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(-) Description

Title :  STRUCTURE OF GH84 WITH LIGAND
 
Authors :  M. Bergeron-Brlek, J. Goodwin-Tindall, N. Cekic, V. Varghese, W. F. Za X. Shan, C. Roth, S. Chan, G. J. Davies, D. J. Vocadlo, R. Britton
Date :  05 Aug 15  (Deposition) - 18 Nov 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Tim-Barrel, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Bergeron-Brlek, J. Goodwin-Tindall, N. Cekic, C. Roth, W. F. Zandberg, X. Shan, V. Varghese, S. Chan, G. J. Davies, D. J. Vocadlo, R. Britton
A Convenient Approach To Stereoisomeric Iminocyclitols: Generation Of Potent Brain-Permeable Oga Inhibitors.
Angew. Chem. Int. Ed. Engl. V. 54 15429 2015
PubMed-ID: 26545827  |  Reference-DOI: 10.1002/ANIE.201507985

(-) Compounds

Molecule 1 - O-GLCNACASE BT_4395
    Chains: A
    EC Number: 3.2.1.169
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: GOLD
    Fragment: UNP RESIDUES 22-737
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 818
    Synonym: BETA-N-ACETYLGLUCOSAMINIDASE, BETA-N-ACETYLHEXOSAMINIDASE, BETA-HEXOSAMINIDASE, HEXOSAMINIDASE B, N-ACETYL-BETA- GLUCOSAMINIDASE, GLYCOSIDE HYDROLASE
 
Molecule 2 - O-GLCNACASE BT_4395
    Chains: B
    EC Number: 3.2.1.169
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: GOLD
    Fragment: UNP RESIDUES 22-737
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 818
    Synonym: BETA-N-ACETYLGLUCOSAMINIDASE, BETA-N-ACETYLHEXOSAMINIDASE, BETA-HEXOSAMINIDASE, HEXOSAMINIDASE B, N-ACETYL-BETA-GLUCOSAMINIDA 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, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3XRJ2Ligand/Ion2-[(2S,3R,4R,5R)-5-(HYDROXYMETHYL)-3,4-BIS(OXIDANYL)-1-PENTYL-PYRROLIDIN-2-YL]-N-METHYL-ETHANAMIDE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3XRJ1Ligand/Ion2-[(2S,3R,4R,5R)-5-(HYDROXYMETHYL)-3,4-BIS(OXIDANYL)-1-PENTYL-PYRROLIDIN-2-YL]-N-METHYL-ETHANAMIDE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3XRJ1Ligand/Ion2-[(2S,3R,4R,5R)-5-(HYDROXYMETHYL)-3,4-BIS(OXIDANYL)-1-PENTYL-PYRROLIDIN-2-YL]-N-METHYL-ETHANAMIDE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:32 , GLU B:61 , ASP B:64 , HOH B:2011 , HOH B:2012 , HOH B:2020BINDING SITE FOR RESIDUE CA B1715
2AC2SOFTWAREARG A:347 , GLU A:375 , HIS A:376 , ASN A:546 , ASN A:548 , HOH A:2098BINDING SITE FOR RESIDUE EDO A1716
3AC3SOFTWAREARG B:347 , GLU B:375 , HIS B:376 , ASN B:546 , ASN B:548 , HOH B:2097 , HOH B:2101BINDING SITE FOR RESIDUE EDO B1716
4AC4SOFTWAREGLY B:135 , PHE B:136 , TYR B:137 , LYS B:166 , ASP B:242 , ASP B:243 , CYS B:278 , TYR B:282 , TRP B:286 , THR B:310 , VAL B:314 , TRP B:337 , ASN B:339 , VAL B:342 , ASP B:344 , TYR B:345 , ASN B:372BINDING SITE FOR RESIDUE XRJ B1717
5AC5SOFTWAREGLY A:135 , PHE A:136 , TYR A:137 , LYS A:166 , ASP A:242 , ASP A:243 , CYS A:278 , TYR A:282 , TRP A:286 , THR A:310 , TRP A:337 , ASN A:339 , VAL A:342 , ASP A:344 , ASN A:372 , HIS A:433BINDING SITE FOR RESIDUE XRJ A1717

(-) SS Bonds  (0, 0)

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

(-) 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 5ABF)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ABF)

(-) 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:663
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee...eeeee.....hhhhhhhhhhhhh..ee....eeeeeee..hhhhhhhh.........eeeee...eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee..........hhhhh..hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeee.............hhhhhhhhhh....eeee.........hhhhhhhhhhhhh..eeeee.......................hhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..................hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh.............eee.....eeee..eeee..eeeeeeeeeeeeeeeeeeeee......ee.....ee....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5abf A   4 SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMISNNLPLQVKANRVLISVEIELDAIYPGENIQIGRLEISTDGKEWKTVDLKSAGLQKAPVKFVRFVLTIEK 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       631       641    || 661       671  ||   687     ||712   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            598|          617|            646|              674|         693|      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             604           631             657               681          709      


Chain B from PDB  Type:PROTEIN  Length:651
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               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..........hhhhh..hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeee.............hhhhhhhhhh....eeee.........hhhhhhhhhhhhh..eeeee.......................hhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..................hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh.................eeee..eeee..eeeeeeeeeeeeeee.......eee....eeeeee..eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5abf B   2 QVSLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMLPLQVKANRVLISVEIELDAIYPGENIQINRLEISLSAGLQKAPVKFVRFQFVLTIE 714
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591   ||  610      |633       643   ||  680       690   ||  713 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           595|         617|             647| 662|           694|      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            605          631              658  680            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 5ABF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 5abg 5abh 5fky 5fl0 5fl1

(-) Related Entries Specified in the PDB File

5abe STRUCTURE OF GH84 WITH LIGAND
5abg STRUCTURE OF GH84 WITH LIGAND
5abh STRUCTURE OF GH84 WITH LIGAND