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(-) Description

Title :  CRYSTAL STRUCTURE OF A GH29 ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH A 5-MEMBERED IMINOCYCLITOL INHIBITOR
 
Authors :  D. W. Wright
Date :  04 Feb 13  (Deposition) - 08 May 13  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
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 :  D. W. Wright, A. J. Moreno-Vargas, A. T. Carmona, I. Robina, G. J. Davie
Three Dimensional Structure Of A Bacterial Alpha-L-Fucosidase With A 5-Membered Iminocyclitol Inhibitor.
Bioorg. Med. Chem. V. 21 4751 2013
PubMed-ID: 23830696  |  Reference-DOI: 10.1016/J.BMC.2013.05.056

(-) Compounds

Molecule 1 - ALPHA-L-FUCOSIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21
    Expression System Taxid: 511693
    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, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1EAT2Ligand/Ion(2S,3S,4R,5S)-2-(1H-BENZIMIDAZOL-2-YL)-5-METHYLPYRROLIDINE-3,4-DIOL
2GOL2Ligand/IonGLYCEROL
3IMD6Ligand/IonIMIDAZOLE
4SO44Ligand/IonSULFATE ION
Biological Unit 1 (4, 10)
No.NameCountTypeFull Name
1EAT1Ligand/Ion(2S,3S,4R,5S)-2-(1H-BENZIMIDAZOL-2-YL)-5-METHYLPYRROLIDINE-3,4-DIOL
2GOL1Ligand/IonGLYCEROL
3IMD5Ligand/IonIMIDAZOLE
4SO43Ligand/IonSULFATE ION
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
1EAT1Ligand/Ion(2S,3S,4R,5S)-2-(1H-BENZIMIDAZOL-2-YL)-5-METHYLPYRROLIDINE-3,4-DIOL
2GOL1Ligand/IonGLYCEROL
3IMD1Ligand/IonIMIDAZOLE
4SO41Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
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 , IMD A:505BINDING SITE FOR RESIDUE EAT A 501
02AC2SOFTWAREALA A:63 , TRP A:117 , MET A:120 , TYR A:168 , PHE A:359BINDING SITE FOR RESIDUE IMD A 502
03AC3SOFTWARETRP A:88 , HOH A:720 , HOH A:990BINDING SITE FOR RESIDUE IMD A 503
04AC4SOFTWAREGLU A:288 , THR A:310 , GLU A:313 , ASN A:314 , TRP A:316BINDING SITE FOR RESIDUE IMD A 504
05AC5SOFTWARETRP A:232 , EAT A:501 , SO4 A:507BINDING SITE FOR RESIDUE IMD A 505
06AC6SOFTWAREARG A:399 , VAL A:405BINDING SITE FOR RESIDUE IMD A 506
07AC7SOFTWARETRP A:232 , ARG A:262 , ARG A:271 , HIS A:272 , IMD A:505BINDING SITE FOR RESIDUE SO4 A 507
08AC8SOFTWARELYS A:90 , ALA A:97 , HOH A:806BINDING SITE FOR RESIDUE SO4 A 508
09AC9SOFTWARELYS A:145 , GLU A:215 , THR A:218 , HOH A:707 , GLU B:252BINDING SITE FOR RESIDUE SO4 A 509
10BC1SOFTWAREASN A:169 , GLY A:172 , ASP A:174 , LYS A:224 , HOH A:621 , HOH A:917BINDING SITE FOR RESIDUE GOL A 510
11BC2SOFTWAREHIS 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:792BINDING SITE FOR RESIDUE EAT B 501
12BC3SOFTWARETRP B:117 , MET B:120 , TYR B:168 , PHE B:359BINDING SITE FOR RESIDUE IMD B 502
13BC4SOFTWARETRP B:232 , ARG B:262 , ARG B:271 , HIS B:272BINDING SITE FOR RESIDUE SO4 B 503
14BC5SOFTWAREGLU B:416 , VAL B:454 , PRO B:455 , LYS B:456 , ASN B:458 , HOH B:620 , HOH B:839 , HOH B:840 , HOH B:897BINDING SITE FOR RESIDUE GOL B 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J28)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J28)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J28)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J28)

(-) Exons   (0, 0)

(no "Exon" information available for 4J28)

(-) 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:438
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               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...................ee...........hhhhhhh.eeeee...........hhhhh...hhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhhhhhh.............eeeee.....eeeee.......eeeee....eeeeeeee.....ee.eeeee..eeeee.........eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j28 A  35 EIPLKYGATNEGKRQDPAMQKFRDNRLGAFIHWGLYAIPGGEWNGKVYGGAAEWLKSWAKVPADEWLKLMDQWNPTKFDAKKWAKMAKEMGTKYVKITTKHHEGFCLWPSKYTKYTVANTPYKRDILGELVKAYNDEGIDVHFYFSVMDWSNPDYRYDIKSKEDSIAFSRFLEFTDNQLKELATRYPTVKDFWFDGTWDASVKKNGWWTAHAEQMLKELVPGVAINSRLRADDKGKRHFDSNGRLMGDYESGYERRLPDPVKDLKVTQWDWEACMTIPENQWGYHKDWSLSYVKTPIEVIDRIVHAVSMGGNMVVNFGPQADGDFRPEEKAMATAIGKWMNRYGKAVYACDYAGFEKQDWGYYTRGKNDEVYMVVFNQPYSERLIVKTPKGITVEKATLLTTGEDITVVETTRNEYNVSVPKKNPGEPYVIQLKVRAA 472
                                    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:438
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               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...................ee...........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
                 4j28 B  35 EIPLKYGATNEGKRQDPAMQKFRDNRLGAFIHWGLYAIPGGEWNGKVYGGAAEWLKSWAKVPADEWLKLMDQWNPTKFDAKKWAKMAKEMGTKYVKITTKHHEGFCLWPSKYTKYTVANTPYKRDILGELVKAYNDEGIDVHFYFSVMDWSNPDYRYDIKSKEDSIAFSRFLEFTDNQLKELATRYPTVKDFWFDGTWDASVKKNGWWTAHAEQMLKELVPGVAINSRLRADDKGKRHFDSNGRLMGDYESGYERRLPDPVKDLKVTQWDWEACMTIPENQWGYHKDWSLSYVKTPIEVIDRIVHAVSMGGNMVVNFGPQADGDFRPEEKAMATAIGKWMNRYGKAVYACDYAGFEKQDWGYYTRGKNDEVYMVVFNQPYSERLIVKTPKGITVEKATLLTTGEDITVVETTRNEYNVSVPKKNPGEPYVIQLKVRAA 472
                                    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 4J28)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J28)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J28)

(-) Gene Ontology  (3, 3)

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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 4jfs 4jft 4jfu 4jfv 4jfw 4jl1 4jl2 4pcs 4pct 4pee 4wsj 4wsk 5hdr 5i5r

(-) Related Entries Specified in the PDB File

4j27 4jfs 4jft 4jfu 4jfv 4jfw 4jl1 4jl2