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 :  COMPLEX OF ATP-ACTIN WITH THE C-TERMINAL ACTIN-BINDING DOMAIN OF TROPOMODULIN
 
Authors :  J. N. Rao, R. Dominguez
Date :  14 May 14  (Deposition) - 30 Jul 14  (Release) - 06 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,G
Keywords :  Tmod, Actin Filament, Pointed-End Capping Protein, Tropomyosin, Contractile Protein, Actin-Binding Protein, Contractile Protein- Actin-Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. N. Rao, Y. Madasu, R. Dominguez
Actin Cytoskeleton. Mechanism Of Actin Filament Pointed-End Capping By Tropomodulin.
Science V. 345 463 2014
PubMed-ID: 25061212  |  Reference-DOI: 10.1126/SCIENCE.1256159

(-) Compounds

Molecule 1 - ACTIN, ALPHA SKELETAL MUSCLE
    Chains: A
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Synonym: ALPHA-ACTIN-1
    Tissue: SKELETAL MUSCLE
 
Molecule 2 - GELSOLIN,TROPOMODULIN-1 CHIMERA
    Chains: G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTYB11
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: GELSOLIN (UNP RESIDUES 12-136), GGSGGSGGS LINKER, TMOD1 ACTIN-BINDING SITE 2 (UNP RESIDUES 160-349)
    Gene: GSN, TMOD1, D9S57E, TMOD
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AGEL,ACTIN-DEPOLYMERIZING FACTOR,ADF,BREVIN,ERYTHROCYTE TROPOMODULIN,E-TMOD

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CA3Ligand/IonCALCIUM ION
3HIC1Mod. Amino Acid4-METHYL-HISTIDINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:13 , SER A:14 , GLY A:15 , LEU A:16 , LYS A:18 , GLY A:156 , ASP A:157 , GLY A:158 , VAL A:159 , GLY A:182 , ARG A:210 , LYS A:213 , GLU A:214 , GLY A:301 , GLY A:302 , THR A:303 , MET A:305 , TYR A:306 , LYS A:336 , CA A:402 , HOH A:517 , HOH A:532 , HOH A:533 , HOH A:541 , HOH A:545binding site for residue ATP A 401
2AC2SOFTWAREATP A:401 , HOH A:510 , HOH A:511 , HOH A:512 , HOH A:532 , HOH A:541binding site for residue CA A 402
3AC3SOFTWAREGLU A:167 , ASP G:136 , GLY G:141 , ALA G:143 , HOH G:1525 , HOH G:1528binding site for residue CA A 403
4AC4SOFTWAREGLY G:92 , ASP G:93 , GLU G:124 , VAL G:172 , HOH G:1521 , HOH G:1574binding site for residue CA G 1401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:244 -Gly A:245

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PKI)

(-) 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:371
                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeeee.......eeee..eeee.....hhhhh....eehhhhhhh...eeee..ee..ee.hhhhhhhhhhhhhhh....hhhhh.eeeee....hhhhhhhhhhhhhhh....eeeeeehhhhhhhhh....eeeeee....eeeeeee..ee.hhhheee..hhhhhhhhhhhhhhh.........hhhhhhhhhhhhh....hhhhhhhhhhhh....eeee.....eeee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.eeeehhhhh..hhhhhhhhhhhhhh.......ee......hhhhhhhhhhhhh.......eehhhhhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4pki A    5 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEhGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF  375
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374 
                                                                                               73-HIC                                                                                                                                                                                                                                                                                                          


Chain G from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhh....eeeeeeee..eeee.hhhhh.eee...eeeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhh......eee.....................hhhhhhhhhhh......eee.......hhhhhhhhhhhhh......eee......hhhhhhhhhhhhh......eee......hhhhhhhhhhhhhhh....eee........hhhhhhhhhhhhh......eee....hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4pki G   52 MVVEHPEFLKAGKEPGLQIWRVEKFDLVPVPTNLYGDFFTGDAYVILKTVQLRNGNLQYDLHYWLGNECSQDESGAAAIFTVQLDDYLNGRAVQHREVQGFESATFLGYFKSGLKYKKGGVASGFGYKPVPDEEPNSTDVEETLERIKNNDPKLEEVNLNNIRNIPIPTLKAYAEALKENSYVKKFSIVGTRSNDPVAYALAEMLKENKVLKTLNVESNFISGAGILRLVEALPYNTSLVEMKIDNQSQPLGNKVEMEIVSMLEKNATLLKFGYHFTQQGPRLRASNAMMNNNDLVRKRRLADLTG 1349
                                    61        71        81        91       101       111       121       131       141       151       161       171     |1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323      1333      1343      
                                                                                                                                                       177|                                                                                                                                                                                   
                                                                                                                                                       1170
   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 4PKI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (92, 103)

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
    ATP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HIC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:244 - Gly A:245   [ RasMol ]  
 

(-) 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
  4pki
    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
  ACTS_RABIT | P68135
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  GELS_HUMAN | P06396
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  TMOD1_HUMAN | P28289
    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
  ACTS_RABIT | P68135
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  GELS_HUMAN | P06396
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TMOD1_HUMAN | P28289
    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
        ACTS_RABIT | P68135: 1alm 1atn 1eqy 1esv 1h1v 1ijj 1j6z 1kxp 1lcu 1lot 1m8q 1ma9 1mvw 1nwk 1o18 1o19 1o1a 1o1b 1o1c 1o1d 1o1e 1o1f 1o1g 1p8z 1qz5 1qz6 1rdw 1rfq 1rgi 1s22 1sqk 1t44 1uy5 1wua 1y64 1yxq 2a3z 2a40 2a41 2a42 2a5x 2asm 2aso 2asp 2d1k 2ff3 2ff6 2fxu 2gwj 2gwk 2hmp 2pav 2pbd 2q0r 2q0u 2q1n 2q31 2q36 2q97 2v51 2v52 2vcp 2vyp 2w49 2w4u 2y83 2yje 2yjf 2zwh 3b5u 3buz 3cjb 3cjc 3daw 3ffk 3g37 3hbt 3j4k 3j8a 3j8i 3j8j 3j8k 3jbi 3jbj 3jbk 3m1f 3m3n 3m6g 3mfp 3mn5 3sjh 3tpq 3tu5 3u8x 3u9z 3ue5 4a7f 4a7h 4a7l 4a7n 4b1v 4b1w 4b1x 4b1y 4b1z 4eah 4gy2 4h03 4h0t 4h0v 4h0x 4h0y 4k41 4k42 4k43 4pkg 4pkh 4pl8 4v0u 4wyb 4z94 5h53 5jlf 5kg8
        GELS_HUMAN | P06396: 1c0f 1c0g 1d4x 1dej 1eqy 1esv 1h1v 1kcq 1mdu 1nlv 1nm1 1nmd 1p8x 1p8z 1sol 1t44 1yag 1yvn 2ff3 2ff6 2fh1 2fh2 2fh3 2fh4 3a5l 3a5m 3a5n 3a5o 3ci5 3cip 3cjb 3cjc 3ffk 3ffn 3tu5 4pkg 4pkh 4s10 4z94 5dd2 5fae 5faf
        TMOD1_HUMAN | P28289: 4pkg 4pkh 4z8g 4z94

(-) Related Entries Specified in the PDB File

4pkg 4pkh