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(-) Description

Title :  STRUCTURE OF LIGAND BOUND GLYCOSYLHYDROLASE
 
Authors :  J. F. Darby, J. Landstroem, C. Roth, Y. He, M. Schultz, G. J. Davies, R. E.
Date :  27 Jun 14  (Deposition) - 25 Feb 15  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
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 :  J. F. Darby, J. Landstrom, C. Roth, Y. He, G. J. Davies, R. E. Hubbard
Discovery Of Selective Small-Molecule Activators Of A Bacterial Glycoside Hydrolase.
Angew. Chem. Int. Ed. Engl. V. 53 13419 2014
PubMed-ID: 25291993  |  Reference-DOI: 10.1002/ANIE.201407081

(-) Compounds

Molecule 1 - O-GLCNACASE BT_4395
    Chains: A, B
    EC Number: 3.2.1.169
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 22-737
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 818
    Synonym: N-ACETYL BETA-GLUCOSAMINIDASE, BETA-N-ACETYLHEXOSAMINIDASE, BETA-HEXOSAMINIDASE, GH84, HEXOSAMINIDASE B, N-ACETYL-BETA-GLUCOSAMINIDASE

 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, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1BK92Ligand/Ion4-ETHOXYQUINAZOLINE
2CA1Ligand/IonCALCIUM ION
3OAN2Ligand/IonO-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE)AMINO-N-PHENYLCARBAMATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1BK91Ligand/Ion4-ETHOXYQUINAZOLINE
2CA-1Ligand/IonCALCIUM ION
3OAN1Ligand/IonO-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE)AMINO-N-PHENYLCARBAMATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1BK91Ligand/Ion4-ETHOXYQUINAZOLINE
2CA-1Ligand/IonCALCIUM ION
3OAN1Ligand/IonO-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE)AMINO-N-PHENYLCARBAMATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:137 , ASP A:344 , ARG A:347 , TYR A:550 , OAN A:1718BINDING SITE FOR RESIDUE BK9 A1717
2AC2SOFTWARETYR B:137 , ASP B:344 , ARG B:347 , TYR B:550 , OAN B:1718BINDING SITE FOR RESIDUE BK9 B1717
3AC3SOFTWAREGLY A:135 , PHE A:136 , TYR A:137 , LYS A:166 , ASP A:242 , ASP A:243 , TYR A:282 , TRP A:286 , VAL A:314 , TRP A:337 , ASN A:339 , ASP A:344 , TYR A:345 , ASN A:372 , BK9 A:1717BINDING SITE FOR RESIDUE OAN A1718
4AC4SOFTWAREGLY B:135 , PHE B:136 , TYR B:137 , LYS B:166 , ASP B:242 , ASP B:243 , TYR B:282 , TRP B:286 , VAL B:314 , ASN B:339 , ASP B:344 , TYR B:345 , ASN B:372 , HIS B:433 , BK9 B:1717BINDING SITE FOR RESIDUE OAN B1718
5AC5SOFTWAREGLU B:32 , GLU B:61 , ASP B:64 , HOH B:2014 , HOH B:2015 , HOH B:2028BINDING SITE FOR RESIDUE CA B1719

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UR9)

(-) 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 4UR9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UR9)

(-) Exons   (0, 0)

(no "Exon" information available for 4UR9)

(-) 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:685
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee...eeeee.....hhhhhhhhhhhh...ee....eeeeeee..hhhhhhhh.........eeeee...eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee..........hhhhh..hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeee....hhhhh.....hhhhhhhhh....eeee.........hhhhhhhhhhhhh..eeeee.......................hhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..................hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhh............eee......eeee..eeee..........eeeeeeeeeeeeeeeeee..eee.....eee..............eeeeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ur9 A   4 SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMISIKNLPLQVKANRVLISPANEVVKGNSVEIELDAIYPGENIQINFLEISTDGKEWKTVDLKSRLSAGLQKAPVKFVRFTNYLRQFVLTIEKK 716
                                    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   ||  607       617      |630       640       660       670   ||  683       693  ||   711     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           597|                   624|                 648|            674|               696|           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            602                    628                  659             678                705           


Chain B from PDB  Type:PROTEIN  Length:667
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeee....eeee.....hhhhhhhhhhhh.........eeeeeee..hhhhhhhh.........eeeee...eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee.................hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeee..............hhhhhhhhh....eeee.........hhhhhhhhhhhhh..eeeee.......................hhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..................hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh.................eeee..eeee....eeeeeeeeeeeeee..eee......ee......eeee....eeeeee....eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ur9 B   3 VSLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMLPLQVKANRVLISPVEIELDAIYPGENIQIRLEISTDGKEWKTVDLKSRLSAGLQKAPVKFVRLRQFVLTIEKK 716
                                    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  ||   611      |633       643  ||   664       674|      687     ||709       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          595|          618|            646|             674|            693|          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           605           631             658              678             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 4UR9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UR9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UR9)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        OGA_BACTN | Q89ZI2: 2chn 2cho 2j47 2j4g 2jiw 2vvn 2vvs 2w4x 2w66 2w67 2wca 2wzh 2wzi 2x0h 2xj7 2xm1 2xm2 4ais 4aiu 5abe 5abf 5abg 5abh 5fky 5fl0 5fl1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4UR9)