Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ALPHA-GLUCOSIDASE (TM0752) FROM THERMOTOGA MARITIMA AT 2.50 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  22 Mar 04  (Deposition) - 30 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Tm0752, Alpha-Glucosidase, Structural Genomics, Jcsg, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Alpha-Glucosidase (Tm0752) From Thermotoga Maritima At 2. 50 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALPHA-GLUCOSIDASE
    ChainsA
    EC Number3.2.1.139
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneTM0752
    Organism ScientificTHERMOTOGA MARITIMA
    Organism Taxid2336

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1MSE15Mod. Amino AcidSELENOMETHIONINE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (2, 32)
No.NameCountTypeFull Name
1MSE30Mod. Amino AcidSELENOMETHIONINE
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:7 , GLY A:9 , SER A:10 , MSE A:37 , ASP A:38 , HIS A:40 , ARG A:43 , THR A:83 , ALA A:84 , TYR A:85 , PRO A:86 , THR A:158 , ALA A:159 , ASN A:160 , ARG A:310BINDING SITE FOR RESIDUE NAD A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VJT)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:160 -Pro A:161
2Glu A:397 -Pro A:398

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VJT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VJT)

(-) Exons   (0, 0)

(no "Exon" information available for 1VJT)

(-) 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:471
 aligned with Q9WZL1_THEMA | Q9WZL1 from UniProtKB/TrEMBL  Length:471

    Alignment length:471
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       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 
         Q9WZL1_THEMA     - --MKISIIGAGSVRFALQLVGDIAQTEELSREDTHIYMMDVHERRLNASYILARKYVEELNSPVKIVKTSSLDEAIDGADFIINTAYPYDPRYHDSGSQRWDEVTKVGEKHGYYRGIDSQELNMVSTYTYVLSSYPDMKLALEIAEKMKKMAPKAYLMQTANPVFEITQAVRRWTGANIVGFCHGVAGVYEVFEKLDLDPEEVDWQVAGVNHGIWLNRFRYRGEDAYPLLDEWIEKKLPEWEPKNPWDTQMSPAAMDMYKFYGMLPIGDTVRNGSWKYHYNLETKKKWFGKFGGIDNEVERPKFHEQLRRARERLIKLAEEVQQNPGMKLTEEHPEIFPKGKLSGEQHIPFINAIANNKRVRLFLNVENQGTLKDFPDDVVMELPVWVDCCGIHREKVEPDLTHRIKIFYLWPRILRMEWNLEAYISRDRKVLEEILIRDPRTKSYEQIVQVLDEIFNLPFNEELRRYYKE 469
               SCOP domains --d1vjta1 A:1-181 Putative alpha-glucosidase TM0752                                                                                                                                    d1vjta2 A:182-469 Putative alpha-glucosidase TM0752                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhh...eeee...........hhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh...eee..hhhhhhhhhhhhh..hhh.eeeeeeee..eeeeeeeee..eehhhhhhhhhhhhhhhh..........hhhhhhhhhhhh..eehhhh...hhhhh.hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh............hhhhhhhhhhhh..eeeeeeee............eeeeeeeee..eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vjt A  -1 HHmKISIIGAGSVRFALQLVGDIAQTEELSREDTHIYmmDVHERRLNASYILARKYVEELNSPVKIVKTSSLDEAIDGADFIINTAYPYDPRYHDSGSQRWDEVTKVGEKHGYYRGIDSQELNmVSTYTYVLSSYPDmKLALEIAEKmKKmAPKAYLmQTANPVFEITQAVRRWTGANIVGFCHGVAGVYEVFEKLDLDPEEVDWQVAGVNHGIWLNRFRYRGEDAYPLLDEWIEKKLPEWEPKNPWDTQmSPAAmDmYKFYGmLPIGDTVRNGSWKYHYNLETKKKWFGKFGGIDNEVERPKFHEQLRRARERLIKLAEEVQQNPGmKLTEEHPEIFPKGKLSGEQHIPFINAIANNKRVRLFLNVENQGTLKDFPDDVVmELPVWVDCCGIHREKVEPDLTHRIKIFYLWPRILRmEWNLEAYISRDRKVLEEILIRDPRTKSYEQIVQVLDEIFNLPFNEELRRYYKE 469
                              |      8        18        28       |38        48        58        68        78        88        98       108       118   |   128       138       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 
                              |                                 36-MSE                                                                               122-MSE       136-MSE   146-MSE     |                                                                                          249-MSE| |     |                                                             326-MSE                                               380-MSE                             416-MSE                                                 
                              1-MSE                              37-MSE                                                                                                         149-MSE  |                                                                                               254-MSE   |                                                                                                                                                                                                               
                                                                                                                                                                                       156-MSE                                                                                             256-MSE |                                                                                                                                                                                                               
                                                                                                                                                                                                                                                                                                 262-MSE                                                                                                                                                                                                           

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1VJT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1VJT)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9WZL1_THEMA | Q9WZL1)
molecular function
    GO:0004558    alpha-1,4-glucosidase activity    Catalysis of the hydrolysis of terminal, non-reducing alpha-(1->4)-linked alpha-D-glucose residues with release of alpha-D-glucose.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0032450    maltose alpha-glucosidase activity    Catalysis of the reaction: alpha-maltose + H2O = 2 alpha-D-glucose.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0000023    maltose metabolic process    The chemical reactions and pathways involving the disaccharide maltose (4-O-alpha-D-glucopyranosyl-D-glucopyranose), an intermediate in the catabolism of glycogen and starch.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

 Visualization

(-) Interactive Views

Asymmetric 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:160 - Pro A:161   [ RasMol ]  
    Glu A:397 - Pro A:398   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1vjt
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q9WZL1_THEMA | Q9WZL1
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.139
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q9WZL1_THEMA | Q9WZL1
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1VJT)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1VJT)