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 THE CATALYTIC DOMAIN OF THE INOSINE MONOPHOSPHATE DEHYDROGENASE FROM LISTERIA MONOCYTOGENES IN THE PRESENCE OF XANTHOSINE MONOPHOSPHATE
 
Authors :  Y. Kim, M. Makowska-Grzyska, J. Osipiuk, W. F. Anderson, A. Joachimiak For Structural Genomics Of Infectious Diseases (Csgid)
Date :  04 Feb 17  (Deposition) - 05 Apr 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Alpha-Beta Structure, Tim Barrel, Impdh, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, M. Makowska-Grzyska, J. Osipiuk, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of The Catalytic Domain Of The Inosine Monophosphate Dehydrogenase From Listeria Monocytogenes In The Presence Of Xanthosine Monophosphate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.205
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG50
    Expression System Strain: BL21(DE3) MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GUAB
    Organism Scientific: LISTERIA MONOCYTOGENES SEROVAR 1/2A (STRAIN ATCC BAA-679 / EGD-E)
    Organism Taxid: 169963
    Strain: ATCC BAA-679 / EGD-E
    Synonym: IMPDH

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2XMP1Ligand/IonXANTHOSINE-5'-MONOPHOSPHATE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2XMP4Ligand/IonXANTHOSINE-5'-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:49 , MET A:51 , GLY A:305 , SER A:306 , ILE A:307 , CYS A:308 , THR A:310 , ASP A:341 , GLY A:342 , GLY A:343 , MET A:362 , GLY A:364 , SER A:365 , TYR A:388 , GLY A:390 , MET A:391 , GLY A:392 , GLU A:416 , GLY A:417 , HOH A:634 , HOH A:644 , HOH A:661 , HOH A:677 , HOH A:680 , HOH A:697binding site for residue XMP A 500
2AC2SOFTWAREHIS A:254 , SER A:441 , GLY A:444 , TYR A:445binding site for residue GOL A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:279 -Asn A:280

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UPX)

(-) 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:380
                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.......hhh.eee.......hhhhh...eeee..eee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh...ee....ee..............eeee....hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhh....eeee........hhhhhhh...hhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhh...eeee..............eee..eeeeeee...hhhhhh..................eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.eee.hhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5upx A  -2 SNAMWETKFAKEGLTFDDVLLVPAKSDVLPNDVDLSVEMAPSLKLNVPIWSAGMDTITEAKMAIAIARQGGIGVVHKNMSIEQQAEEIEKVKRSESGGIKDKVIEFPNSAKDKHGRLLAAAAVGITNDTFVRVEKLIEAGVDAIVIDTAHGHSAGVINKISEIRQTFKDVVIVAGNVATAEGARALFEVGVDIVKVGIGPGSICTTRVVAGVGVPQITAIYDCATVAREFGKTIIADGGIKYSGDIVKALAAGGNAVMLGSMLAGTDESPGETEIFQGRQFKTYRGMGSLAAMEHGDRYFQADAKKLVPEGIEGRVPYKGSVADIIFQLVGGIRSGMGYTGSPDLRHLREEAAFVRMTGAGLRESHPHDIQITKEAPNYS 486
                                     7        17        27        37        47        57        67        77        87        97||     214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394     ||406       416       426       436       446       456       466       476       486
                                                                                                                               98|                                                                                                                                                                                               400|                                                                                   
                                                                                                                               206                                                                                                                                                                                                403
   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 5UPX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    XMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:279 - Asn A:280   [ 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
[ 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
  5upx
    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
  Q926Y9_LISMO | Q926Y9
    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)
  1.1.1.205
    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
  Q926Y9_LISMO | Q926Y9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q926Y9_LISMO | Q926Y9: 5upy

(-) Related Entries Specified in the PDB File

5upy