Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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 :  1.65 ANGSTROM STRUCTURE OF THE DYNEIN LIGHT CHAIN 1 FROM PLASMODIUM FALCIPARUM
 
Authors :  J. R. Walker, J. Lew, M. Amani, Z. Alam, G. Wasney, K. Boulanger, M. Sunds C. Arrowsmith, A. Edwards, R. Hui, A. Bochkarev, M. Vedadi, Structura Genomics Consortium (Sgc)
Date :  26 Jan 05  (Deposition) - 15 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (2x)
Keywords :  Structural Genomics Consortium, Dynein Light Chain, Microtubule, Malaria, Sgc, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Vedadi, J. Lew, J. Artz, M. Amani, Y. Zhao, A. Dong, G. A. Wasney, M. Gao, T. Hills, S. Brokx, W. Qiu, S. Sharma, A. Diassiti, Z. Alam, M. Melone, A. Mulichak, A. Wernimont, J. Bray, P. Loppnau, O. Plotnikova, K. Newberry, E. Sundararajan, S. Houston, J. Walker, W. Tempel, A. Bochkarev, I. Kozieradzki, A. Edwards, C. Arrowsmith, D. Roos, K. Kain, R. Hui
Genome-Scale Protein Expression And Structural Biology Of Plasmodium Falciparum And Related Apicomplexan Organisms.
Mol. Biochem. Parasitol. V. 151 100 2007
PubMed-ID: 17125854  |  Reference-DOI: 10.1016/J.MOLBIOPARA.2006.10.011

(-) Compounds

Molecule 1 - DYNEIN LIGHT CHAIN 1
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-LIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PFL0660W
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A C
Biological Unit 2 (2x):  B 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1YO3)

(-) Sites  (0, 0)

(no "Site" information available for 1YO3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YO3)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Pro A:46 -Thr A:47
2Pro B:46 -Thr B:47
3Pro C:46 -Thr C:47

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YO3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YO3)

(-) Exons   (0, 0)

(no "Exon" information available for 1YO3)

(-) 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:85
 aligned with Q8I5R9_PLAF7 | Q8I5R9 from UniProtKB/TrEMBL  Length:93

    Alignment length:85
                                    18        28        38        48        58        68        78        88     
          Q8I5R9_PLAF7    9 NAVVKNVDMTEEMQIDAIDCANQALQKYNVEKDIAAHIKKEFDRKYDPTWHCVVGRNFGSYVTHETKNFIYFYIGQVAILLFKSG 93
               SCOP domains d1yo3a_ A: automated matches                                                          SCOP domains
               CATH domains 1yo3A00 A:-1-83 Protein Inhibitor Of Neuronal Nitric Oxide Synthase;                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeee......eee....eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                  1yo3 A -1 GSVVKNVDMTEEMQIDAIDCANQALQKYNVEKDIAAHIKKEFDRKYDPTWHCVVGRNFGSYVTHETKNFIYFYIGQVAILLFKSG 83
                                     8        18        28        38        48        58        68        78     


Chain B from PDB  Type:PROTEIN  Length:85
 aligned with Q8I5R9_PLAF7 | Q8I5R9 from UniProtKB/TrEMBL  Length:93

    Alignment length:85
                                    18        28        38        48        58        68        78        88     
          Q8I5R9_PLAF7    9 NAVVKNVDMTEEMQIDAIDCANQALQKYNVEKDIAAHIKKEFDRKYDPTWHCVVGRNFGSYVTHETKNFIYFYIGQVAILLFKSG 93
               SCOP domains d1yo3b_ B: automated matches                                                          SCOP domains
               CATH domains 1yo3B00 B:-1-83 Protein Inhibitor Of Neuronal Nitric Oxide Synthase;                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeee.........eeeeeeeeeee..eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                  1yo3 B -1 GSVVKNVDMTEEMQIDAIDCANQALQKYNVEKDIAAHIKKEFDRKYDPTWHCVVGRNFGSYVTHETKNFIYFYIGQVAILLFKSG 83
                                     8        18        28        38        48        58        68        78     


Chain C from PDB  Type:PROTEIN  Length:85
 aligned with Q8I5R9_PLAF7 | Q8I5R9 from UniProtKB/TrEMBL  Length:93

    Alignment length:85
                                    18        28        38        48        58        68        78        88     
          Q8I5R9_PLAF7    9 NAVVKNVDMTEEMQIDAIDCANQALQKYNVEKDIAAHIKKEFDRKYDPTWHCVVGRNFGSYVTHETKNFIYFYIGQVAILLFKSG 93
               SCOP domains d1yo3c_ C: automated matches                                                          SCOP domains
               CATH domains 1yo3C00 C:-1-83 Protein Inhibitor Of Neuronal Nitric Oxide Synthase;                  CATH domains
           Pfam domains (1) --Dynein_light-1yo3C01 C:1-83                                                         Pfam domains (1)
           Pfam domains (2) --Dynein_light-1yo3C02 C:1-83                                                         Pfam domains (2)
           Pfam domains (3) --Dynein_light-1yo3C03 C:1-83                                                         Pfam domains (3)
         Sec.struct. author ...eee...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeee......eeeeeeeeeeeeee..eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                  1yo3 C -1 GSVVKNVDMTEEMQIDAIDCANQALQKYNVEKDIAAHIKKEFDRKYDPTWHCVVGRNFGSYVTHETKNFIYFYIGQVAILLFKSG 83
                                     8        18        28        38        48        58        68        78
   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  (1, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: Dynein_light] (6)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q8I5R9_PLAF7 | Q8I5R9)
molecular function
    GO:0003777    microtubule motor activity    Catalysis of movement along a microtubule, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP).
    GO:0003774    motor activity    Catalysis of the generation of force resulting either in movement along a microfilament or microtubule, or in torque resulting in membrane scission, coupled to the hydrolysis of a nucleoside triphosphate.
biological process
    GO:0007018    microtubule-based movement    A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
    GO:0007017    microtubule-based process    Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins.
cellular component
    GO:0005868    cytoplasmic dynein complex    Any dynein complex with a homodimeric dynein heavy chain core that catalyzes movement along a microtubule. Cytoplasmic dynein complexes participate in many cytoplasmic transport activities in eukaryotes, such as mRNA localization, intermediate filament transport, nuclear envelope breakdown, apoptosis, transport of centrosomal proteins, mitotic spindle assembly, virus transport, kinetochore functions, and movement of signaling and spindle checkpoint proteins. Some complexes participate in intraflagellar transport. Subunits associated with the dynein heavy chain mediate association between dynein heavy chain and cargoes, and may include light chains and light intermediate chains.
    GO:0030286    dynein complex    Any of several large complexes that contain two or three dynein heavy chains and several light chains, and have microtubule motor activity.
    GO:0005875    microtubule associated complex    Any multimeric complex connected to a microtubule.

 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 1yo3)
 
  Sites
(no "Sites" information available for 1yo3)
 
  Cis Peptide Bonds
    Pro A:46 - Thr A:47   [ RasMol ]  
    Pro B:46 - Thr B:47   [ RasMol ]  
    Pro C:46 - Thr C:47   [ 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
  1yo3
    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
  Q8I5R9_PLAF7 | Q8I5R9
    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)
  (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
  Q8I5R9_PLAF7 | Q8I5R9
    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 1YO3)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1YO3)