Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  COMPUTATIONAL DESIGN OF SELF-ASSEMBLING CYCLIC PROTEIN HOMOOLIGOMERS
 
Authors :  B. Sankaran, P. H. Zwart, J. A. Fallas, J. H. Pereira, G. Ueda, D. Baker
Date :  02 Jun 16  (Deposition) - 12 Apr 17  (Release) - 12 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Rosetta, De Novo Design, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Fallas, G. Ueda, W. Sheffler, V. Nguyen, D. E. Mcnamara, B. Sankaran, J. H. Pereira, F. Parmeggiani, T. J. Brunette, D. Cascio, T. R. Yeates, P. Zwart, D. Baker
Computational Design Of Self-Assembling Cyclic Protein Homo-Oligomers.
Nat Chem V. 9 353 2017
PubMed-ID: 28338692  |  Reference-DOI: 10.1038/NCHEM.2673

(-) Compounds

Molecule 1 - DESIGNED PROTEIN ANK1C2
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5KBA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ser B:0 -Ser B:1
2Ser B:1 -Glu B:2
3Ser C:1 -Glu C:2

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KBA)

(-) 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:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhh.............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kba A   0 SSELGKRLIEAAENGNKDRVKDLIENGADVNASDSDGRTPLHHAAENGHAEVVALLIEKGADVNAKDSDGRTPLHHAAENGHDEVVLILLLKGADVNAKDSDGRTPLHHAAENGHKRVVLVLILAGADVNTSDSDGRTPLDLAREHGNEEVVKALEKQ 157
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149        


Chain B from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kba B  -2 WGSSELGKRLIEAAENGNKDRVKDLIENGADVNASDSDGRTPLHHAAENGHAEVVALLIEKGADVNAKDSDGRTPLHHAAENGHDEVVLILLLKGADVNAKDSDGRTPLHHAAENGHKRVVLVLILAGADVNTSDSDGRTPLDLAREHGNEEVVKALEKQ 157
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157


Chain C from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhh.............hhhhhhhhh.hhhhhhhhhhhh...........hhhhhhhhh.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kba C   0 SSELGKRLIEAAENGNKDRVKDLIENGADVNASDSDGRTPLHHAAENGHAEVVALLIEKGADVNAKDSDGRTPLHHAAENGHDEVVLILLLKGADVNAKDSDGRTPLHHAAENGHKRVVLVLILAGADVNTSDSDGRTPLDLAREHGNEEVVKALEKQ 157
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149        


Chain D from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhh.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kba D   1 SELGKRLIEAAENGNKDRVKDLIENGADVNASDSDGRTPLHHAAENGHAEVVALLIEKGADVNAKDSDGRTPLHHAAENGHDEVVLILLLKGADVNAKDSDGRTPLHHAAENGHKRVVLVLILAGADVNTSDSDGRTPLDLAREHGNEEVVKALEKQ 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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 5KBA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5KBA)

 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
(no "Ligands, Modified Residues, Ions" information available for 5kba)
 
  Sites
(no "Sites" information available for 5kba)
 
  Cis Peptide Bonds
    Ser B:0 - Ser B:1   [ RasMol ]  
    Ser B:1 - Glu B:2   [ RasMol ]  
    Ser C:1 - Glu C:2   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 1 PNG format | Biol. Unit 2 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
  5kba
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 5KBA)

(-) Related Entries Specified in the PDB File

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