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

(-) Description

Title :  1.4 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF PUTATIVE ALPHA AMYLASE FROM SALMONELLA TYPHIMURIUM.
 
Authors :  G. Minasov, L. Shuvalova, I. Dubrovska, J. Winsor, L. Papazisi, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  02 Mar 10  (Deposition) - 16 Mar 10  (Release) - 16 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Putative Alpha Amylase, Idp00968, Csgid, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, L. Shuvalova, I. Dubrovska, J. Winsor, L. Papazisi, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 4 Angstrom Resolution Crystal Structure Of Putative Alpha Amylase From Salmonella Typhimurium.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE ALPHA AMYLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NP_460519, STM1560
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 14)

Asymmetric/Biological Unit (5, 14)
No.NameCountTypeFull Name
1BTB1Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2CL4Ligand/IonCHLORIDE ION
3MG6Ligand/IonMAGNESIUM ION
4PG42Ligand/IonTETRAETHYLENE GLYCOL
5PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:297 , GLU A:319 , TRP A:320 , HOH A:632 , HOH A:633 , HOH A:634BINDING SITE FOR RESIDUE MG A 595
02AC2SOFTWAREGLU A:371 , HOH A:635 , HOH A:636 , HOH A:637 , HOH A:638 , HOH A:639BINDING SITE FOR RESIDUE MG A 596
03AC3SOFTWAREHOH A:640 , HOH A:641 , HOH A:642 , HOH A:643 , HOH A:644 , HOH A:645BINDING SITE FOR RESIDUE MG A 597
04AC4SOFTWAREHOH A:646 , HOH A:647 , HOH A:648 , HOH A:649 , HOH A:650 , HOH A:651BINDING SITE FOR RESIDUE MG A 598
05AC5SOFTWAREHOH A:652 , HOH A:653 , HOH A:654 , HOH A:655 , HOH A:656 , HOH A:657BINDING SITE FOR RESIDUE MG A 599
06AC6SOFTWAREHOH A:658 , HOH A:659 , HOH A:660 , HOH A:661 , HOH A:662 , HOH A:663BINDING SITE FOR RESIDUE MG A 600
07AC7SOFTWAREGLN A:390 , LEU A:404 , ILE A:405 , HOH A:723 , HOH A:787 , HOH A:867BINDING SITE FOR RESIDUE CL A 601
08AC8SOFTWARETRP A:110 , HOH A:659 , HOH A:1035BINDING SITE FOR RESIDUE CL A 602
09AC9SOFTWARESER A:298 , ASP A:322 , ARG A:373 , HOH A:632BINDING SITE FOR RESIDUE CL A 603
10BC1SOFTWAREARG A:283 , PRO A:290 , ILE A:291 , HOH A:783 , HOH A:999BINDING SITE FOR RESIDUE CL A 604
11BC2SOFTWARETYR A:163 , HIS A:203 , TRP A:227 , ASP A:261 , ALA A:262 , GLU A:296 , HIS A:392 , ASP A:393 , HOH A:641 , HOH A:644 , HOH A:976 , HOH A:1199 , HOH A:1200BINDING SITE FOR RESIDUE BTB A 605
12BC3SOFTWARELYS A:39 , PHE A:331 , ALA A:332 , THR A:333 , ALA A:408 , ARG A:412 , HOH A:1215BINDING SITE FOR RESIDUE PG4 A 606
13BC4SOFTWAREHIS A:273 , ARG A:299 , SER A:303 , HOH A:829BINDING SITE FOR RESIDUE PG4 A 607
14BC5SOFTWARETYR A:14 , ASP A:94 , HOH A:627 , HOH A:657BINDING SITE FOR RESIDUE PGE A 608

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M07)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:570 -Pro A:571

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M07)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M07)

(-) Exons   (0, 0)

(no "Exon" information available for 3M07)

(-) 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:584
 aligned with Q8ZPF0_SALTY | Q8ZPF0 from UniProtKB/TrEMBL  Length:594

    Alignment length:584
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585    
         Q8ZPF0_SALTY     6 FCKSWGAEYIAADVVRFRLWATGQQKVMLRLAGKDQEMQANGDGWFTLDVAGVTPGTEYNFVLSDGMVVPDPASRAQKTDVNGPSYVVDPGSYTWRNTGWKGSRWEQAVVYEMHTGTFTPEGTFRAAIAKLPYLAELGVTVIEVMPVAQFGGERGWGYDGVLLYAPHSAYGTPDDFKAFIDAAHGYGLSVVLDIVLNHFGPEGNYLPLLAPAFFHKERMTPWGNGIAYDVDAVRRYIIEAPLYWLTEYHLDGLRFDAIDQIEDSSARHVLVEIAQRIREDITDRPIHLTTEDSRNIISLHPRDQDGNAPLFTAEWNDDFHNAVHVFATGETQAYYNDFADAPEKHLARALAEGFAYQGEISPQTGEPRGVKSTGQPPVAFVDFIQNHDQVGNRAQGDRLITLAGAERTKVLLATLLLSPHIPLLFMGEEYGESRPFLFFTDFHGDLARAVREGRAKEFADHAGENVPDPNAPETFQRSKLNWKQQHSEEGKAWLAFTRELLLLRQKHIVPLLSAARESSGTVLQTAPGFIAVSWRFPGGTLSLALNISATTVLLPDLPGKTLFAWPNESTGSLSQHSLIVRLAQ 589
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Alpha-amylase-3m07A02 A:229-439                                                                                                                                                                                    -------------------------------------------------------------DUF3459-3m07A01 A:501-586                                                             --- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Alpha-amylase-3m07A03 A:229-439                                                                                                                                                                                    ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .....eeeeee..eeeeeee......eeeee..eeee.ee....eeeeeee......eeeeee....ee...............ee.................hhhhh.eeeehhhhhh...hhhhhhhhhhhhhhhh..eeee...ee............eeeee.....hhhhhhhhhhhhhhh..eeeeee..........hhhhhh...eeeeeee..eeee...hhhhhhhhhhhhhhhhhhh...eeee.hhhhh......hhhhhhhhhhhhhh.....eeee......................eeehhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhhhh......................hhh.eee...hhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh...........hhhhhhhhhhhhhhhhhhhh........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee..eeeeeeee..eeeeeeee.....ee......eeeeee......ee...eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m07 A   6 FCKSWGAEYIAADVVRFRLWATGQQKVMLRLAGKDQEMQANGDGWFTLDVAGVTPGTEYNFVLSDGMVVPDPASRAQKTDVNGPSYVVDPGSYTWRNTGWKGSRWEQAVVYEMHTGTFTPEGTFRAAIAKLPYLAELGVTVIEVMPVAQFGGERGWGYDGVLLYAPHSAYGTPDDFKAFIDAAHGYGLSVVLDIVLNHFGPEGNYLPLLAPAFFHKERMTPWGNGIAYDVDAVRRYIIEAPLYWLTEYHLDGLRFDAIDQIEDSSARHVLVEIAQRIREDITDRPIHLTTEDSRNIISLHPRDQDGNAPLFTAEWNDDFHNAVHVFATGETQAYYNDFADAPEKHLARALAEGFAYQGEISPQTGEPRGVKSTGQPPVAFVDFIQNHDQVGNRAQGDRLITLAGAERTKVLLATLLLSPHIPLLFMGEEYGESRPFLFFTDFHGDLARAVREGRAKEFADHAGENVPDPNAPETFQRSKLNWKQQHSEEGKAWLAFTRELLLLRQKHIVPLLSAARESSGTVLQTAPGFIAVSWRFPGGTLSLALNISATTVLLPDLPGKTLFAWPNESTGSLSQHSLIVRLAQ 589
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585
   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 3M07)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M07)

(-) Pfam Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Clan: GHD (106)
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8ZPF0_SALTY | Q8ZPF0)
molecular function
    GO:0033942    4-alpha-D-(1->4)-alpha-D-glucanotrehalose trehalohydrolase activity    Catalysis of the hydrolysis of alpha-(1->4)-D-glucosidic linkage in 4-alpha-D-{(1->4)-alpha-D-glucanosyl}n trehalose to yield trehalose and alpha-(1->4)-D-glucan.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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: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:0005992    trehalose biosynthetic process    The chemical reactions and pathways resulting in the formation of trehalose, a disaccharide isomeric with sucrose and obtained from certain lichens and fungi.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    BTB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PGE  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Trp A:570 - Pro A:571   [ 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
  3m07
    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
  Q8ZPF0_SALTY | Q8ZPF0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  Q8ZPF0_SALTY | Q8ZPF0
    Protein Disorder Prediction: DisEMBL | 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 3M07)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3M07)