Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF AGD31B, ALPHA-TRANSGLUCOSYLASE IN GLYCOSIDE HYDROLASE FAMILY 31, IN COMPLEX WITH CYCLOPHELLITOL AZIRIDINE PROBE CF021
 
Authors :  L. Wu, G. J. Davies
Date :  08 Feb 16  (Deposition) - 04 May 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha Glycosidase, Cyclophellitol Aziridine, Inhibitor, Probe, Hydrolase (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
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Gene: AGD31B, CJA_3248
    Organism Scientific: CELLVIBRIO JAPONICUS (STRAIN UEDA107)
    Organism Taxid: 498211
    Strain: UEDA107
    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  (5, 11)

Asymmetric/Biological Unit (5, 11)
No.NameCountTypeFull Name
166U1Ligand/Ion(1R,2S,3S,4R,5S,6R)-5-AMINO-6-(HYDROXYMETHYL)CYCLOHEXANE-1,2,3,4-TETROL
2EDO3Ligand/Ion1,2-ETHANEDIOL
3PG41Ligand/IonTETRAETHYLENE GLYCOL
4SO45Ligand/IonSULFATE ION
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:58 , ARG A:231 , HOH A:1288binding site for residue SO4 A 901
02AC2SOFTWAREARG A:797 , HOH A:1379 , HOH A:1440binding site for residue SO4 A 902
03AC3SOFTWARETHR A:323 , PRO A:324 , LEU A:325 , ASP A:326 , HOH A:1173 , HOH A:1264binding site for residue SO4 A 903
04AC4SOFTWARETHR A:732 , ASP A:733 , ASN A:734 , GLN A:735binding site for residue SO4 A 904
05AC5SOFTWAREARG A:123 , GLY A:239 , ASN A:240 , SER A:244 , ASN A:248 , HOH A:1245binding site for residue SO4 A 905
06AC6SOFTWARELEU A:566 , ARG A:569 , TYR A:674 , GLU A:690 , EDO A:910 , HOH A:1011binding site for residue PG4 A 906
07AC7SOFTWAREPHE A:271 , ASP A:299 , ILE A:341 , TRP A:410 , ASP A:412 , ARG A:463 , TRP A:477 , ASP A:480 , PHE A:513 , HIS A:540 , HOH A:1016 , HOH A:1030 , HOH A:1031binding site for residue 66U A 907
08AC8SOFTWAREGLN A:77 , LEU A:78 , SER A:229 , GLY A:230binding site for residue EDO A 908
09AC9SOFTWAREARG A:176 , HIS A:178 , GLN A:187 , HOH A:1002binding site for residue EDO A 909
10AD1SOFTWAREPHE A:640 , TRP A:641 , PG4 A:906binding site for residue EDO A 910
11AD2SOFTWAREHIS A:731 , SER A:764 , GLN A:766 , ARG A:798 , LYS A:817 , HOH A:1078 , HOH A:1195 , HOH A:1359binding site for residue TRS A 911

(-) 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 5I24)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I24)

(-) Exons   (0, 0)

(no "Exon" information available for 5I24)

(-) 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..eeeeeeeeee..eeeeee......eeeee..........eeeee.................eeeeeee...eeeee.....eeeee......eeeeee.....eeeeee..hhhhhhhhhhhhhh.....hhhhhh.ee......hhhhhhhhhhhhhhh.....eeeehhhhhh..................hhhhhhhhhhhh..eeeeee..eee....hhhhhhhh.............eee..eeeee....hhhhhhhhhhhhhhhhhh...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....hhhhh...eeee....eeeeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i24 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 5I24)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I24)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I24)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    66U  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TRS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:115 - Pro A:116   [ RasMol ]  
    Glu A:415 - Pro A:416   [ RasMol ]  
    Phe A:271 - Gly A:272   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5i24
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  OL4AG_CELJU | B3PEE6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.4.1.161
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  OL4AG_CELJU | B3PEE6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        OL4AG_CELJU | B3PEE6: 4b9y 4b9z 4ba0 5i23

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5I24)