Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  C. ELEGANS CLP1 BOUND TO AMP-PNP, AND MG2+
 
Authors :  A. Dikfidan, B. Loll, C. Zeymer, T. Clausen, A. Meinhart
Date :  18 Jan 14  (Deposition) - 14 May 14  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Polynucleotide Kinase, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Dikfidan, B. Loll, C. Zeymer, I. Magler, T. Clausen, A. Meinhart
Rna Specificity And Regulation Of Catalysis In The Eukaryotic Polynucleotide Kinase Clp1.
Mol. Cell V. 54 975 2014
PubMed-ID: 24813946  |  Reference-DOI: 10.1016/J.MOLCEL.2014.04.005

(-) Compounds

Molecule 1 - PROTEIN CLPF-1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CLPF-1, F59A2.4
    Organism Common: NEMATODE
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
12PE1Ligand/IonNONAETHYLENE GLYCOL
2ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3MG1Ligand/IonMAGNESIUM ION
4MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:16 , ARG A:18 , PHE A:39 , ARG A:56 , ALA A:58 , THR A:123 , ASP A:124 , VAL A:125 , GLY A:126 , LYS A:127 , THR A:128 , THR A:129 , ASP A:151 , SER A:282 , GLY A:284 , GLU A:286 , ARG A:288 , ARG A:293 , MG A:502 , HOH A:601 , HOH A:602 , HOH A:603 , HOH A:604 , HOH A:607 , HOH A:657BINDING SITE FOR RESIDUE ANP A 501
2AC2SOFTWARETHR A:128 , ANP A:501 , HOH A:601 , HOH A:602 , HOH A:603BINDING SITE FOR RESIDUE MG A 502
3AC3SOFTWARETRP A:62 , LEU A:88 , TYR A:137 , GLN A:141BINDING SITE FOR RESIDUE 2PE A 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OHV)

(-) Sequences/Alignments

Asymmetric/Biological 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:396
                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee...eeeeeee.....eeeeeeee..ee..ee.....eeee....eeeeee...eeeeee..eeeeeee...hhhhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhhhhh....eeee............eeeeee................eeee....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhheeee......hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhhhhhhhh........eeeeee.hhheeee....eee..hhhhh.eeeeee.....hhhhh...eeeeeeeeeee....eeeeee........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ohv A   3 EENVQEFVLKEDCELRFAAGDDSDVCLELVKGYAEIFGTELLLNKKYTFPAKSRVAAFTWKGATIELVGTTESAYVAESTPmVIYLNIHAAmEEVRKKREEQAKAKGPRLLLVGPTDVGKTTVSRILCNYSVRQGRTPIFVELDVGQNSVSVPGTVAAVLVQKTADVIDGFERNQPIVFNFGHTSPSANLSLYEALFKEmATTLNAQIQENDEAKIGGmIINTCGWVDGEGYKCIVKAASAFEVDVVIVLDHERLYSDLSKELPEFVRLTHVPKSGGVEQRTGQIRSKmRGENVHRYFYGTRANNLYPFTFDVSFDDVTLCKIGKLVImEPSADIKHHLFAFSRSTKADENVLKSPVFGFCLVTEVDLEKRTmSILCPQRTIPSKVLVFSDITHLD 423
                                    12        22        32        42        52        62        72        82 |      92 |     102  ||   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327   ||  357       367       377       387       397  |    407       417      
                                                                                                            84-MSE    94-MSE    105|                                                                                             207-MSE            226-MSE                                                               296-MSE                            331|   |                                         400-MSE                   
                                                                                                                                 111                                                                                                                                                                                                                          352   |                                                                   
                                                                                                                                                                                                                                                                                                                                                                  356-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 4OHV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    2PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ANP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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
(no "Cis Peptide Bonds" information available for 4ohv)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  4ohv
    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
  CLP1_CAEEL | P52874
    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
  CLP1_CAEEL | P52874
    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
        CLP1_CAEEL | P52874: 4ohw 4ohx 4ohy 4ohz 4oi0 4oi1 4oi2

(-) Related Entries Specified in the PDB File

4ohw 4ohx 4ohy 4ohz 4oi0 4oi1 4oi2