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 A PILZ-CONTAINING PROTEIN (PP4397) FROM PSEUDOMONAS PUTIDA KT2440 AT 2.25 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  30 Mar 06  (Deposition) - 25 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Pilz-Containing Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Motor Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Hypothetical Protein (Np_746511. 1) Fro Pseudomonas Putida Kt2440 At 2. 25 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN PP4397
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_746511.1
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 160488
    Strain: KT2440

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:59 , LEU A:61 , TRP A:92 , LEU A:98 , HOH A:273 , HOH A:278BINDING SITE FOR RESIDUE EDO A 248
2AC2SOFTWAREGLU A:116 , HIS A:203 , TYR A:204 , GLU A:205 , GLU A:206 , HOH A:269BINDING SITE FOR RESIDUE EDO A 249
3AC3SOFTWAREPRO A:8 , GLN A:9 , HIS A:120 , GLN A:121 , ARG A:122 , ALA A:125BINDING SITE FOR RESIDUE EDO A 250

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GJG)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:65 -Pro A:66
2Asn A:188 -Pro A:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GJG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GJG)

(-) Exons   (0, 0)

(no "Exon" information available for 2GJG)

(-) 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:247
 aligned with YCGR_PSEPK | Q88EQ6 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:247
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
           YCGR_PSEPK     1 MFNESDAPQPPKVLSTPLEIAANLRQLQESHDPLIITFHDRSHRFQSYVVHVDRESNTLALDEMIPRDGEKFIENGEHFRVEGFHDGVRIAWECDHALKISEVDGHRCYSGPLPQEVTYHQRRNAFRAALKLSQLVDIILDGAHLKGNGAMRGKLLDISATGCKLRFEGNVEDRLQLGQVYERFKAGNPLGLVDTMVELRHLHYEERINTTFAGVRFHNLSGQAQRKIESFVYQLQREARRFDKDDY 247
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------2gjgA01 A:11-121 Electron Transport, Fmn-binding Protein; Chain A                                              2gjgA02 A:122-247 predicted glycosyltransferase like domains                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee.hhhhhhhhhhhhhhh...eeeee......eee.eeeee....eeeee...hhhhhhhhhh...eeeeeee..eeeeeee....eeeee..eeeeee.....eeee.hhhhhhhhh......eeeee.........eeeeeeee...eeeeeee..hhhhh....eeeeeee.....eeeeeeeeeeeeeehhh.eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gjg A   1 mFNESDAPQPPKVLSTPLEIAANLRQLQESHDPLIITFHDRSHRFQSYVVHVDRESNTLALDEmIPRDGEKFIENGEHFRVEGFHDGVRIAWECDHALKISEVDGHRCYSGPLPQEVTYHQRRNAFRAALKLSQLVDIILDGAHLKGNGAmRGKLLDISATGCKLRFEGNVEDRLQLGQVYERFKAGNPLGLVDTmVELRHLHYEERINTTFAGVRFHNLSGQAQRKIESFVYQLQREARRFDKDDY 247
                            |       10        20        30        40        50        60   |    70        80        90       100       110       120       130       140       150|      160       170       180       190     | 200       210       220       230       240       
                            |                                                             64-MSE                                                                                151-MSE                                      196-MSE                                               
                            1-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 2GJG)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GJG)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (YCGR_PSEPK | Q88EQ6)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0035438    cyclic-di-GMP binding    Interacting selectively and non-covalently with cyclic-di-GMP, cyclic dimeric guanosine monophosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0071973    bacterial-type flagellum-dependent cell motility    Cell motility due to the motion of one or more bacterial-type flagella. A bacterial-type flagellum is a motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope.
    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.
    GO:0071945    regulation of bacterial-type flagellum-dependent cell motility by regulation of motor speed    A process that modulates flagellum-dependent motility in bacteria by modulating the speed or direction of rotation of a rotary flagellar motor, mediated by interactions between the braking protein.
cellular component
    GO:0009288    bacterial-type flagellum    A motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope.
    GO:0009425    bacterial-type flagellum basal body    One of the three major substructures of the flagellin-based flagellum; a structure consisting of a rod, a series of rings, the Mot proteins, the switch complex and the flagellum-specific export apparatus. The rings anchor the flagellum to the cytoplasmic membrane (MS ring), the peptidoglycan (P ring) and the outer membrane (L ring). Examples of this component are found in bacteria.

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:188 - Pro A:189   [ RasMol ]  
    Ile A:65 - Pro A:66   [ 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
  2gjg
    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
  YCGR_PSEPK | Q88EQ6
    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)
  (no 'Enzyme Classificator' available)
    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
  YCGR_PSEPK | Q88EQ6
    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
        YCGR_PSEPK | Q88EQ6: 3kyf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2GJG)