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(-) Description

Title :  STRUCTURE OF HUMAN O-GLCNAC HYDROLASE WITH NEW IMINOCYCLITOL TYPE INHIBITOR
 
Authors :  C. Roth, S. Chan, W. A. Offen, G. R. Hemsworth, L. I. Willems, D. King, V. V R. Britton, D. J. Vocadlo, G. J. Davies
Date :  28 Oct 16  (Deposition) - 29 Mar 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Human Glycoside Hydrolase, Glcnac, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Roth, S. Chan, W. A. Offen, G. R. Hemsworth, L. I. Willems, D. T. King, V. Varghese, R. Britton, D. J. Vocadlo, G. J. Davies
Structural And Functional Insight Into Human O-Glcnacase.
Nat. Chem. Biol. V. 13 610 2017
PubMed-ID: 28346405  |  Reference-DOI: 10.1038/NCHEMBIO.2358

(-) Compounds

Molecule 1 - PROTEIN O-GLCNACASE
    Chains: A, B
    EC Number: 3.2.1.169, 3.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: GOLD
    Gene: MGEA5, HEXC, KIAA0679, MEA5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: OGA,BETA-N-ACETYLGLUCOSAMINIDASE,BETA-N- ACETYLHEXOSAMINIDASE,BETA-HEXOSAMINIDASE,MENINGIOMA-EXPRESSED ANTIGEN 5,N-ACETYL-BETA-D-GLUCOSAMINIDASE,N-ACETYL-BETA-GLUCOSAMINIDASE, NUCLEAR CYTOPLASMIC O-GLCNACASE AND ACETYLTRANSFERASE,NCOAT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1XHA2Ligand/Ion2-[(2~{R},3~{S},4~{R},5~{R})-5-(HYDROXYMETHYL)-3,4-BIS(OXIDANYL)-1-[3-[3-(TRIFLUOROMETHYL)PHENYL]PROPYL]PYRROLIDIN-2-YL]-~{N}-METHYL-ETHANAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:67 , PHE A:68 , TYR A:69 , LYS A:98 , ASP A:174 , ASP A:175 , TYR A:219 , THR A:250 , VAL A:254 , TRP A:278 , ASN A:280 , ASP A:285 , TYR A:286 , ASN A:313 , TRP B:645 , SER B:649 , TRP B:679binding site for residue XHA A 1001
2AC2SOFTWARETRP A:645 , SER A:649 , TRP A:679 , GLY B:67 , PHE B:68 , LYS B:98 , ASP B:174 , ASP B:175 , TYR B:219 , THR B:250 , VAL B:254 , TRP B:278 , ASN B:280 , ASP B:285 , TYR B:286 , ASN B:313binding site for residue XHA B 1001

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:663 -B:663

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:225 -Pro A:226
2Tyr B:225 -Pro B:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M7U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M7U)

(-) Exons   (0, 0)

(no "Exon" information available for 5M7U)

(-) 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
(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:448
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......hhhhhhhhhhhhhhh...eeee................hhhhhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhhhh....eeeee........hhhhhhhh.hhhhhhhhhhhhhhhhh.....eeee....hhhhh......hhhhhhhhhhh....eeee..........hhhhhhhhhhhhh...eeee....................hhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh.hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m7u A  59 RFLCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEEAEQLMTLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDDIDHNMCAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSPYLRTVGEKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGPYKGRSTELIPRLKGVLTNPNCEFEANYVAIHTLATWYKSNMNDVLYSPQMALKLALTEWLQEFGVPHQFVPGPNEKPLYTAEPVTLEDLQLLADLFYLPYEHGPKGAQMLREFQWLRANSSVVSSEKIEEWRSRAAKFEEMCGLVMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQWLGCLIGDQEPWAFRGGLAGEFQRLLPI 695
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       371       381       391   ||  542       552       562       572       582       592||     609       619       629       639       649       659   ||  677       687        
                                                                                                                                                                                                                                                                                                                337|                     395|                                                     593|                                                           663|                       
                                                                                                                                                                                                                                                                                                                 371                      537                                                      601                                                            672                       


Chain B from PDB  Type:PROTEIN  Length:448
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......hhhhhhhhhhhhhhh...eeee................hhhhhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhhhh....eeeee........hhhhhhhh.hhhhhhhhhhhhhhhhh.....eeee....hhhhh......hhhhhhhhhhh....eeee..........hhhhhhhhhhhhh...eeee....................hhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh..hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m7u B  59 RFLCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEEAEQLMTLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDDIDHNMCAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSPYLRTVGEKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGPYKGRSTELIPRLKGVLTNPNCEFEANYVAIHTLATWYKSNMNGVDVLYSPQMALKLALTEWLQEFGVPHQFVPGPNEKPLYTAEPVTLEDLQLLADLFYLPYEHGPKGAQMLREFQWLRANSSVVSSEKIEEWRSRAAKFEEMCGLVMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQWLGCRDQEPWAFRGGLAGEFQRLLPI 695
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338||     379       389     ||540       550       560       570       580       590  ||   607       617       627       637       647       657      |677       687        
                                                                                                                                                                                                                                                                                                                  339|                     395|                                                     593|                                                            664|                    
                                                                                                                                                                                                                                                                                                                   371                      537                                                      601                                                             675
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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 5M7U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M7U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M7U)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        OGA_HUMAN | O60502: 2ydq 5m7r 5m7s 5m7t 5tke 5uhk 5uhl 5uho 5uhp 5un8 5un9

(-) Related Entries Specified in the PDB File

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