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 HELICOBACTER PYLORI 5'-METHYLTHIOADENOSINE/S-ADENOSYL HOMOCYSTEINE NUCLEOSIDASE (MTAN) COMPLEXED WITH PYRAZINYLTHIO-DADME-IMMUCILLIN-A
 
Authors :  S. A. Cameron, S. Wang, S. C. Almo, V. L. Schramm
Date :  09 Mar 15  (Deposition) - 25 Nov 15  (Release) - 02 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Wang, S. A. Cameron, K. Clinch, G. B. Evans, Z. Wu, V. L. Schramm, P. C. Tyler
New Antibiotic Candidates Against Helicobacter Pylori.
J. Am. Chem. Soc. V. 137 14275 2015
PubMed-ID: 26494017  |  Reference-DOI: 10.1021/JACS.5B06110
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMINODEOXYFUTALOSINE NUCLEOSIDASE
    Chains: A
    EC Number: 3.2.2.30, 3.2.2.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MTNN, MTN, JHP_0082
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85963
    Strain: J99 / ATCC 700824
    Synonym: AMINOFUTALOSINE NUCLEOSIDASE,5'-METHYLTHIOADENOSINE/S- ADENOSYLHOMOCYSTEINE NUCLEOSIDASE,MTAN,6-AMINO-6-DEOXYFUTALOSINE N- RIBOSYLHYDROLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
14EH1Ligand/Ion(3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-[(PYRAZIN-2-YLSULFANYL)METHYL]PYRROLIDIN-3-OL
2GOL2Ligand/IonGLYCEROL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
14EH2Ligand/Ion(3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-[(PYRAZIN-2-YLSULFANYL)METHYL]PYRROLIDIN-3-OL
2GOL4Ligand/IonGLYCEROL
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:10 , ILE A:53 , VAL A:79 , ALA A:80 , GLY A:81 , LEU A:105 , HIS A:110 , PHE A:154 , VAL A:155 , VAL A:173 , GLU A:174 , MET A:175 , GLU A:176 , SER A:198 , ASP A:199 , ALA A:201 , PHE A:209 , HOH A:464 , HOH A:576binding site for residue 4EH A 301
2AC2SOFTWAREPHE A:114 , ALA A:119 , ILE A:120 , PHE A:121 , HOH A:549 , HOH A:558binding site for residue GOL A 302
3AC3SOFTWAREHIS A:42 , ASN A:43 , LYS A:44 , LYS A:73 , HOH A:589binding site for residue GOL A 303
4AC4SOFTWAREGLN A:153 , HOH A:429 , HOH A:437binding site for residue PEG A 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YNB)

(-) 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:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhh...eeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhh....eeeeeeeeee.........eeeeeeeee....hhhhh...........eee.hhhhhhhhhhhhhhh....eeeeeee......hhhhhhhhhhhhheeeee.hhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ynb A   2 VQKIGILGAMREEITPILELFGVDFEEIPLGGNVFHKGVYHNKEIIVAYSKIGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLKINDLLVATQLVQHDVDLSAFDHPLGFIPESAIFIETSGSLNALAKKIANEQHIALKEGVIASGDQFVHSKERKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISDNADEKAGMSFDEFLEKSAHTSAKFLKSMVDEL 231
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
   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 4YNB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    4EH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ 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 4ynb)
 
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
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  4ynb
    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
  MQMTN_HELPJ | Q9ZMY2
    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)
  3.2.2.30
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  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
  MQMTN_HELPJ | Q9ZMY2
    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
        MQMTN_HELPJ | Q9ZMY2: 3nm4 3nm5 3nm6 4ffs 4ojt 4oy3 4p54 4wkn 4wko 4wkp 4yo8 5ccd 5cce 5jpc 5k1z 5kb3

(-) Related Entries Specified in the PDB File

4ffs 4FFS CONTAINS THE SAME PROTEIN COMPLEXED WITH BUTYLTHIO-DADME- IMMUCILLIN-A
4wkn 4WKN CONTAINS THE SAME PROTEIN COMPLEXED WITH METHYLTHIO-DADME- IMMUCILLIN-A
4wko 4WKO CONTAINS THE SAME PROTEIN COMPLEXED WITH HYDROXYBUTYLTHIO- DADME-IMMUCILLIN-A
4wkp 4WKP CONTAINS THE SAME PROTEIN COMPLEXED WITH 2-(2-HYDROXYETHOXY) ETHYLTHIOMETHYL-DADME-IMMUCILLIN-A