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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
1CA1Ligand/IonCALCIUM ION
2DV12Ligand/Ion(3~{A}~{R},5~{R},6~{S},7~{R},7~{A}~{R})-5-(HYDROXYMETHYL)-2-(PROP-2-ENYLAMINO)-5,6,7,7~{A}-TETRAHYDRO-3~{A}~{H}-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL
3EDO4Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DV11Ligand/Ion(3~{A}~{R},5~{R},6~{S},7~{R},7~{A}~{R})-5-(HYDROXYMETHYL)-2-(PROP-2-ENYLAMINO)-5,6,7,7~{A}-TETRAHYDRO-3~{A}~{H}-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL
3EDO3Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DV11Ligand/Ion(3~{A}~{R},5~{R},6~{S},7~{R},7~{A}~{R})-5-(HYDROXYMETHYL)-2-(PROP-2-ENYLAMINO)-5,6,7,7~{A}-TETRAHYDRO-3~{A}~{H}-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL
3EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:135 , PHE B:136 , TYR B:137 , LYS B:166 , ASP B:242 , ASP B:243 , TYR B:282 , MET B:308 , TRP B:309 , THR B:310 , VAL B:314 , TRP B:337 , ASN B:339 , ASP B:344 , ASN B:372BINDING SITE FOR RESIDUE DV1 B1716
2AC2SOFTWAREGLY A:135 , PHE A:136 , TYR A:137 , LYS A:166 , ASP A:242 , ASP A:243 , TYR A:282 , MET A:308 , THR A:310 , TRP A:337 , ASN A:339 , ASP A:344 , ASN A:372BINDING SITE FOR RESIDUE DV1 A1716
3AC3SOFTWAREARG A:347 , GLU A:375 , HIS A:376 , ASN A:546 , ASN A:548 , HOH A:2148 , HOH A:2150BINDING SITE FOR RESIDUE EDO A1717
4AC4SOFTWAREARG B:347 , GLU B:375 , HIS B:376 , ASN B:546 , ASN B:548 , HOH B:2173BINDING SITE FOR RESIDUE EDO B1717
5AC5SOFTWAREHIS A:593 , VAL A:609 , ALA A:611 , ASN A:612 , ARG A:613 , ILE A:713 , LYS A:715 , HOH A:2304BINDING SITE FOR RESIDUE EDO A1718
6AC6SOFTWARETYR A:137 , ASP A:344 , TYR A:345 , ARG A:347 , TYR A:550 , GLN A:551 , HOH A:2149 , HOH A:2305BINDING SITE FOR RESIDUE EDO A1719
7AC7SOFTWAREGLU B:32 , GLU B:61 , ASP B:64 , HOH B:2021 , HOH B:2022BINDING SITE FOR RESIDUE CA B1718

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FL1)

(-) 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 5FL1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FL1)

(-) Exons   (0, 0)

(no "Exon" information available for 5FL1)

(-) 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:703
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee...eee....eeee.....hhhhhhhhhhhh.....eeeeeee..hhhhhhhh.........eeeee...eeeeee.hhhhhhhhhhhhhhhh...eee.eeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee..........hhhhh..hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeee....hhhhh....hhhhhhhhhh....eeee.........hhhhhhhhhhhhh..eeeee.......................hhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..................hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhh............eeee...hhhhh.eeee..eeee......eee....eeeeeeeeeeeeeeeeee.....eeeeee......eee.........eee....eeeeeeeee.....eee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fl1 A   4 SLQPPPQQLIVNKTIDLPAVYQLNGGEEANPHAVKVLKELLSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMISNVEQIKNLPLQVKANRVLISPANEVVKWAAGNSVEIELDAIYPGENIQINFGCTWGRLEISTDGKEWKTVDLKQKESRLSAGLQKAPVKFVRFTNVSDEEQQVYLRQFVLTIEK 715
                                    13||      24        34        44 ||     58        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       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648||     662       672       682       692       702       712   
                                     14|                            46|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   649|                                                             
                                      16                             51                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    654                                                             


Chain B from PDB  Type:PROTEIN  Length:665
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeee...eeeee.....hhhhhhhhhhhh..ee.....eeeeeee..hhhhhhhhhhh......eeeee...eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee.................hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeee....hhhhh....hhhhhhhhhh....eeee.........hhhhhhhhhhhhh..eeeee.......................hhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..................hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhh............eee.......eeee..eeee...eeeeeeeeeeeeeee...............ee....eeeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fl1 B   3 VSLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMISQIKNLPLQVKANRVLISPVEIELDAIYPGENIQINWGRLEISEWKTVDSAGLQKAPVKFVRFQFVLTIEK 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       462       472       482       492       502       512       522       532       542       552       562       572       582       592    || 605       615  ||   637       647|     |669  ||   687      |710     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            597|              618|             647|   662|  672|          694|       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             601               631              656    667   681           708
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 5FL1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FL1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FL1)

(-) Gene Ontology  (7, 7)

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  3.2.1.169
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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 5fl0

(-) Related Entries Specified in the PDB File

5fky STRUCTURE OF A HYDROLASE BOUND WITH AN INHIBITOR
5fl0 STRUCTURE OF A HYDROLASE WITH AN INHIBITOR