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 :  THE CRYSTAL STRUCTURE OF PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE ATPASE SUBUNIT OF FRANCISELLA TULARENSIS SUBSP. TULARENSIS SCHU S4
 
Authors :  K. Tan, M. Zhou, K. Kwon, W. F. Anderson, A. Joachimiak, Center For Str Genomics Of Infectious Diseases (Csgid)
Date :  15 Aug 13  (Deposition) - 28 Aug 13  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, The Center For Structural Genomics Of Infectious Diseases, Csgid, Niaid, National Institute Of Allergy And Infectious Diseases, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, M. Zhou, K. Kwon, W. F. Anderson, A. Joachimiak
The Crystal Structure Of Phosphoribosylaminoimidazole Carboxylase Atpase Subunit Of Francisella Tularensis Subsp. Tularensis Schu S4
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE, ATPASE SUBUNIT
    Chains: A
    EC Number: 4.1.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG28
    Expression System Strain: BL21(DE3)-MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: FTT_0897, PURK
    Organism Scientific: FRANCISELLA TULARENSIS SUBSP. TULARENSIS
    Organism Taxid: 177416
    Strain: SCHU S4

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 19)

Asymmetric Unit (5, 19)
No.NameCountTypeFull Name
1ACT10Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3FMT1Ligand/IonFORMIC ACID
4MSE5Mod. Amino AcidSELENOMETHIONINE
5NA2Ligand/IonSODIUM ION
Biological Unit 1 (3, 32)
No.NameCountTypeFull Name
1ACT20Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3FMT2Ligand/IonFORMIC ACID
4MSE10Mod. Amino AcidSELENOMETHIONINE
5NA-1Ligand/IonSODIUM ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:37 , VAL A:40 , HOH A:501 , HOH A:550 , HOH A:729BINDING SITE FOR RESIDUE NA A 401
02AC2SOFTWARESER A:95 , GLU A:101 , ILE A:260 , HOH A:604 , HOH A:683BINDING SITE FOR RESIDUE NA A 402
03AC3SOFTWARECYS A:35BINDING SITE FOR RESIDUE CL A 403
04AC4SOFTWAREALA A:18 , SER A:278 , HOH A:503 , HOH A:525 , HOH A:580 , HOH A:609BINDING SITE FOR RESIDUE ACT A 404
05AC5SOFTWAREPHE A:150 , VAL A:151 , LYS A:357 , HOH A:658BINDING SITE FOR RESIDUE ACT A 405
06AC6SOFTWARELYS A:2 , LYS A:232 , ILE A:233 , LYS A:236 , HOH A:561 , HOH A:700 , HOH A:755 , HOH A:803BINDING SITE FOR RESIDUE ACT A 406
07AC7SOFTWAREGLY A:30 , LYS A:31 , ASN A:32 , VAL A:43 , ASP A:45 , HOH A:545BINDING SITE FOR RESIDUE ACT A 407
08AC8SOFTWAREILE A:110 , ALA A:111 , LEU A:255 , HOH A:723BINDING SITE FOR RESIDUE ACT A 408
09AC9SOFTWAREHOH A:553 , HOH A:784BINDING SITE FOR RESIDUE ACT A 409
10BC1SOFTWARELYS A:2 , HIS A:27 , GLN A:60 , HOH A:708 , HOH A:737 , HOH A:758BINDING SITE FOR RESIDUE ACT A 410
11BC2SOFTWARELYS A:328 , HOH A:567 , HOH A:626 , HOH A:654 , HOH A:655 , HOH A:718BINDING SITE FOR RESIDUE ACT A 411
12BC3SOFTWARETHR A:296 , SER A:297 , ARG A:298 , HOH A:689BINDING SITE FOR RESIDUE ACT A 412
13BC4SOFTWAREASN A:80 , SER A:88 , ALA A:89 , HOH A:519 , HOH A:538 , HOH A:774BINDING SITE FOR RESIDUE ACT A 413
14BC5SOFTWAREARG A:334BINDING SITE FOR RESIDUE FMT A 414

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M9U)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Tyr A:86 -Pro A:87
2Leu A:133 -Pro A:134
3Ala A:216 -Pro A:217

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M9U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M9U)

(-) Exons   (0, 0)

(no "Exon" information available for 4M9U)

(-) 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:365
                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh.eeeee......hhhhh.eee.....hhhhhhhhhh...eeee.....hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhh..eeeee.........eeee...hhhhhhhhhhh.....eeeee.....eeeeeeeee.....eee...eeeeee..eeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeeeeee..eeeeeeee...hhhhhhhhhhh..hhhhhhhhhhh...........eeeeeee....hhhhhhh....eeee.........eeeeeeee..hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m9u A   1 mKIGIIGAGQLARmLSLAGTPLGLEFHCLGKNGDCAEEVVKTVTDIELTKVNDVVAWAKQFDVITFENENISHELIKAINHEVSVYPSAKAIAISQDRLLEKSFmQDHGIATAKFVNIDSLAKLQSAVDDHGLPAILKTRRFGYDGKGQFVIRSQEDITKAWDVLKDAPDGLIYEAFVDFDYEVSQICTADLKGNIAFYPLARNTHKQGIIVESEAPFENVVLAEKAQQIAKILVKEFAYVGTLAIEFFVKGDELIVNEIAPRVHNSGHWSIDGAVTSQFENHVRAIAGLILGDTTSRKTVmLNCIGGmPATKDLAALDRVKIHSYNKEPRKGRKVGHLNLNLNDETDEYQLLQVKKLIALSEEI 365
                            |       10   |    20        30        40        50        60        70        80        90       100    |  110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 |     310       320       330       340       350       360     
                            |           14-MSE                                                                                    105-MSE                                                                                                                                                                                              302-MSE  |                                                        
                            1-MSE                                                                                                                                                                                                                                                                                                             309-MSE
   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 4M9U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M9U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M9U)

(-) 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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
    Ala A:216 - Pro A:217   [ RasMol ]  
    Leu A:133 - Pro A:134   [ RasMol ]  
    Tyr A:86 - Pro A:87   [ 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
  4m9u
    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
  Q5NGE8_FRATT | Q5NGE8
    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)
  4.1.1.21
    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
  Q5NGE8_FRATT | Q5NGE8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q5NGE8_FRATT | Q5NGE8: 4ma0 4ma5 4mam 5jqw

(-) Related Entries Specified in the PDB File

4ma0 4ma5 4mam