Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  N-TERMINAL DOMAIN OF DNA BINDING PROTEIN
 
Authors :  M. A. Schumacher, N. Chinnam, N. K. Tonthat
Date :  03 Mar 14  (Deposition) - 11 Jun 14  (Release) - 23 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Schumacher, N. K. Tonthat, S. M. Kwong, N. B. Chinnam, M. A. Liu, R. A. Skurray, N. Firth
Mechanism Of Staphylococcal Multiresistance Plasmid Replication Origin Assembly By The Repa Protein.
Proc. Natl. Acad. Sci. Usa V. 111 9121 2014
PubMed-ID: 24927575  |  Reference-DOI: 10.1073/PNAS.1406065111

(-) Compounds

Molecule 1 - TRUNCATED REPLICATION PROTEIN REPA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 2-132
    Gene: CA347_2788
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 15)

Asymmetric Unit (1, 15)
No.NameCountTypeFull Name
1EDO15Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 30)
No.NameCountTypeFull Name
1EDO30Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:34 , ASN B:34BINDING SITE FOR RESIDUE EDO A 201
02AC2SOFTWAREARG A:15 , PHE A:16 , GLN A:18BINDING SITE FOR RESIDUE EDO A 202
03AC3SOFTWARETYR A:17 , GLN A:18 , ALA A:41 , ARG A:44BINDING SITE FOR RESIDUE EDO A 203
04AC4SOFTWAREGLU A:124 , ASN A:128 , LYS B:52 , PRO B:132BINDING SITE FOR RESIDUE EDO A 204
05AC5SOFTWARELYS A:30 , ASN B:76BINDING SITE FOR RESIDUE EDO A 205
06AC6SOFTWARELYS A:70 , LYS A:125 , EDO A:207 , ASP B:129BINDING SITE FOR RESIDUE EDO A 206
07AC7SOFTWARESER A:67 , LYS A:70 , EDO A:206BINDING SITE FOR RESIDUE EDO A 207
08AC8SOFTWAREARG A:118 , LYS A:122BINDING SITE FOR RESIDUE EDO A 208
09AC9SOFTWAREPHE A:24 , TYR B:17 , ILE B:74 , HOH B:311BINDING SITE FOR RESIDUE EDO B 201
10BC1SOFTWAREGLU B:14 , ARG B:15 , PHE B:16 , GLN B:18BINDING SITE FOR RESIDUE EDO B 202
11BC2SOFTWARETYR B:17 , GLN B:18 , ALA B:41 , ARG B:44 , ASP B:45 , HOH B:314BINDING SITE FOR RESIDUE EDO B 203
12BC3SOFTWAREGLU A:14 , GLU B:10 , LYS B:112BINDING SITE FOR RESIDUE EDO B 204
13BC4SOFTWAREASP B:35 , ILE B:38 , LEU B:75 , ILE B:85BINDING SITE FOR RESIDUE EDO B 205
14BC5SOFTWAREASN B:68 , LYS B:79 , THR B:83 , LYS B:86 , GLN B:97 , ARG B:99 , ASN B:106BINDING SITE FOR RESIDUE EDO B 206
15BC6SOFTWAREASN B:68 , GLU B:69BINDING SITE FOR RESIDUE EDO B 207

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:131 -Pro A:132

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PQL)

(-) 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:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh.eeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee........eeee.....hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pql A   2 QNQYFTVQENYKERFYQIPKVFFTSENYKNLTNDMKIAYAILRDRLNLSIKNSWVDEDGNIYFVYSNEKLMEILNCKKEKLTKIKKGLENDGLLIQKRRGLNKPNILYLMKPIVTERDIYKIEKEENDVEP 132
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 


Chain B from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.eeeeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee........eeee.....hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pql B   3 NQYFTVQENYKERFYQIPKVFFTSENYKNLTNDMKIAYAILRDRLNLSIKNSWVDEDGNIYFVYSNEKLMEILNCKKEKLTKIKKGLENDGLLIQKRRGLNKPNILYLMKPIVTERDIYKIEKEENDVEP 132
                                    12        22        32        42        52        62        72        82        92       102       112       122       132
   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 4PQL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4PQL)

 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
    EDO  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:131 - Pro A:132   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  4pql
    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
  B1B3N7_STAAU | B1B3N7
    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
  B1B3N7_STAAU | B1B3N7
    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 4PQL)

(-) Related Entries Specified in the PDB File

4pqk