE FOR RESIDUE ACT A 4
05AC5SOFTWARETYR A:436 , NAG A:776BINDING SITE FOR RESIDUE ACT A 5
06AC6SOFTWAREGLY A:201 , ASN A:405 , TYR A:436 , ASN A:437 , GLY A:469 , GLY A:470 , GCU A:775 , HOH A:1143 , HOH A:1145 , HOH A:1147 , HOH A:1152 , HOH A:1153BINDING SITE FOR RESIDUE NAG A 774
07AC7SOFTWAREASP A:145 , HIS A:406 , TYR A:429 , NAG A:774 , NAG A:776 , HOH A:1153 , HOH A:1177BINDING SITE FOR RESIDUE GCU A 775
08AC8SOFTWAREACT A:5 , ARG A:96 , ASP A:145 , ARG A:148 , GCU A:775 , GCD A:777 , HOH A:1038BINDING SITE FOR RESIDUE NAG A 776
09AC9SOFTWAREARG A:96 , NAG A:776 , HOH A:1144 , HOH A:1191BINDING SITE FOR RESIDUE GCD A 777
10BC1SOFTWAREHIS B:408 , ASP B:425 , HIS B:451 , HOH B:1249 , HOH B:1287 , HOH B:1347BINDING SITE FOR RESIDUE ZN B 2
11BC2SOFTWAREASP B:273 , ARG B:274BINDING SITE FOR RESIDUE ACT B 773
12BC3SOFTWAREASN B:405 , TYR B:436 , ASN B:437 , GLY B:469 , GLY B:470 , GCU B:775 , HOH B:1194 , HOH B:1258 , HOH B:1259 , HOH B:1271BINDING SITE FOR RESIDUE NAG B 774
13BC4SOFTWAREASP B:145 , HIS B:406 , TYR B:429 , NAG B:774 , NAG B:776BINDING SITE FOR RESIDUE GCU B 775
14BC5SOFTWAREPHE B:95 , ARG B:96 , ASP B:145 , ARG B:148 , GCU B:775 , GCD B:777BINDING SITE FOR RESIDUE NAG B 776
15BC6SOFTWAREARG B:96 , NAG B:776 , HOH B:1283BINDING SITE FOR RESIDUE GCD B 777

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E7J)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1His A:48 -Pro A:49
2Tyr A:191 -Pro A:192
3Ser A:376 -Pro A:377
4Gly A:515 -Pro A:516
5Leu A:610 -Pro A:611
6His B:48 -Pro B:49
7Tyr B:191 -Pro B:192
8Ser B:376 -Pro B:377
9Gly B:515 -Pro B:516
10Leu B:610 -Pro B:611

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E7J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E7J)

(-) Exons   (0, 0)

(no "Exon" information available for 3E7J)

(-) 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:743
 aligned with HEPB_PEDHD | C6XZB6 from UniProtKB/Swiss-Prot  Length:772

    Alignment length:743
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       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       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769   
           HEPB_PEDHD    30 DVVWKDVDGVSMPIPPKTHPRLYLREQQVPDLKNRMNDPKLKKVWADMIKMQEDWKPADIPEVKDFRFYFNQKGLTVRVELMALNYLMTKDPKVGREAITSIIDTLETATFKPAGDISRGIGLFMVTGAIVYDWCYDQLKPEEKTRFVKAFVRLAKMLECGYPPVKDKSIVGHASEWMIMRDLLSVGIAIYDEFPEMYNLAAGRFFKEHLVARNWFYPSHNYHQGMSYLNVRFTNDLFALWILDRMGAGNVFNPGQQFILYDAIYKRRPDGQILAGGDVDYSRKKPKYYTMPALLAGSYYKDEYLNYEFLKDPNVEPHCKLFEFLWRDTQLGSRKPDDLPLSRYSGSPFGWMIARTGWGPESVIAEMKVNEYSFLNHQHQDAGAFQIYYKGPLAIDAGSYTGSSGGYNSPHNKNFFKRTIAHNSLLIYDPKETFSSSGYGGSDHTDFAANDGGQRLPGKGWIAPRDLKEMLAGDFRTGKILAQGFGPDNQTPDYTYLKGDITAAYSAKVKEVKRSFLFLNLKDAKVPAAMIVFDKVVASNPDFKKFWLLHSIEQPEIKGNQITIKRTKNGDSGMLVNTALLPDAANSNITSIGGKGKDFWVFGTNYTNDPKPGTDEALERGEWRVEITPKKAAAEDYYLNVIQIADNTQQKLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVVGKGTFKFVMTDLLPGTWQVLKDGKILYPALSAKGDDGALYFEGTEGTYRFLR 772
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....eee...........hhhhhhhhhhhhhh..hhhhhhhhhhhh............hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.......hhhhh..eeee.....eeeee.......eeeeee................eeeee..eee..............hhhhhhh..hhhhh..eeee.....................................hhhhhhh......eeeeeeee.......eeeeeee.hhhh...eeeeeeeeeeee.......eeeeeeeeeee.....eeeeeeee....eee..eeeee.......eeeeeeeee.hhh.eeeeeee......ee..ee.................eeeeeee.....eeeeeeeeeeee.........eeee...eeeeee..eeeeee.........eeeee.....eeeee.....eeeeeee..eeeeeeeee......eeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e7j A  30 DVVWKDVDGVSMPIPPKTHPRLYLREQQVPDLKNRMNDPKLKKVWADMIKMQEDWKPADIPEVKDFRFYFNQKGLTVRVELMALNYLMTKDPKVGREAITSIIDTLETATFKPAGDISRGIGLFMVTGAIVYDWCYDQLKPEEKTRFVKAFVRLAKMLECGYPPVKDKSIVGAASEWMIMRDLLSVGIAIYDEFPEMYNLAAGRFFKEHLVARNWFYPSHNYHQGMSALNVRFTNDLFALWILDRMGAGNVFNPGQQFILYDAIYKRRPDGQILAGGDVDYSRKKPKYYTMPALLAGSYYKDEYLNYEFLKDPNVEPHCKLFEFLWRDTQLGSRKPDDLPLSRYSGSPFGWMIARTGWGPESVIAEMKVNEYSFLNHQHQDAGAFQIYYKGPLAIDAGSYTGSSGGYNSPHNKNFFKRTIAHNSLLIYDPKETFSSSGYGGSDHTDFAANDGGQRLPGKGWIAPRDLKEMLAGDFRTGKILAQGFGPDNQTPDYTYLKGDITAAYSAKVKEVKRSFLFLNLKDAKVPAAMIVFDKVVASNPDFKKFWLLHSIEQPEIKGNQITIKRTKNGDSGMLVNTALLPDAANSNITSIGGKGKDFWVFGTNYTNDPKPGTDEALERGEWRVEITPKKAAAEDYYLNVIQIADNTQQKLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVVGKGTFKFVMTDLLPGTWQVLKDGKILYPALSAKGDDGALYFEGTEGTYRFLR 772
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       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       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769   

Chain B from PDB  Type:PROTEIN  Length:743
 aligned with HEPB_PEDHD | C6XZB6 from UniProtKB/Swiss-Prot  Length:772

    Alignment length:743
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       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       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769   
           HEPB_PEDHD    30 DVVWKDVDGVSMPIPPKTHPRLYLREQQVPDLKNRMNDPKLKKVWADMIKMQEDWKPADIPEVKDFRFYFNQKGLTVRVELMALNYLMTKDPKVGREAITSIIDTLETATFKPAGDISRGIGLFMVTGAIVYDWCYDQLKPEEKTRFVKAFVRLAKMLECGYPPVKDKSIVGHASEWMIMRDLLSVGIAIYDEFPEMYNLAAGRFFKEHLVARNWFYPSHNYHQGMSYLNVRFTNDLFALWILDRMGAGNVFNPGQQFILYDAIYKRRPDGQILAGGDVDYSRKKPKYYTMPALLAGSYYKDEYLNYEFLKDPNVEPHCKLFEFLWRDTQLGSRKPDDLPLSRYSGSPFGWMIARTGWGPESVIAEMKVNEYSFLNHQHQDAGAFQIYYKGPLAIDAGSYTGSSGGYNSPHNKNFFKRTIAHNSLLIYDPKETFSSSGYGGSDHTDFAANDGGQRLPGKGWIAPRDLKEMLAGDFRTGKILAQGFGPDNQTPDYTYLKGDITAAYSAKVKEVKRSFLFLNLKDAKVPAAMIVFDKVVASNPDFKKFWLLHSIEQPEIKGNQITIKRTKNGDSGMLVNTALLPDAANSNITSIGGKGKDFWVFGTNYTNDPKPGTDEALERGEWRVEITPKKAAAEDYYLNVIQIADNTQQKLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVVGKGTFKFVMTDLLPGTWQVLKDGKILYPALSAKGDDGALYFEGTEGTYRFLR 772
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....eee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.......hhhhh..eeee.....eeeee........eeeee................eeee...eee..............hhhhhhh..hhhhh..eeee.....................................hhhhhhh......eeeeeeee.......eeeeeee.hhhh...eeeeeeeeeeee.......eeeeeeeeeee.....eeeeeeee....eee..eeeee.......eeeeeeeee.hhh.eeeeeee......ee..ee.................eeeeeee.....eeeeeeeeeeee.........eeee...eeeeee..eeeeee.........eeeee.....eeeee.....eeeeeee..eeeeeeeee......eeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e7j B  30 DVVWKDVDGVSMPIPPKTHPRLYLREQQVPDLKNRMNDPKLKKVWADMIKMQEDWKPADIPEVKDFRFYFNQKGLTVRVELMALNYLMTKDPKVGREAITSIIDTLETATFKPAGDISRGIGLFMVTGAIVYDWCYDQLKPEEKTRFVKAFVRLAKMLECGYPPVKDKSIVGAASEWMIMRDLLSVGIAIYDEFPEMYNLAAGRFFKEHLVARNWFYPSHNYHQGMSALNVRFTNDLFALWILDRMGAGNVFNPGQQFILYDAIYKRRPDGQILAGGDVDYSRKKPKYYTMPALLAGSYYKDEYLNYEFLKDPNVEPHCKLFEFLWRDTQLGSRKPDDLPLSRYSGSPFGWMIARTGWGPESVIAEMKVNEYSFLNHQHQDAGAFQIYYKGPLAIDAGSYTGSSGGYNSPHNKNFFKRTIAHNSLLIYDPKETFSSSGYGGSDHTDFAANDGGQRLPGKGWIAPRDLKEMLAGDFRTGKILAQGFGPDNQTPDYTYLKGDITAAYSAKVKEVKRSFLFLNLKDAKVPAAMIVFDKVVASNPDFKKFWLLHSIEQPEIKGNQITIKRTKNGDSGMLVNTALLPDAANSNITSIGGKGKDFWVFGTNYTNDPKPGTDEALERGEWRVEITPKKAAAEDYYLNVIQIADNTQQKLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVVGKGTFKFVMTDLLPGTWQVLKDGKILYPALSAKGDDGALYFEGTEGTYRFLR 772
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       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       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769   

   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 3E7J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E7J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E7J)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HEPB_PEDHD | C6XZB6)
molecular function
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0047488    heparin lyase activity    Catalysis of the eliminative cleavage of polysaccharides containing 1,4-linked D-glucuronate or L-iduronate residues and 1,4-alpha-linked 2-sulfoamino-2-deoxy-6-sulfo-D-glucose residues to give oligosaccharides with terminal 4-deoxy-alpha-D-gluc-4-enuronosyl groups at their nonreducing ends.
    GO:0015021    heparin-sulfate lyase activity    Catalysis of the elimination of sulfate; appears to act on linkages between N-acetyl-D-glucosamine and uronate. Product is an unsaturated sugar.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0030211    heparin catabolic process    The chemical reactions and pathways resulting in the breakdown of heparin, any member of a group of glycosaminoglycans of average Mr (6000-20000), consisting predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        HEPB_PEDHD | C6XZB62fuq 2fut 3e80

(-) Related Entries Specified in the PDB File

3e80 HEPARINASE II COMPLEXED WITH HEPARAN SULFATE DEGRADATION DISACCHARIDE PRODUCT