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(-) Description

Title :  ALPHA-L-FUCOSIDASE COMPLEXED WITH INHIBITOR, PH-6FNJ
 
Authors :  H. -J. Wu, T. -P. Ko, C. -W. Ho, C. -H. Lin, A. H. -J. Wang
Date :  22 Dec 08  (Deposition) - 08 Dec 09  (Release) - 02 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Tim Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Wu, C. W. Ho, T. P. Ko, S. D. Popat, C. H. Lin, A. H. Wang
Structural Basis Of Alpha-Fucosidase Inhibition By Iminocyclitols With K(I) Values In The Micro- To Picomolar Range.
Angew. Chem. Int. Ed. Engl. V. 49 337 2010
PubMed-ID: 19967696  |  Reference-DOI: 10.1002/ANIE.200905597

(-) Compounds

Molecule 1 - ALPHA-L-FUCOSIDASE, PUTATIVE
    Chains: A, B
    EC Number: 3.2.1.51
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Strain: MSB8

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZXB2Ligand/Ion(2S,3R,4S,5R)-2-BENZYLPIPERIDINE-3,4,5-TRIOL
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1ZXB6Ligand/Ion(2S,3R,4S,5R)-2-BENZYLPIPERIDINE-3,4,5-TRIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:34 , TYR A:64 , GLU A:66 , TRP A:67 , HIS A:128 , ASP A:224 , ARG A:254 , GLU A:266 , PHE A:290 , HOH A:578BINDING SITE FOR RESIDUE ZXB A 901
2AC2SOFTWAREHIS B:34 , TYR B:64 , GLU B:66 , TRP B:67 , HIS B:128 , ASP B:224 , ARG B:254 , GLU B:266BINDING SITE FOR RESIDUE ZXB B 902

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:364 -A:365
2A:380 -B:380
3B:364 -B:365

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZXB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZXB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZXB)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZXB)

(-) Sequences/Alignments

Asymmetric 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:442
 aligned with Q9WYE2_THEMA | Q9WYE2 from UniProtKB/TrEMBL  Length:449

    Alignment length:442
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446  
         Q9WYE2_THEMA     7 RYKPDWESLREHTVPKWFDKAKFGIFIHWGIYSVPGWATPTGELGKVPMDAWFFQNPYAEWYENSLRIKESPTWEYHVKTYGENFEYEKFADLFTAEKWDPQEWADLFKKAGAKYVIPTTKHHDGFCLWGTKYTDFNSVKRGPKRDLVGDLAKAVREAGLRFGVYYSGGLDWRFTTEPIRYPEDLSYIRPNTYEYADYAYKQVMELVDLYLPDVLWNDMGWPEKGKEDLKYLFAYYYNKHPEGSVNDRWGVPHWDFKTAEYHVNYPGDLPGYKWEFTRGIGLSFGYNRNEGPEHMLSVEQLVYTLVDVVSKGGNLLLNVGPKGDGTIPDLQKERLLGLGEWLRKYGDAIYGTSVWERCCAKTEDGTEIRFTRKCNRIFVIFLGIPTGEKIVIEDLNLSAGTVRHFLTGERLSFKNVGKNLEITVPKKLLETDSITLVLEAVE 448
               SCOP domains d2zxba1 A:7-356 automated matches                                                                                                                                                                                                                                                                                                                             d2zxba2 A:357-448 automated matches                                                          SCOP domains
               CATH domains 2zxbA01 A:7-356 Glycosidases                                                                                                                                                                                                                                                                                                                                  2zxbA02 A:357-448 Golgi alpha-mannosidase II                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh....hhhhhhhheeeee..hhhhh................hhhhh..hhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhh.....hhhhhhhhhhhh...eeee...........................hhhhhhhhhhhhh..eeeeee....hhhhh.....hhhhhhh....hhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhh...ee...........eeee.............eeeeee.................hhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhhhhhhhhh.........eee.....eeeeeee..eeeeee.......eeee........eeee.....ee.eeee..eeeee.hhhhhh......eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zxb A   7 RYKPDWESLREHTVPKWFDKAKFGIFIHWGIYSVPGWATPTGELGKVPMDAWFFQNPYAEWYENSLRIKESPTWEYHVKTYGENFEYEKFADLFTAEKWDPQEWADLFKKAGAKYVIPTTKHHDGFCLWGTKYTDFNSVKRGPKRDLVGDLAKAVREAGLRFGVYYSGGLDWRFTTEPIRYPEDLSYIRPNTYEYADYAYKQVMELVDLYLPDVLWNDMGWPEKGKEDLKYLFAYYYNKHPEGSVNDRWGVPHWDFKTAEYHVNYPGDLPGYKWEFTRGIGLSFGYNRNEGPEHMLSVEQLVYTLVDVVSKGGNLLLNVGPKGDGTIPDLQKERLLGLGEWLRKYGDAIYGTSVWERCCAKTEDGTEIRFTRKCNRIFVIFLGIPTGEKIVIEDLNLSAGTVRHFLTGERLSFKNVGKNLEITVPKKLLETDSITLVLEAVE 448
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446  


Chain B from PDB  Type:PROTEIN  Length:442
 aligned with Q9WYE2_THEMA | Q9WYE2 from UniProtKB/TrEMBL  Length:449

    Alignment length:442
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446  
         Q9WYE2_THEMA     7 RYKPDWESLREHTVPKWFDKAKFGIFIHWGIYSVPGWATPTGELGKVPMDAWFFQNPYAEWYENSLRIKESPTWEYHVKTYGENFEYEKFADLFTAEKWDPQEWADLFKKAGAKYVIPTTKHHDGFCLWGTKYTDFNSVKRGPKRDLVGDLAKAVREAGLRFGVYYSGGLDWRFTTEPIRYPEDLSYIRPNTYEYADYAYKQVMELVDLYLPDVLWNDMGWPEKGKEDLKYLFAYYYNKHPEGSVNDRWGVPHWDFKTAEYHVNYPGDLPGYKWEFTRGIGLSFGYNRNEGPEHMLSVEQLVYTLVDVVSKGGNLLLNVGPKGDGTIPDLQKERLLGLGEWLRKYGDAIYGTSVWERCCAKTEDGTEIRFTRKCNRIFVIFLGIPTGEKIVIEDLNLSAGTVRHFLTGERLSFKNVGKNLEITVPKKLLETDSITLVLEAVE 448
               SCOP domains d2zxbb1 B:7-356 automated matches                                                                                                                                                                                                                                                                                                                             d2zxbb2 B:357-448 automated matches                                                          SCOP domains
               CATH domains 2zxbB01 B:7-356 Glycosidases                                                                                                                                                                                                                                                                                                                                  2zxbB02 B:357-448 Golgi alpha-mannosidase II                                                 CATH domains
           Pfam domains (1) Alpha_L_fucos-2zxbB01 B:7-357                                                                                                                                                                                                                                                                                                                                  ------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) Alpha_L_fucos-2zxbB02 B:7-357                                                                                                                                                                                                                                                                                                                                  ------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhhhh....hhhhhhhheeeee..hhhhh.............hhhhhh....hhhhhhhhhhh..hhhhhhhhhhh....hhhhhhhhh.....hhhhhhhhhhhhh..eeeeeee........................hhhhhhhhhhhhh..eeeeee....hhhhh.....hhhhhhh....hhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhh...ee...........eeee.............eeeeee...........hhhhh.hhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhhhhhhhhh.........eee.....eeeeeee..eeeeee.......eeee........eeee.....ee.ee.....eeee.hhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zxb B   7 RYKPDWESLREHTVPKWFDKAKFGIFIHWGIYSVPGWATPTGELGKVPMDAWFFQNPYAEWYENSLRIKESPTWEYHVKTYGENFEYEKFADLFTAEKWDPQEWADLFKKAGAKYVIPTTKHHDGFCLWGTKYTDFNSVKRGPKRDLVGDLAKAVREAGLRFGVYYSGGLDWRFTTEPIRYPEDLSYIRPNTYEYADYAYKQVMELVDLYLPDVLWNDMGWPEKGKEDLKYLFAYYYNKHPEGSVNDRWGVPHWDFKTAEYHVNYPGDLPGYKWEFTRGIGLSFGYNRNEGPEHMLSVEQLVYTLVDVVSKGGNLLLNVGPKGDGTIPDLQKERLLGLGEWLRKYGDAIYGTSVWERCCAKTEDGTEIRFTRKCNRIFVIFLGIPTGEKIVIEDLNLSAGTVRHFLTGERLSFKNVGKNLEITVPKKLLETDSITLVLEAVE 448
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9WYE2_THEMA | Q9WYE2)
molecular function
    GO:0004560    alpha-L-fucosidase activity    Catalysis of the reaction: an alpha-L-fucoside + H2O = an alcohol + L-fucose.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006004    fucose metabolic process    The chemical reactions and pathways involving fucose, or 6-deoxygalactose, which has two enantiomers, D-fucose and L-fucose.

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  2zxb
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 Related Entries

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

UniProtKB/TrEMBL
        Q9WYE2_THEMA | Q9WYE2: 1hl8 1hl9 1odu 2wsp 2zwy 2zwz 2zx5 2zx6 2zx7 2zx8 2zx9 2zxa 2zxd

(-) Related Entries Specified in the PDB File

1hl8 MODEL FOR MOLECULAR REPLACEMENT
2zwy NATIVE CRYSTAL
2zwz LEAD COMPOUND
2zx5
2zx6
2zx7
2zx8
2zx9
2zxa
2zxd