Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF INOSINE 5' MONOPHOSPHATE DEHYDROGENASE FROM LEGIONELLA PNEUMOPHILA
 
Authors :  R. Agarwal, S. C. Almo, S. Swaminathan, New York Structural Genomic Research Consortium (Nysgrc)
Date :  14 Mar 11  (Deposition) - 06 Apr 11  (Release) - 06 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (4x)
Keywords :  Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Agarwal, S. C. Almo, S. Swaminathan
Crystal Structure Of Inosine 5' Monophosphate Dehydrogenase From Legionella Pneumophila
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: PET
    Expression System Strain: BL21(DE3)RIPL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: IPG2843, LPG2843
    Organism Scientific: LEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA
    Organism Taxid: 272624
    Strain: PHILADELPHIA 1 / ATCC 33152 / DSM 7513

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3R2G)

(-) Sites  (0, 0)

(no "Site" information available for 3R2G)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R2G)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:147 -Asn A:148

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R2G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R2G)

(-) Exons   (0, 0)

(no "Exon" information available for 3R2G)

(-) 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:323
 aligned with Q5ZRN7_LEGPH | Q5ZRN7 from UniProtKB/TrEMBL  Length:337

    Alignment length:323
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323   
         Q5ZRN7_LEGPH     4 QAITFDDVLLVPSYNHHESRRVVETTSTDRLGKLTLNLPVISANMDTITESNMANFMHSKGAMGALHRFMTIEENIQEFKKCKGPVFVSVGCTENELQRAEALRDAGADFFCVDVAHAHAKYVGKTLKSLRQLLGSRCIMAGNVATYAGADYLASCGADIIKAGIGGGSVCSTRIKTGFGVPMLTCIQDCSRADRSIVADGGIKTSGDIVKALAFGADFVMIGGMLAGSAPTPGEVFQKDDGSKVKRYRGMASREAQEAFLGQMHEWKTAEGVATEVPFKENPDGIIADIIGGLRSGLTYAGADSISELQRKLNYVIVTQAGR 326
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains IMPDH-3r2gA01 A:6-328                                                                                                                                                                                                                                                                                                               Pfam domains
         Sec.struct. author ...hhh.eee................ee......ee...eee.......hhhhhhhhhhh..ee......hhhhhhhhhhh......eee..hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh...eeee......hhhhhhhhh...hhhhhhhhhh....eeeee....hhhhhhhhhhh...eeeehhhhh........eee.....eeeee..hhhhhhhhhhh.............eeee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhh..eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r2g A   6 QAITFDDVLLVPSYNHHESRRVVETTSTDRLGKLTLNLPVISANMDTITESNMANFMHSKGAMGALHRFMTIEENIQEFKKCKGPVFVSVGCTENELQRAEALRDAGADFFCVDVAHAHAKYVGKTLKSLRQLLGSRCIMAGNVATYAGADYLASCGADIIKAGIGGGSVCSTRIKTGFGVPMLTCIQDCSRADRSIVADGGIKTSGDIVKALAFGADFVMIGGMLAGSAPTPGEVFQKDDGSKVKRYRGMASREAQEAFLGQMHEWKTAEGVATEVPFKENPDGIIADIIGGLRSGLTYAGADSISELQRKLNYVIVTQAGR 328
                                    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
   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 3R2G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R2G)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5ZRN7_LEGPH | Q5ZRN7)
molecular function
    GO:0003938    IMP dehydrogenase activity    Catalysis of the reaction: inosine 5'-phosphate + NAD+ + H2O = xanthosine 5'-phosphate + NADH + H+.
    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:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    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
(no "Ligands, Modified Residues, Ions" information available for 3r2g)
 
  Sites
(no "Sites" information available for 3r2g)
 
  Cis Peptide Bonds
    Gly A:147 - Asn A:148   [ RasMol ]  
 
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 | Biol. Unit 1 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
  3r2g
    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
  Q5ZRN7_LEGPH | Q5ZRN7
    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
  Q5ZRN7_LEGPH | Q5ZRN7
    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 3R2G)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3R2G)