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(-) Description

Title :  STRUCTURE OF A HYDROLASE WITH AN INHIBITOR
 
Authors :  N. Cekic, J. E. Heinonen, K. A. Stubbs, C. Roth, E. J. Mceachern, G. J. Dav D. J. Vocadlo
Date :  20 Oct 15  (Deposition) - 31 Aug 16  (Release) - 31 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Cekic, J. E. Heinonen, K. A. Stubbs, C. Roth, Y. He, A. J. Bennet, E. J. Mceachern, G. J. Davies, D. J. Vocadlo
Analysis Of Transition State Mimicry By Tight Binding Aminothiazoline Inhibitors Provides Insight Into Catalysis By Human O-Glcnacase
Chem. Sci. V. 7 3742 2016
PubMed: search  |  Reference-DOI: 10.1039/C6SC00370B

(-) Compounds

Molecule 1 - O-GLCNACASE BT_4395
    Chains: A, B
    EC Number: 3.2.1.169
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 818
    Synonym: BETA-N-ACETYLGLUCOSAMINIDASE, BETA-N-ACETYLHEXOSAMINIDASE, BETA-HEXOSAMINIDASE, HEXOSAMINIDASE B, N-ACETYL-BETA-GLUCOSAMINIDASE, GLYCOSIDE HYDROLASE

 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, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
171I2Ligand/Ion(3~{A}~{R},5~{R},6~{S},7~{R},7~{A}~{R})-2-(BUTYLAMINO)-5-(HYDROXYMETHYL)-5,6,7,7~{A}-TETRAHYDRO-3~{A}~{H}-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL
2CA1Ligand/IonCALCIUM ION
3EDO4Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
171I1Ligand/Ion(3~{A}~{R},5~{R},6~{S},7~{R},7~{A}~{R})-2-(BUTYLAMINO)-5-(HYDROXYMETHYL)-5,6,7,7~{A}-TETRAHYDRO-3~{A}~{H}-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL
2CA-1Ligand/IonCALCIUM ION
3EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
171I1Ligand/Ion(3~{A}~{R},5~{R},6~{S},7~{R},7~{A}~{R})-2-(BUTYLAMINO)-5-(HYDROXYMETHYL)-5,6,7,7~{A}-TETRAHYDRO-3~{A}~{H}-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL
2CA-1Ligand/IonCALCIUM ION
3EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:32 , GLU B:61 , ASP B:64 , HOH B:2019 , HOH B:2020 , HOH B:2038BINDING SITE FOR RESIDUE CA B1716
2AC2SOFTWAREARG A:347 , GLU A:375 , HIS A:376 , ASN A:546 , ASN A:548 , HOH A:2150 , HOH A:2153BINDING SITE FOR RESIDUE EDO A1716
3AC3SOFTWARETYR A:137 , ASP A:344 , TYR A:345 , ARG A:347 , GLN A:551 , HOH A:2152BINDING SITE FOR RESIDUE EDO A1717
4AC4SOFTWAREARG B:347 , GLU B:375 , HIS B:376 , ASN B:546 , ASN B:548 , HOH B:2163BINDING SITE FOR RESIDUE EDO B1717
5AC5SOFTWAREPRO B:303 , GLN B:306 , ARG B:332 , SER B:367BINDING SITE FOR RESIDUE EDO B1718
6AC6SOFTWAREGLY A:135 , PHE A:136 , TYR A:137 , LYS A:166 , ASP A:242 , ASP A:243 , CYS A:278 , TYR A:282 , MET A:308 , TRP A:309 , THR A:310 , TRP A:337 , ASN A:339 , ASP A:344 , TYR A:345 , ASN A:372 , HOH A:2193BINDING SITE FOR RESIDUE 71I A1718
7AC7SOFTWAREGLY B:135 , PHE B:136 , TYR B:137 , LYS B:166 , ASP B:242 , ASP B:243 , CYS B:278 , TYR B:282 , MET B:308 , TRP B:309 , THR B:310 , VAL B:314 , TRP B:337 , ASN B:339 , ASP B:344 , TYR B:345 , ASN B:372 , HOH B:2211BINDING SITE FOR RESIDUE 71I B1719

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FL0)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gln A:6 -Pro A:7
2Ala A:173 -Pro A:174
3Phe A:340 -Pro A:341
4Gln B:6 -Pro B:7
5Ala B:173 -Pro B:174
6Phe B:340 -Pro B:341

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FL0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FL0)

(-) Exons   (0, 0)

(no "Exon" information available for 5FL0)

(-) 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:668
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee...eeeee.....hhhhhhhhhhhh...ee....eeeeeee..hhhhh............eeeee...eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee..........hhhhh..hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeee....hhhhh....hhhhhhhhhh....eeee.........hhhhhhhhhhhhh..eeeee.......................hhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..................hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhh............eee.....eeee..eeee......eeeeeeeeeeeeeee..eee.....eee....eee....eeeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fl0 A   4 SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMISKNLPLQVKANRVLISPANEVEIELDAIYPGENIQINLEISTDGKEWKTVDLLSAGLQKAPVKFVRFQFVLTIEK 715
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593   ||  608       618  ||   637       647|      668    || 684       694|       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           597|               621|             647|           673|           694|       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            603                631              659            680            708       


Chain B from PDB  Type:PROTEIN  Length:682
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeee....eeee.....hhhhhhhhhhhh.........eeeeeee..hhhhhhhhhhh......eeeee...eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee.................hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeee.............hhhhhhhhhh....eeee.........hhhhhhhhhhhhh..eeeee.......................hhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..................hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhh............eee..hhhhhh..eeee..eeee...eeeeeeeeeeeeeeeeeeeeee......eee..ee....eeee....eeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fl0 B   3 VSLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMISNVEQIKNLPLQVKANRVLISPVEIELDAIYPGENIQINGRLEISTDGKEWKTVDLKQKESRLSAGLQKAPVKFVRFTNLRQFVLTIEK 715
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452 ||    463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613    || 635       645 ||    664       674       684       694 ||    713  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             454|                                                                                                                                                               618|             647|                                    696|         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              456                                                                                                                                                                631              657                                     706
   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 5FL0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FL0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FL0)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        OGA_BACTN | Q89ZI2: 2chn 2cho 2j47 2j4g 2jiw 2vvn 2vvs 2w4x 2w66 2w67 2wca 2wzh 2wzi 2x0h 2xj7 2xm1 2xm2 4ais 4aiu 4ur9 5abe 5abf 5abg 5abh 5fky 5fl1

(-) Related Entries Specified in the PDB File

5fky STRUCTURE OF A HYDROLASE BOUND WITH AN INHIBITOR
5fl1 STRUCTURE OF A HYDROLASE WITH AN INHIBITOR