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(-) Description

Title :  CRYSTAL STRUCTURE OF A BACTERIAL FUCOSIDASE WITH A MULTIVALENT IMINOCYCLITOL INHIBITOR
 
Authors :  D. W. Wright, G. J. Davies
Date :  12 Mar 13  (Deposition) - 22 Jan 14  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.68
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha-L-Fucosidase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Moreno-Clavijo, A. T. Carmona, A. J. Moreno-Varga, L. Molina, D. W. Wright, G. J. Davies, I. Robina
Exploring A Multivalent Approach To Alpha-L-Fucosidase Inhibition
Eur. J. Org. Chem. V. 2013 7328 2013
PubMed: search  |  Reference-DOI: 10.1002/EJOC.201300878

(-) Compounds

Molecule 1 - ALPHA-L-FUCOSIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-YSBLIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 35-484
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 226186
    Strain: VPI-5482

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2IMD6Ligand/IonIMIDAZOLE
3LM52Ligand/Ion(3S,4R,5S)-N-BENZYL-3,4-DIHYDROXY-5-METHYL-D-PROLINAMIDE
4SO46Ligand/IonSULFATE ION
Biological Unit 1 (4, 9)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2IMD3Ligand/IonIMIDAZOLE
3LM51Ligand/Ion(3S,4R,5S)-N-BENZYL-3,4-DIHYDROXY-5-METHYL-D-PROLINAMIDE
4SO43Ligand/IonSULFATE ION
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2IMD3Ligand/IonIMIDAZOLE
3LM51Ligand/Ion(3S,4R,5S)-N-BENZYL-3,4-DIHYDROXY-5-METHYL-D-PROLINAMIDE
4SO43Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:66 , GLU A:87 , TRP A:88 , HIS A:135 , HIS A:136 , TYR A:178 , ASP A:229 , TRP A:232 , TRP A:316 , HOH A:820 , HOH A:840 , HOH A:1164BINDING SITE FOR RESIDUE LM5 A 501
02AC2SOFTWARETRP A:232 , ARG A:262 , ARG A:271 , HIS A:272BINDING SITE FOR RESIDUE SO4 A 502
03AC3SOFTWARELYS A:90 , ALA A:97 , HOH A:772BINDING SITE FOR RESIDUE SO4 A 503
04AC4SOFTWAREVAL A:81 , TYR A:82 , GLY A:83 , HOH A:676 , HOH A:955 , HOH A:1124BINDING SITE FOR RESIDUE SO4 A 504
05AC5SOFTWARETRP A:117 , MET A:120 , TYR A:168 , PHE A:359BINDING SITE FOR RESIDUE IMD A 505
06AC6SOFTWARELYS A:90 , SER A:91 , TRP A:184 , TYR A:191 , HOH A:1125BINDING SITE FOR RESIDUE IMD A 506
07AC7SOFTWAREASN A:375 , ARG A:376BINDING SITE FOR RESIDUE IMD A 507
08AC8SOFTWAREASN A:169 , GLY A:172 , ASP A:174 , LYS A:224 , HOH A:602 , HOH A:984BINDING SITE FOR RESIDUE GOL A 508
09AC9SOFTWARETHR A:310 , GLU A:313 , ASN A:314BINDING SITE FOR RESIDUE GOL A 509
10BC1SOFTWAREHIS B:66 , GLU B:87 , TRP B:88 , HIS B:135 , HIS B:136 , TYR B:178 , TRP B:227 , ASP B:229 , TRP B:232 , TRP B:316 , HOH B:711BINDING SITE FOR RESIDUE LM5 B 501
11BC2SOFTWARETRP B:232 , ARG B:262 , ARG B:271 , HIS B:272 , HOH B:1079BINDING SITE FOR RESIDUE SO4 B 502
12BC3SOFTWARETYR B:82 , GLY B:83 , GLY B:84 , TRP B:92 , HOH B:766 , HOH B:807 , HOH B:834BINDING SITE FOR RESIDUE SO4 B 503
13BC4SOFTWARELYS B:90 , PRO B:96 , ALA B:97 , HOH B:810 , HOH B:811 , HOH B:1082BINDING SITE FOR RESIDUE SO4 B 504
14BC5SOFTWARETRP B:117 , MET B:120 , TYR B:168 , PHE B:359BINDING SITE FOR RESIDUE IMD B 505
15BC6SOFTWAREARG B:399 , ASP B:403 , VAL B:469BINDING SITE FOR RESIDUE IMD B 506
16BC7SOFTWAREGLN B:354 , ASP B:358 , PHE B:359 , ARG B:360 , PRO B:361 , HOH B:926BINDING SITE FOR RESIDUE IMD B 507
17BC8SOFTWARETRP B:241 , HOH B:1080BINDING SITE FOR RESIDUE GOL B 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4JL1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JL1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JL1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JL1)

(-) Exons   (0, 0)

(no "Exon" information available for 4JL1)

(-) 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:439
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhheeeee..hhhhh...ee..ee...hhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhh..eeeeeee...............hhhhh....hhhhhhhhhhhhh..eeeeeee..............hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhhhhhh...ee.hhhh...................eee..........hhhhhhh.eeeee...........hhhhh...hhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhhhhh.............eeeee.....eeeee.......eeeee....eeeeeeee.....ee.eeeee..eeeee.........eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jl1 A  35 EIPLKYGATNEGKRQDPAMQKFRDNRLGAFIHWGLYAIPGGEWNGKVYGGAAEWLKSWAKVPADEWLKLMDQWNPTKFDAKKWAKMAKEMGTKYVKITTKHHEGFCLWPSKYTKYTVANTPYKRDILGELVKAYNDEGIDVHFYFSVMDWSNPDYRYDIKSKEDSIAFSRFLEFTDNQLKELATRYPTVKDFWFDGTWDASVKKNGWWTAHAEQMLKELVPGVAINSRLRADDKGKRHFDSNGRLMGDYESGYERRLPDPVKDLKVTQWDWEACMTIPENQWGYHKDWSLSYVKTPIEVIDRIVHAVSMGGNMVVNFGPQADGDFRPEEKAMATAIGKWMNRYGKAVYACDYAGFEKQDWGYYTRGKNDEVYMVVFNQPYSERLIVKTPKGITVEKATLLTTGEDITVVETTRNEYNVSVPKKNPGEPYVIQLKVRAAK 473
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464         


Chain B from PDB  Type:PROTEIN  Length:439
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhheeeee..hhhhh...ee..ee...hhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhh..eeeeeee...............hhhhh....hhhhhhhhhhhhh..eeeeeee..............hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhhhhhh...ee.hhhh...................eee..........hhhhhhh.eeeee...........hhhhh...hhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhhhhhh.............eeeee.....eeeee.......eeeee....eeeeeeee........eeeee..eeeee.........eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jl1 B  35 EIPLKYGATNEGKRQDPAMQKFRDNRLGAFIHWGLYAIPGGEWNGKVYGGAAEWLKSWAKVPADEWLKLMDQWNPTKFDAKKWAKMAKEMGTKYVKITTKHHEGFCLWPSKYTKYTVANTPYKRDILGELVKAYNDEGIDVHFYFSVMDWSNPDYRYDIKSKEDSIAFSRFLEFTDNQLKELATRYPTVKDFWFDGTWDASVKKNGWWTAHAEQMLKELVPGVAINSRLRADDKGKRHFDSNGRLMGDYESGYERRLPDPVKDLKVTQWDWEACMTIPENQWGYHKDWSLSYVKTPIEVIDRIVHAVSMGGNMVVNFGPQADGDFRPEEKAMATAIGKWMNRYGKAVYACDYAGFEKQDWGYYTRGKNDEVYMVVFNQPYSERLIVKTPKGITVEKATLLTTGEDITVVETTRNEYNVSVPKKNPGEPYVIQLKVRAAK 473
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464
   Legend:   → Mismatch (orange background)
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    → 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 4JL1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JL1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JL1)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        Q8A3I4_BACTN | Q8A3I4: 2wvs 2wvt 2wvu 2wvv 2xib 2xii 4j27 4j28 4jfs 4jft 4jfu 4jfv 4jfw 4jl2 4pcs 4pct 4pee 4wsj 4wsk 5hdr 5i5r

(-) Related Entries Specified in the PDB File

2wvv 4j27 4j28 4jfs 4jft 4jfu 4jfv 4jfw 4jl2