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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE GLYCOSYL HYDROLASE (BDI_2473) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 1.85 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  23 May 11  (Deposition) - 15 Jun 11  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Concanavalin A-Like Lectins/Glucanases, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Hypothetical Glycosyl Hydrolase (Bdi_2473) From Parabacteroides Distasonis Atcc 8503 At 1. 8 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE GLYCOSYLHYDROLASE
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidSPEEDET
    Expression System StrainHK100
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSEQUENCE DATABASE RESIDUES 29-223
    GeneBDI_2473
    Organism ScientificPARABACTEROIDES DISTASONIS
    Organism Taxid435591
    StrainATCC 8503 / DSM 20701 / NCTC 11152

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2IOD3Ligand/IonIODIDE ION
3MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:-11 , ASN A:84 , TYR A:127BINDING SITE FOR RESIDUE IOD A 300
2AC2SOFTWAREGLU A:184BINDING SITE FOR RESIDUE IOD A 301
3AC3SOFTWAREHIS A:-7BINDING SITE FOR RESIDUE IOD A 302
4AC4SOFTWARELYS A:130 , ASN A:133 , SER A:167 , HOH A:394BINDING SITE FOR RESIDUE EDO A 303
5AC5SOFTWAREASN A:51 , ASN A:179 , PRO A:180 , ASP A:181 , HOH A:450 , HOH A:451 , HOH A:452BINDING SITE FOR RESIDUE EDO A 304
6AC6SOFTWAREILE A:-13 , THR A:174 , EDO A:306 , HOH A:340BINDING SITE FOR RESIDUE EDO A 305
7AC7SOFTWARETHR A:178 , ASN A:179 , PRO A:180 , ARG A:216 , EDO A:305 , HOH A:319 , HOH A:465BINDING SITE FOR RESIDUE EDO A 306
8AC8SOFTWARELEU A:32 , PHE A:33 , PHE A:49 , ASN A:217 , ILE A:218 , HOH A:321BINDING SITE FOR RESIDUE EDO A 307
9AC9SOFTWAREVAL A:81 , HIS A:111 , THR A:198 , HOH A:364 , HOH A:370 , HOH A:373BINDING SITE FOR RESIDUE EDO A 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S5Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3S5Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S5Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S5Q)

(-) Exons   (0, 0)

(no "Exon" information available for 3S5Q)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:213
 aligned with A6LES9_PARD8 | A6LES9 from UniProtKB/TrEMBL  Length:223

    Alignment length:218
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215        
         A6LES9_PARD8     6 NVKRVFTVLIILLLLISCRVETDYRPLFDKDLSNADYDSSVWTFKNGILTATADQSIWTKVQYENFILDLEFKTDVNTNSGVVIYCTDKGNWIPSSIEIQIADDHHPEWQSYPEYWRCGSIYGHKGANEQLVVKKPGEWNRMIITAKGQQIDIELNGKHIVSANLADWTSGTTNPDGTEIPEWLPIPYANMPTKGYIGLQGKHGESNIWFRNIQLKQL 223
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------DUF1080-3s5qA01 A:29-221                                                                                                                                                                         -- Pfam domains
         Sec.struct. author ............hhhhh.-----eee........ee.....eeee..eeee.....eee......eeeeeeeee....eeeeeeee.....hhhhheeeeee...hhhhhhhhhhhh.....................eeeeeeeee..eeeeee..eeeeeee.hhh..................hhhhh....eeee........eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s5q A -17 GSDKIHHHHHHENLYFQG-----YRPLFDKDLSNADYDSSVWTFKNGILTATADQSIWTKVQYENFILDLEFKTDVNTNSGVVIYCTDKGNWIPSSIEIQIADDHHPEWQSYPEYWRCGSIYGHKGANEQLVVKKPGEWNRmIITAKGQQIDIELNGKHIVSANLADWTSGTTNPDGTEIPEWLPIPYANmPTKGYIGLQGKHGESNIWFRNIQLKQL 223
                                    -8       | -   |    35        45        55        65        75        85        95       105       115       125       135       145 |     155       165       175       185       195|      205       215        
                                             0    29                                                                                                                   147-MSE                                          196-MSE                       

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  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 3S5Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S5Q)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A6LES9_PARD8 | A6LES9)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.

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