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(-) Description

Title :  CRYSTAL STRUCTURE OF A GH29 ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON IN A NOVEL CRYSTAL FORM
 
Authors :  D. W. Wright
Date :  04 Feb 13  (Deposition) - 08 May 13  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha-L-Fucosidase, Hydrolase (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  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2IMD5Ligand/IonIMIDAZOLE
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2IMD2Ligand/IonIMIDAZOLE
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2IMD3Ligand/IonIMIDAZOLE
3SO42Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:117 , MET A:120 , TYR A:168 , PHE A:359BINDING SITE FOR RESIDUE IMD A 501
02AC2SOFTWARETRP A:232 , HOH A:1162BINDING SITE FOR RESIDUE IMD A 502
03AC3SOFTWARETRP A:232 , ARG A:262 , ARG A:271 , HIS A:272 , HOH A:1001 , HOH A:1162BINDING SITE FOR RESIDUE SO4 A 503
04AC4SOFTWARELYS A:90 , PRO A:96 , ALA A:97 , HOH A:858BINDING SITE FOR RESIDUE SO4 A 504
05AC5SOFTWARELYS A:145 , TYR A:146 , GLU A:215 , THR A:218 , ARG A:219 , HOH A:659 , HOH A:912 , GLU B:252 , HOH B:630BINDING SITE FOR RESIDUE GOL A 505
06AC6SOFTWAREHIS A:66 , HIS A:135 , TYR A:178 , TRP A:227 , ASP A:229 , GLU A:288 , TRP A:316 , HOH A:720 , HOH A:973 , HOH A:1146 , HOH A:1176BINDING SITE FOR RESIDUE GOL A 506
07AC7SOFTWARETRP B:117 , MET B:120 , TYR B:168 , PHE B:359BINDING SITE FOR RESIDUE IMD B 501
08AC8SOFTWARETHR B:422 , GLU B:444 , THR B:446 , ARG B:447 , ASN B:448 , GLU B:449 , TYR B:450BINDING SITE FOR RESIDUE IMD B 502
09AC9SOFTWARETRP B:241BINDING SITE FOR RESIDUE IMD B 503
10BC1SOFTWARETRP B:232 , ARG B:262 , ARG B:271 , HIS B:272 , HOH B:765BINDING SITE FOR RESIDUE SO4 B 504
11BC2SOFTWARELYS B:90 , PRO B:96 , ALA B:97 , HOH B:730 , HOH B:755BINDING SITE FOR RESIDUE SO4 B 505
12BC3SOFTWAREHIS B:66 , GLU B:87 , TRP B:88 , HIS B:135 , TYR B:178 , ASP B:229 , TRP B:316 , HOH B:768 , HOH B:1082BINDING SITE FOR RESIDUE GOL B 506
13BC4SOFTWAREGLN B:354 , PHE B:359 , ARG B:360 , PRO B:361 , HOH B:957 , HOH B:1077 , HOH B:1083BINDING SITE FOR RESIDUE GOL B 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J27)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J27)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J27)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J27)

(-) Exons   (0, 0)

(no "Exon" information available for 4J27)

(-) 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..eeeeee........hhhhhhhhhhhhhhhhhhhhhh.............eeeee.....eeeee.......eeeee....eeeeeeee.....ee.eeeee..eeeee.........eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j27 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: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...................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
                 4j27 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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  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 4J27)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J27)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J27)

(-) 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 4j28 4jfs 4jft 4jfu 4jfv 4jfw 4jl1 4jl2 4pcs 4pct 4pee 4wsj 4wsk 5hdr 5i5r

(-) Related Entries Specified in the PDB File

4j28 4jfs 4jft 4jfu 4jfv 4jfw 4jl1 4jl2