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 :  STRUCTURE OF GH36 ALPHA-GALACTOSIDASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH INTACT CYCLOPROPYL-CARBASUGAR.
 
Authors :  R. Pengelly, T. Gloster
Date :  07 Oct 16  (Deposition) - 09 Nov 16  (Release) - 30 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Galactosidase, Glycoside Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Adamson, R. J. Pengelly, S. Shamsi Kazem Abadi, S. Chakladar, J. Draper, R. Britton, T. M. Gloster, A. J. Bennet
Structural Snapshots For Mechanism-Based Inactivation Of A Glycoside Hydrolase By Cyclopropyl Carbasugars.
Angew. Chem. Int. Ed. Engl. V. 55 14978 2016
PubMed-ID: 27783466  |  Reference-DOI: 10.1002/ANIE.201607431

(-) Compounds

Molecule 1 - ALPHA-GALACTOSIDASE
    Chains: A
    EC Number: 3.2.1.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GALA
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Other Details: DIFFERENCES AT THE N-TERMINUS ARISE FROM THE VECTOR USED FOR EXPRESSION (PRIMARILY A HIS TAG). DIFFERENCES AT THE C- TERMINUS ARISE FROM THE LACK OF ELECTRON DENSITY MEANING THIS PART COULD NOT BE MODELLED.

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
17D01Ligand/Ion(1~{R},2~{S},3~{S},4~{R},5~{S},6~{S})-5-[3,5-BIS(FLUORANYL)PHENOXY]-1-(HYDROXYMETHYL)BICYCLO[4.1.0]HEPTANE-2,3,4-TRIOL
2MG1Ligand/IonMAGNESIUM ION
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:9 , PHE A:391 , GLY A:393 , GLU A:394 , HIS A:395 , HOH A:720 , HOH A:781 , HOH A:810 , HOH A:910 , HOH A:957binding site for residue SO4 A 601
2AC2SOFTWARELYS A:302 , ASP A:303 , GLU A:304 , LYS A:339binding site for residue SO4 A 602
3AC3SOFTWAREASP A:419 , ASP A:454 , HOH A:760 , HOH A:916 , HOH A:951 , HOH A:993binding site for residue MG A 603
4AC4SOFTWAREARG A:-6 , GLY A:-5 , SER A:-4 , PRO A:-7 , TRP A:65 , TRP A:85 , TRP A:190 , TYR A:191 , ASP A:220 , ASP A:221 , TRP A:257 , ASN A:290 , LYS A:325 , ASP A:327 , PHE A:328 , CYS A:368 , ARG A:383 , ASP A:387binding site for residue 7D0 A 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5M12)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5M12)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M12)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M12)

(-) Exons   (0, 0)

(no "Exon" information available for 5M12)

(-) 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:534
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhh.ee..ee...eeeeee...eeeeeeeeee..eeeeeeeeee...eeeeeeee...eeeee.......eeeee............hhhhhh.hhhhhh..eeee.eeee..eeeee......eeeeeee..eeeeeee.....eeeeee...eeeee..hhhhhhhhhhhhhhhhhh........eeeehhhhhhhhhhhhhhhhhhhhhhhh...eeee...................hhhhhhhhhhhh..eeeeee...eee..hhhhhhhhhhh.ee..ee.eeeee..eeeee....hhhhhhhhhhhhhhhhhh...eeee.hhhhhhh........hhhhhhhhhhhhhhhhhh...eeee....hhhhh....eee...................hhhhhhhhhhhhhhhh....eee.............hhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh....eeee........eeeeeeeee..eeeeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5m12 A  -8 VPRGSHMASMEIFGKTFREGRFVLKEKNFTVEFAVEKIHLGWKISGRVKGSPGRLEVLRTKAPEKVLVNNWQSWGPCRVVDAFSFKPPEIDPNWRYTASVVPDVLERNLQSDYFVAEEGKVYGFLSSKIAHPFFAVEDGELVAYLEYFDVEFDDFVPLEPLVVLEDPNTPLLLEKYAELVGMENNARVPKHTPTGWCSWYHYFLDLTWEETLKNLKLAKNFPFEVFQIDDAYEKDIGDWLVTRGDFPSVEEMAKVIAENGFIPGIWTAPFSVSETSDVFNEHPDWVVKENGEPKMAYRNWNKKIYALDLSKDEVLNWLFDLFSSLRKMGYRYFKIDFLFAGAVPGERKKNITPIQAFRKGIETIRKAVGEDSFILGCGSPLLPAVGCVDGMRIGPDTAPFWGEHIEDNGAPAARWALRNAITRYFMHDRFWLNDPDCLILREEKTDLTQKEKELYSYTCGVLDNMIIESDDLSLVRDHGKKVLKETLELLGGRPRVQNIMSEDLRYEIVSSGTLSGNVKIVVDLNSREYHLEKE 525
                                     1        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
   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 5M12)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M12)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M12)

(-) Gene Ontology  (8, 16)

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
    7D0  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5m12)
 

(-) 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
  5m12
    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
  AGAL_THEMA | G4FEF4
    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)
  3.2.1.22
    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
  AGAL_THEMA | G4FEF4
    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
        AGAL_THEMA | G4FEF4: 1zy9 5m0x 5m16 5m1i

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5M12)