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(-) Description

Title :  CRYSTAL STRUCTURE OF AGD31B, ALPHA-TRANSGLUCOSYLASE IN GLYCOSIDE HYDROLASE FAMILY 31, IN COMPLEX WITH CYCLOPHELLITOL AZIRIDINE PROBE CF022
 
Authors :  L. Wu, G. J. Davies
Date :  08 Feb 16  (Deposition) - 04 May 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha Glycosidase, Cyclophellitol Aziridine, Inhibitor, Probe, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Jiang, C. L. Kuo, L. Wu, C. Franke, W. W. Kallemeijn, B. I. Florea, E. Van Meel, G. A. Van Der Marel, J. D. Codee, R. G. Boot, G. J. Davies, H. S. Overkleeft, J. M. Aerts
Detection Of Active Mammalian Gh31 Alpha-Glucosidases In Health And Disease Using In-Class, Broad-Spectrum Activity-Based Probes.
Acs Cent. Sci. V. 2 351 2016
PubMed-ID: 27280170  |  Reference-DOI: 10.1021/ACSCENTSCI.6B00057

(-) Compounds

Molecule 1 - OLIGOSACCHARIDE 4-ALPHA-D-GLUCOSYLTRANSFERASE
    Chains: A
    EC Number: 2.4.1.161
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: AGD31B, CJA_3248
    Organism Scientific: CELLVIBRIO JAPONICUS (STRAIN UEDA107)
    Organism Taxid: 498211
    Synonym: ALPHA-GLUCOSIDASE 31B,CJAGD31B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
166V1Ligand/Ion1-(8-{[(1S,2R,3S,4S,5R,6R)-2,3,4,5-TETRAHYDROXY-6-(HYDROXYMETHYL)CYCLOHEXYL]AMINO}OCTYL)TRIAZA-1,2-DIEN-2-IUM
2EDO2Ligand/Ion1,2-ETHANEDIOL
3PG41Ligand/IonTETRAETHYLENE GLYCOL
4SO46Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:569 , TRP A:641 , TYR A:674 , EDO A:908 , HOH A:1001 , HOH A:1565binding site for residue PG4 A 901
02AC2SOFTWARETHR A:732 , ASN A:734 , GLN A:735binding site for residue SO4 A 902
03AC3SOFTWAREARG A:58 , ARG A:231 , HOH A:1297binding site for residue SO4 A 903
04AC4SOFTWAREARG A:797 , HOH A:1383 , HOH A:1471binding site for residue SO4 A 904
05AC5SOFTWARESER A:396 , LYS A:399 , HOH A:1158 , HOH A:1201binding site for residue SO4 A 905
06AC6SOFTWARETHR A:323 , PRO A:324 , LEU A:325 , ASP A:326 , HOH A:1116 , HOH A:1268 , HOH A:1360binding site for residue SO4 A 906
07AC7SOFTWARETHR A:107 , ASP A:124 , GLY A:239 , ASN A:240 , SER A:244 , ASN A:248 , HOH A:1332binding site for residue SO4 A 907
08AC8SOFTWARETRP A:641 , PG4 A:901binding site for residue EDO A 908
09AC9SOFTWARESER A:764 , GLN A:766 , LYS A:817 , HOH A:1377binding site for residue EDO A 909
10AD1SOFTWAREPHE A:271 , ASP A:299 , ILE A:341 , TYR A:376 , TRP A:410 , ASP A:412 , ARG A:463 , TRP A:477 , ASP A:480 , PHE A:513 , HIS A:540 , HOH A:1026 , HOH A:1040 , HOH A:1077 , HOH A:1277binding site for residue 66V A 910

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:784 -A:792

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Arg A:115 -Pro A:116
2Phe A:271 -Gly A:272
3Glu A:415 -Pro A:416

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I23)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I23)

(-) Exons   (0, 0)

(no "Exon" information available for 5I23)

(-) 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:779
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..eeeeee...eeeeeeee..eeeeee.....................eeee...eeeee...eeeeee....eeeeee..eeeeeeeeeee.eeeeee......eeeee..........eeeee.................eeeeeee...eeeee.....eeeee......eeeeee.....eeeeee..hhhhhhhhhhhhhh.....hhhhhh.ee......hhhhhhhhhhhhhhh.....eeeehhhhh...................hhhhhhhhhhhh..eeeeee..eee....hhhhhhhh.............eee..eeeee....hhhhhhhhhhhhhhhhhhh..eeee............ee..eehhhhh.hhhhhhhhhhhhhhhhhh......eee.....hhhhh.eee.......hhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.hhhh..hhhhhhh...eee...eee.........eeee....eeeee.....eeee....eeee.......eeee...eeee.....hhhhh...eeeeeee......eeeeeeee..............eeeeeeeee...eeeeeeeee..........eeeeeeee.......eeee..eeee............eeee....eeeeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i23 A  35 AVFYKEHKLRNDGLVITTNQGNIRLQFKSEAAIEVLYRADSKQLPSFALAQPESAIKAQLTETENHLQFSGGTLTARIQKRPFAISYYRDSELLLAEESGFQKINFRFYLSPGEKILGGGQRILGMDRRGQRFPLYNRAHYGYSDHSGQMYFGLPAIMSSKQYILVFDNSASGAMDIGKTESDILQLEAKSGRSAYILVAGNSYPSLIENFTQVTGRQPLPPRWALGSFASRFGYRSEAETRATVQKYKTEDFPLDTIVLDLYWFGKDIKGHMGNLDWDKENFPTPLDMMADFKQQGVKTVLITEPFVLTSSKRWDDAVKAKALAKDPQGQPKAFELYFGNGGIIDVFSKEGSRWFSSIYKDLSKQGVAGWWGDLGEPEMHPEDTQHAIGDADTVHNAYGHRWAEMLYQQQLDQFPELRPFIMMRAGFVGSQRYGMIPWTGDVSRTWGGLASQVELALQMSLLGFGYIHSDLGGFADGETLDKEMYIRWLQYGVFQPVYRPHGQDHIPSEPVFQDEETKAILRPLVKLRYRMLPYIYTAAYQNTLTGMPLMRPLFFSDEKNPALIDNKTSYFWGDSLLVTPITQAGVESVSIPAPKGVWFDFWKDTRYQTDGAPLTLPTDLHTIPVLVKAGAFMPYVPAVSTTEDYRSDSLEIHYYADASVPLAQGEIFEDDGKDPNSIKRNQFDLLTLQATHTDNQLHFQLARTGKGYRGMPERRATTLVIHNASDQYQHLDINGKTIAIAQADCASTPALACYDQERRQLQLVFTWGREALNLRLHK 817
                                    44        54        64        74        84        94       104       114       124       134 ||    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       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808         
                                                                                                                               136|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                                                                                                                141
   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 5I23)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I23)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I23)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:115 - Pro A:116   [ RasMol ]  
    Glu A:415 - Pro A:416   [ RasMol ]  
    Phe A:271 - Gly A:272   [ RasMol ]  
 

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 Related Entries

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        OL4AG_CELJU | B3PEE6: 4b9y 4b9z 4ba0 5i24

(-) Related Entries Specified in the PDB File

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