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 :  STRUCTURE OF THE AEROPYRUM PERNIX ORC1 PROTEIN IN COMPLEX WITH DNA
 
Authors :  M. Gaudier, B. S. Schuwirth, S. L. Westcott, D. B. Wigley
Date :  30 May 07  (Deposition) - 18 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Replication, Nucleotide-Binding, Replication, Archaea, Atp-Binding, Phosphorylation, Dna Replication Initiation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Gaudier, B. S. Schuwirth, S. L. Westcott, D. B. Wigley
Structural Basis Of Dna Replication Origin Recognition By An Orc Protein.
Science V. 317 1213 2007
PubMed-ID: 17761880  |  Reference-DOI: 10.1126/SCIENCE.1143664

(-) Compounds

Molecule 1 - CELL DIVISION CONTROL PROTEIN 6 HOMOLOG
    Chains: A
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 56636
    Synonym: CDC6 HOMOLOG, ORC1
 
Molecule 2 - 5'-D(*TP*CP*TP*CP*CP*AP*CP*AP*GP*GP *AP*AP*AP*CP*GP*GP*AP*GP*GP*GP*GP*T)-3'
    Chains: B
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 56636
    Synonym: 22BP ORB4 ELEMENT
    Synthetic: YES
 
Molecule 3 - 5'-D(*AP*CP*CP*CP*CP*TP*CP*CP*GP*TP *TP*TP*CP*CP*TP*GP*TP*GP*GP*AP*GP*A)-3'
    Chains: C
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 56636
    Synonym: 22BP ORB4 ELEMENT
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:33 , PRO A:34 , GLY A:66 , THR A:67 , GLY A:68 , LYS A:69 , THR A:70 , ALA A:71 , TYR A:213 , ILE A:221 , ARG A:225 , ALA A:254 , ARG A:255 , LEU A:258 , MG A:1401BINDING SITE FOR RESIDUE ADP A1400
2AC2SOFTWARETHR A:70 , ADP A:1400BINDING SITE FOR RESIDUE MG A1401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V1U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V1U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V1U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V1U)

(-) Exons   (0, 0)

(no "Exon" information available for 2V1U)

(-) 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:382
 aligned with CDC61_AERPE | Q9YEV6 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:387
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       
          CDC61_AERPE     9 LESKIFRKRWVLLPDYVPDVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKSSLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARRALDLLRVAGEIAERRREERVRREHVYSARAEIERDRVSEVVRTLPLHAKLVLLSIMMLEDGGRPASTGEIYERYKELTSTLGLEHVTLRRVSGIISELDMLGIVKSRVVSRGRYGKTREVSLDADRLAVENALSEDPFVARLL 395
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh..........hhhhhhhhhhhhhhhh.......eee......hhhhhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhhh........hhhhhhhhhhhhhh....eeeeeee..hhhhhh.hhhhhhhhhhhhhhh.-----.eeeee..........hhhhhh....ee......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeeeee.hhh.eeeeeee..hhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v1u A  13 LESKIFRKRWVLLPDYVPDVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQEL-----VSLVGITNSLGFVENLEPRVKSSLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARRALDLLRVAGEIAERRREERVRREHVYSARAEIERDRVSEVVRTLPLHAKLVLLSIMMLEDGGRPASTGEIYERYKELTSTLGLEHVTLRRVSGIISELDMLGIVKSRVVSRGRYGKTREVSLDADRLAVENALSEDPFVARLL 399
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172 |     182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       
                                                                                                                                                                                           174   180                                                                                                                                                                                                                           


Chain B from PDB  Type:DNA  Length:22
                                                      
                 2v1u B   1 TCTCCACAGGAAACGGAGGGGT  22
                                    10        20  


Chain C from PDB  Type:DNA  Length:22
                                                      
                 2v1u C   1 ACCCCTCCGTTTCCTGTGGAGA  22
                                    10        20
   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 2V1U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V1U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2V1U)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CDC61_AERPE | Q9YEV6)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.

 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2v1u)
 

(-) 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
  2v1u
    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
  CDC61_AERPE | Q9YEV6
    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
  CDC61_AERPE | Q9YEV6
    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 2V1U)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2V1U)