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

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PCNA IN COMPLEX WITH THE PIP BOX OF DVC1
 
Authors :  T. Jiang, M. Xu, Y. Wang
Date :  24 Mar 16  (Deposition) - 08 Jun 16  (Release) - 08 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Pcna, Pip Box, Dvc1, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Wang, M. Xu, T. Jiang
Crystal Structure Of Human Pcna In Complex With The Pip Box Of Dvc1
Biochem. Biophys. Res. Commun. V. 474 264 2016
PubMed-ID: 27084448  |  Reference-DOI: 10.1016/J.BBRC.2016.04.053

(-) Compounds

Molecule 1 - PROLIFERATING CELL NUCLEAR ANTIGEN
    Chains: A, C, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PCNA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PCNA,CYCLIN
 
Molecule 2 - DVC1 PIP BOX
    Chains: B, D, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5IY4)

(-) Sites  (0, 0)

(no "Site" information available for 5IY4)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:135 -A:162
2C:135 -C:162

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5IY4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IY4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IY4)

(-) Exons   (0, 0)

(no "Exon" information available for 5IY4)

(-) 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:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhh....eeeeeee..eeeeeee.....eeeeeeee.hhh.eeee...eeeeeehhhhhhhhh......eeeeee.....eeeeeee.....eeeeeeee.................eeeeeehhhhhhhhhhhhhh..eeeeeee..eeeeeee...eeeeeeee.......eeee...eeeeeehhhhhhhhhhhhhh.eeeeee.....eeeeeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iy4 A   1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKI 255
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     ||195       205       215       225       235       245       255
                                                                                                                                                                                                                   186|                                                               
                                                                                                                                                                                                                    192                                                               


Chain B from PDB  Type:PROTEIN  Length:14
                                              
               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
                 5iy4 B 323 SHQNVLSNYFPRVS 336
                                   332    


Chain C from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhh......eeeeeee..eeeeeee.....eeeeeeee.hhh.eeee...eeeeeehhhhhhhhh......eeeeee.....eeeeeee.....eeeeeeee.................eeeeeehhhhhhhhhhhhhh..eeeeeee..eeeeeee...eeeeeee.........eeee...eeeeeehhhhhhhhhhhhhh.eeeeee.....eeeeeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iy4 C   1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKI 255
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     ||194       204       214       224       234       244       254 
                                                                                                                                                                                                                   186|                                                                
                                                                                                                                                                                                                    191                                                                


Chain D from PDB  Type:PROTEIN  Length:14
                                              
               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
                 5iy4 D 323 SHQNVLSNYFPRVS 336
                                   332    


Chain E from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhh......eeeeeee..eeeeeee.....eeeeeeee.hhh.eeee...eeeeeehhhhhhhhhh.....eeeeee.....eeeeeee.....eeeeeeee.................eeeeeehhhhhhhhhhhhhh..eeeeeee..eeeeeee...eeeeeee........eeee...eeeeeehhhhhhhhhhhhhh.eeeeee.....eeeeeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iy4 E   1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKI 255
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     ||195       205       215       225       235       245       255
                                                                                                                                                                                                                   186|                                                               
                                                                                                                                                                                                                    192                                                               


Chain F from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 5iy4 F 323 SHQNVLSNYFP 333
                                   332
   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 5IY4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IY4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IY4)

(-) Gene Ontology  (64, 72)

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
(no "Ligands, Modified Residues, Ions" information available for 5iy4)
 
  Sites
(no "Sites" information available for 5iy4)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5iy4)
 

(-) 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 ](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
  5iy4
    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
  PCNA_HUMAN | P12004
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SPRTN_HUMAN | Q9H040
    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
  PCNA_HUMAN | P12004
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SPRTN_HUMAN | Q9H040
    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
        PCNA_HUMAN | P12004: 1axc 1u76 1u7b 1ul1 1vyj 1vym 1w60 2zvk 2zvl 2zvm 3ja9 3p87 3tbl 3vkx 3wgw 4d2g 4rjf 4ztd 5e0t 5e0u 5e0v 5l7c 5mlo 5mlw 5mom

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5IY4)