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 FULL-LENGTH E.COLI TOPOISOMERASE I IN COMPLEX WITH SSDNA
 
Authors :  K. Tan, B. Chen, Y. C. Tse-Dinh
Date :  20 Nov 14  (Deposition) - 04 Nov 15  (Release) - 06 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Topoisomerase 1A, Isomerase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, Q. Zhou, B. Cheng, Z. Zhang, A. Joachimiak, Y. C. Tse-Dinh
Structural Basis For Suppression Of Hypernegative Dna Supercoiling By E. Coli Topoisomerase I.
Nucleic Acids Res. V. 43 11031 2015
PubMed-ID: 26490962  |  Reference-DOI: 10.1093/NAR/GKV1073

(-) Compounds

Molecule 1 - DNA TOPOISOMERASE 1
    Chains: A
    EC Number: 5.99.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLIC-HK
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ECDH1ME8569_1213, ECDH1_2375, ESCHERICHIA COLI, TOPA
    Organism Scientific: ESCHERICHIA COLI DH1
    Organism Taxid: 536056
    Strain: DH1
    Synonym: DNA TOPOISOMERASE I
 
Molecule 2 - SINGLE STRAND DNA
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION
3ZN4Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:599 , CYS A:602 , CYS A:619 , CYS A:630 , THR A:632BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWARECYS A:662 , CYS A:665 , CYS A:683 , CYS A:689BINDING SITE FOR RESIDUE ZN A 1002
3AC3SOFTWARECYS A:711 , CYS A:714 , CYS A:731 , CYS A:736BINDING SITE FOR RESIDUE ZN A 1003
4AC4SOFTWAREHIS A:566 , ASP A:570BINDING SITE FOR RESIDUE ZN A 1004
5AC5SOFTWAREARG A:169 , ARG A:173 , TYR A:177 , HOH A:1129BINDING SITE FOR RESIDUE SO4 A 1005
6AC6SOFTWAREARG A:114 , ARG A:161 , ALA A:554 , HOH A:1118BINDING SITE FOR RESIDUE SO4 A 1006
7AC7SOFTWAREGLY A:300 , GLU A:479 , ARG A:515BINDING SITE FOR RESIDUE SO4 A 1007
8AC8SOFTWAREARG A:515 , ARG A:516 , HOH A:1128BINDING SITE FOR RESIDUE SO4 A 1008
9AC9SOFTWARETYR A:83 , TRP A:121 , ASN A:163 , GLN A:166 , TRP A:560BINDING SITE FOR RESIDUE GOL A 1009

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:686 -Pro A:687
2Phe A:786 -Pro A:787

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RUL)

(-) 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:823
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhh.....eeeee.....ee....hhhhhhhhhhh...........ee...hhhhhhhhhhhhhheeeeee....hhhhhhhhhhhhhhhh.hhh.eee......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh....eeeeeeeeee.....eee.eeeee........hhhhhhhhhhhhhh..eeeeeeeeeeeee......hhhhhhhhhhhh...hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhh........................hhhhh...hhhhhhhhhhhhhhhhhh....eeeeeeeeeeee..eeeeeeeeeeeehhhhhh....................eeeeeeeeeeeee.......hhhhhhhhhhhh......hhhhhhhhh.....eeee..eeeehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee......eeeeee....eeeee.....hhhhh...eee.ee........hhhhhhhhhhhh..........eeeeeee..eeeeee........eee..............ee......eeeeee....eeeee........ee.hhhhh........eeeeeee......eeeeeee..eeeeee........ee......hhhhhhhhhhhhhh...eeee..........eeee..eeeee....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rul A   2 GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTKDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMVLTSIDCPTCGRKMGIRTASTGVFLGCSGYALPPKERCKTTINLVPENEVLNVLEGEDAETNALRAKRRCPKCGTAMDSYLIDPKRKLHVCGNNPTCDGYEIEEGEFRIKGYDGPIVECEKCGSEMHLKMGRFGKYMACTNEECKNTRKILRNGEVAPPKEDPVPLPELPCEKSDAYFVLRDGAAGVFLAANTFPKSRETRAPLVEEFRDRLPEKLRYLADAPNKTMVRFSRKTKQQYVSSEKGWSAFYVDGKWVE 862
                                    11        21        31       |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     ||365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795   ||  808       818|      834       844|      859   
                                                                39|                                                                                                                                                                                                                                                                                                      358|                                                                                                                                                                                                                                                                                                                                                                                                                                                  799|            818|                844|            
                                                                 61                                                                                                                                                                                                                                                                                                       362                                                                                                                                                                                                                                                                                                                                                                                                                                                   803             825                 850            


Chain B from PDB  Type:DNA  Length:13
                                             
                 4rul B  17 TATGCGATTTGGG  29
                                    26
   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 4RUL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:686 - Pro A:687   [ RasMol ]  
    Phe A:786 - Pro A:787   [ 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
  4rul
    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
  TOP1_ECOLI | P06612
    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)
  5.99.1.2
    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
  TOP1_ECOLI | P06612
    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
        TOP1_ECOLI | P06612: 1cy0 1cy1 1cy2 1cy4 1cy6 1cy7 1cy8 1cy9 1cyy 1ecl 1mw8 1mw9 1yua 3pwt 3px7

(-) Related Entries Specified in the PDB File

3pwt A N-TERMINAL DOMAINS MUTANT OF E.COLI TOPOISOMERASE I
3px7 A COVALENT COMPLEX OF E.COLI TOPOISOMERASE I N-TERMINAL DOMAINS IN COMPLEX WITH CLEAVED SSDNA