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 :  PROLIFERATING CELL NUCLEAR ANTIGEN HOMOLOG 1 BOUND TO FEN-1 PEPTIDE
 
Authors :  J. E. Ladner, A. S. Altieri, Z. Kelman
Date :  20 Aug 15  (Deposition) - 11 May 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Complex, Pip Box Binder, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Altieri, J. E. Ladner, Z. Li, H. Robinson, Z. F. Sallman, J. P. Marino, Z. Kelman
A Small Protein Inhibits Proliferating Cell Nuclear Antigen By Breaking The Dna Clamp.
Nucleic Acids Res. V. 44 6232 2016
PubMed-ID: 27141962  |  Reference-DOI: 10.1093/NAR/GKW351

(-) Compounds

Molecule 1 - DNA POLYMERASE SLIDING CLAMP 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PCN1, TK0535
    Organism Scientific: THERMOCOCCUS KODAKARENSIS (STRAIN ATCC BAA-918 / JCM 12380 / KOD1)
    Organism Taxid: 69014
    Strain: ATCC BAA-918 / JCM 12380 / KOD1
    Synonym: PROLIFERATING CELL NUCLEAR ANTIGEN HOMOLOG 1,PCNA 1
 
Molecule 2 - C-TERMINUS OF FEN-1 PROTEIN
    Chains: B
    Engineered: YES
    Organism Scientific: THERMOCOCCUS KODAKARENSIS KOD1
    Organism Taxid: 69014
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 11)

Asymmetric Unit (1, 11)
No.NameCountTypeFull Name
1SO411Ligand/IonSULFATE ION
Biological Unit 1 (1, 33)
No.NameCountTypeFull Name
1SO433Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:193 , GLU A:194binding site for residue SO4 A 301
02AC2SOFTWARELYS A:11 , LYS A:84 , ALA A:85binding site for residue SO4 A 302
03AC3SOFTWAREGLY A:212 , LYS A:213 , HOH A:404 , HOH A:443binding site for residue SO4 A 303
04AC4SOFTWAREASN A:22 , LYS A:77 , LYS A:81 , HOH A:434binding site for residue SO4 A 304
05AC5SOFTWAREGLU A:55 , SER A:59 , LYS A:60 , TYR A:61 , HOH A:410 , HOH A:458binding site for residue SO4 A 305
06AC6SOFTWARELYS A:156 , ILE A:158 , LYS A:167 , LYS A:196binding site for residue SO4 A 306
07AC7SOFTWAREGLU A:67 , THR A:68 , HOH A:403binding site for residue SO4 A 307
08AC8SOFTWARETHR A:68 , ILE A:69 , GLY A:70 , ILE A:116 , ASP A:117 , VAL A:118binding site for residue SO4 A 308
09AC9SOFTWARELYS A:142 , LYS A:209binding site for residue SO4 A 309
10AD1SOFTWAREPHE A:130 , GLU A:190 , GLU A:192binding site for residue SO4 A 310
11AD2SOFTWARELYS B:330 , ARG B:332 , THR B:333 , HOH B:502binding site for residue SO4 B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DAI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DAI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DAI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DAI)

(-) Exons   (0, 0)

(no "Exon" information available for 5DAI)

(-) 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:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhhhhhh...eeeeee...eeeeeee.....eeeeeeee.hhh.eee....eeeeeehhhhhhhhh......eeeeee....eeeeeee...eeeeeee.................eeeeeehhhhhhhhhhhhh...eeeeeee..eeeeeee....eeeeeee.....eeeeee...eeeeeehhhhhhhhh......eeeeee.....eeeeeee...eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dai A   2 PFEVVFDGAKEFADLIATASNLIDEAAFKFTEEGISMRAMDPSRVVLIDLNLPESIFSKYEVEEPETIGINMDQFKKILKRGKAKDTLILRKGDENFLEITFEGTAKRTFRLPLIDVEELELELPELPFTAKVVLLGEVLKEGIKDASLVSDAIKFIAKENEFTMKAEGETNEVEIRLTLEDEGLLDLEVEEETKSAYGIRYLSDMVKGIGKADEVILRFGNEMPLQMEYMIRDEGRLTFLLAPRVE 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       


Chain B from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ....hhhhh Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 5dai B 330 KQRTLESWF 338
   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 5DAI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DAI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DAI)

(-) Gene Ontology  (18, 20)

Asymmetric Unit(hide GO term definitions)

 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
    SO4  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5dai)
 
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
  5dai
    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
  FEN_THEKO | Q5JGN0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  PCNA1_THEKO | Q5JF32
    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
  FEN_THEKO | Q5JGN0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PCNA1_THEKO | Q5JF32
    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
        PCNA1_THEKO | Q5JF32: 3lx1 5da7

(-) Related Entries Specified in the PDB File

3lx1 THE PCNA WITH NOTHING BOUND.
5da7 THE PCNA WITH BINDING INHIBITOR PROTEIN.