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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE FROM BACILLUS ANTHRACIS
 
Authors :  K. F. Tarique, S. Devi, S. A. Abdul Rehman, S. Gourinath
Date :  19 May 14  (Deposition) - 18 Jun 14  (Release) - 18 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Amino-Acid Biosynthesis, Methionine Biosynthesis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. F. Tarique, S. Devi, S. A. Abdul Rehman, S. Gourinath
Crystal Structure Of 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase From Bacillus Anthracis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE
    Chains: B, A, C
    EC Number: 3.2.2.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28(B)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MTNN, BA_4602, GBAA_4602, BAS4270
    Organism Common: ANTHRAX, ANTHRAX BACTERIUM
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 1392
    Strain: STERNE
    Synonym: MTA/SAH NUCLEOSIDASE, MTAN, 5'-METHYLTHIOADENOSINE NUCLEOSIDASE, MTA NUCLEOSIDASE, S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE, ADOHCY NUCLEOSIDASE, SAH NUCLEOSIDASE, SRH NUCLEOSIDASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1ADE3Ligand/IonADENINE
2TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ADE2Ligand/IonADENINE
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ADE2Ligand/IonADENINE
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA B:77 , GLY B:78 , PHE B:152 , MET B:153 , VAL B:172 , GLU B:173 , SER B:197 , ASP B:198 , TRS B:302BINDING SITE FOR RESIDUE ADE B 301
2AC2SOFTWAREALA B:8 , GLU B:12 , SER B:76 , GLU B:173 , MET B:174 , GLU B:175 , ARG B:194 , ADE B:301 , HIS C:236BINDING SITE FOR RESIDUE TRS B 302
3AC3SOFTWAREALA A:77 , GLY A:78 , PHE A:152 , MET A:153 , VAL A:172 , GLU A:173 , SER A:197 , ASP A:198 , TRS A:302BINDING SITE FOR RESIDUE ADE A 301
4AC4SOFTWAREALA A:8 , GLU A:12 , SER A:76 , GLU A:173 , MET A:174 , GLU A:175 , ARG A:194 , PHE A:208 , ADE A:301 , HIS B:236BINDING SITE FOR RESIDUE TRS A 302
5AC5SOFTWAREALA C:8 , GLU C:12 , SER C:76 , GLU C:173 , MET C:174 , GLU C:175 , ARG C:194 , PHE C:208 , ADE C:302BINDING SITE FOR RESIDUE TRS C 301
6AC6SOFTWAREALA C:77 , GLY C:78 , PHE C:152 , MET C:153 , VAL C:172 , GLU C:173 , SER C:197 , ASP C:198 , PHE C:208 , TRS C:301BINDING SITE FOR RESIDUE ADE C 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QEZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4QEZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QEZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QEZ)

(-) Exons   (0, 0)

(no "Exon" information available for 4QEZ)

(-) 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:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhheeeeeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhhh...eeee..eeee.........eeeeeeeee....hhhhh............ee.hhhhhhhhhhh..eeeeeeee......hhhhhhhhhh....eeeee.hhhhhhhhhhhhh..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qez A   2 RIAVIGAMEEEVRILRDKLEQAETETVAGCEFTKGQLAGHEVILLKSGIGKVNAAMSTTILLERYKPEKVINTGSAGGFHHSLNVGDVVISTEVRHHDVDVTAFNYEYGQVPGMPPGFKADEALVALAEKCMQVVKGMIATGDSFMSDPNRVAAIRDKFENLYAVEMEAAAVAQVCHQYEVPFVIIRALSDIAGKESNVSFDQFLDQAALHSTNFIVKVLEEL 230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 ||    147       157       167       177       187       197       207       217       227   
                                                                                                                                                             133|                                                                                          
                                                                                                                                                              140                                                                                          


Chain B from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhheeeeeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhhh...eeee..eeee.........eeeeeeeee....hhhhh............ee.hhhhhhhhhhhh..eeeeeeee......hhhhhhhhhh....eeeee.hhhhhhhhhhhhh..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qez B   2 RIAVIGAMEEEVRILRDKLEQAETETVAGCEFTKGQLAGHEVILLKSGIGKVNAAMSTTILLERYKPEKVINTGSAGGFHHSLNVGDVVISTEVRHHDVDVTAFNYEYGQVPGMPPGFKADEALVALAEKCMQQVVKGMIATGDSFMSDPNRVAAIRDKFENLYAVEMEAAAVAQVCHQYEVPFVIIRALSDIAGKESNVSFDQFLDQAALHSTNFIVKVLEELKLEHHHH 237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131  ||   146       156       166       176       186       196       206       216       226       236 
                                                                                                                                                              134|                                                                                                 
                                                                                                                                                               140                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhheeeeeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhhh...eeee..eeee.........eeeeeeeee....hhhhh............ee.hhhhhhhhhhh...eeeeeeee......hhhhhhhhhh....eeeee.hhhhhhhhhhhhh..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qez C   2 RIAVIGAMEEEVRILRDKLEQAETETVAGCEFTKGQLAGHEVILLKSGIGKVNAAMSTTILLERYKPEKVINTGSAGGFHHSLNVGDVVISTEVRHHDVDVTAFNYEYGQVPGMPPGFKADEALVALAEKCMQQVVKGMIATGDSFMSDPNRVAAIRDKFENLYAVEMEAAAVAQVCHQYEVPFVIIRALSDIAGKESNVSFDQFLDQAALHSTNFIVKVLEELKLEHHHH 237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131  ||   146       156       166       176       186       196       206       216       226       236 
                                                                                                                                                              134|                                                                                                 
                                                                                                                                                               140
   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 4QEZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QEZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QEZ)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

 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
    ADE  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4qez)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4qez
    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
  MTNN_BACAN | Q81LL4
    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)
  3.2.2.9
    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
  MTNN_BACAN | Q81LL4
    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 4QEZ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4QEZ)