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 :  CRYSTAL STRUCTURE OF THE DNAI
 
Authors :  K. L. Tsai, Y. H. Lo, Y. J. Sun, C. D. Hsiao
Date :  08 Dec 08  (Deposition) - 22 Dec 09  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dnai, Helicase, Atp-Binding, Nucleotide-Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. L. Tsai, Y. H. Lo, Y. J. Sun, C. D. Hsiao
Molecular Interplay Between The Replicative Helicase Dnac And Its Loader Protein Dnai From Geobacillus Kaustophilus.
J. Mol. Biol. V. 393 1056 2009
PubMed-ID: 19744498  |  Reference-DOI: 10.1016/J.JMB.2009.09.002

(-) Compounds

Molecule 1 - PRIMOSOME COMPONENT (HELICASE LOADER)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 108-309
    Organism Scientific: GEOBACILLUS KAUSTOPHILUS HTA426
    Organism Taxid: 235909
    Synonym: DNAI

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:133 , VAL A:134 , GLY A:171 , VAL A:172 , GLY A:173 , LYS A:174 , THR A:175 , TYR A:176 , ARG A:308 , MG A:1311 , HOH A:2071 , HOH A:2072 , HOH A:2074BINDING SITE FOR RESIDUE ADP A1310
2AC2SOFTWAREGLY B:1171 , VAL B:1172 , GLY B:1173 , LYS B:1174 , THR B:1175 , HOH B:2047 , HOH B:2048 , HOH B:2091BINDING SITE FOR RESIDUE PO4 B2305
3AC3SOFTWARETHR A:175 , ADP A:1310 , HOH A:2045 , HOH A:2073 , HOH A:2074BINDING SITE FOR RESIDUE MG A1311

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W58)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2W58)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W58)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W58)

(-) Exons   (0, 0)

(no "Exon" information available for 2W58)

(-) 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:188
 aligned with Q5KWD0_GEOKA | Q5KWD0 from UniProtKB/TrEMBL  Length:313

    Alignment length:199
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300         
        Q5KWD0_GEOKA    111 KRQESLIQSMFMPREILRASLSDVDLNDDGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVYVPELFRELKHSLQDQTMNEKLDYIKKVPVLMLDDLGAEAMSSWVRDDVFGPILQYRMFENLPTFFTSNFDMQQLAHHLTYSQRGEEEKVKAARIMERIRYLAYPIEITGPNRR  309
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2w58A01 A:111-303 P-loop containing nucleotide triphosphate hydrolases                                                                                                                           ------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheeee..hhhhhh.........hhhhhhhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhhhhh....eeeeehhhhhhhh...---..hhhhhhhhhhh.eeeeeee...---.hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhh....-----.hhhhhhhhhhhhheeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2w58 A  111 KRQESLIQSMFMPREILRASLSDVDLNDDGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVYVPELFRELKHS---QTMNEKLDYIKKVPVLMLDDLGAE---SWVRDDVFGPILQYRMFENLPTFFTSNFDMQQLAHHLTYSQ-----KVKAARIMERIRYLAYPIEITGPNRR  309
                                   120       130       140       150       160       170       180       190       200      |  -|      220       230   |   240       250       260       270       | -   |   290       300         
                                                                                                                          207 211                    234 238                                     278   284                         


Chain B from PDB  Type:PROTEIN  Length:188
 aligned with Q5KWD0_GEOKA | Q5KWD0 from UniProtKB/TrEMBL  Length:313

    Alignment length:193
                                   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301   
        Q5KWD0_GEOKA    112 RQESLIQSMFMPREILRASLSDVDLNDDGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVYVPELFRELKHSLQDQTMNEKLDYIKKVPVLMLDDLGAEAMSSWVRDDVFGPILQYRMFENLPTFFTSNFDMQQLAHHLTYSQRGEEEKVKAARIMERIRYLAYPIEIT  304
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2w58B01 B:1112-1303 P-loop containing nucleotide triphosphate hydrolases                                                                                                                        - CATH domains
           Pfam domains (1) ----------------IstB_IS21-2w58B01 B:1128-1296                                                                                                                                            -------- Pfam domains (1)
           Pfam domains (2) ----------------IstB_IS21-2w58B02 B:1128-1296                                                                                                                                            -------- Pfam domains (2)
         Sec.struct. author ......eee..hhhhh............hhhhhhhhhhhhhhh........eeeee.....hhhhhhhhhhhhhhhh....eeeehhhhhhhhh......hhhhhhhhhhhh..eeeeee....-hhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhh.----.hhhhhhhhhhhhhhhheeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2w58 B 1112 RQESLIQSMFMPREILRASLSDVDLNDDGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVYVPELFRELKHSLQDQTMNEKLDYIKKVPVLMLDDLGAEA-SSWVRDDVFGPILQYRMFENLPTFFTSNFDMQQLAHHLTY----EEEKVKAARIMERIRYLAYPIEIT 1304
                                  1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231   | |1241      1251      1261      1271    | 1281      1291      1301   
                                                                                                                                                    1235 |                                   1276 1281                       
                                                                                                                                                      1237
   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 2W58)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5KWD0_GEOKA | Q5KWD0)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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.

 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 ]
    PO4  [ 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 2w58)
 

(-) 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
  2w58
    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
  Q5KWD0_GEOKA | Q5KWD0
    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
  Q5KWD0_GEOKA | Q5KWD0
    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 2W58)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2W58)