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 :  CRYSTAL STRUCTURE OF ENGINEERED PROTEIN. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET OR267.
 
Authors :  S. Vorobiev, M. Su, F. Parmeggiani, J. Seetharaman, P. -S. Huang, M. Mag R. Xiao, D. Lee, J. K. Everett, T. B. Acton, D. Baker, G. T. Montelione, L J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  27 Sep 12  (Deposition) - 10 Oct 12  (Release) - 12 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Psi-Biology, Protein Structure Initiative, Northeast Structural Genomics Consortium (Nesg), 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 - ENGINEERED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: OR267-21.1-SEM-R2
    Expression System Strain: BL21(DE3) +MAGIC
    Expression System Taxid: 469008
    Expression System Vector: PET21
    Expression System Vector Type: PLASMID
    Organism Scientific: ARTIFICIAL GENE
    Organism Taxid: 32630

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4HB5)

(-) Sites  (0, 0)

(no "Site" information available for 4HB5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HB5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HB5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HB5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HB5)

(-) Exons   (0, 0)

(no "Exon" information available for 4HB5)

(-) 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:157
                                                                                                                                                                                             
               SCOP domains d4hb5a_ A: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hb5 A   2 SELGKRLIEAAENGNKDRVKDLLENGADPNASDSDGRTPLHYAAENGHKEIVKLLLSKGADPNAKDSDGRTPLHYAAENGHKEIVKLLLSKGADPNAKDSDGRTPLHYAAENGHKEIVKLLLSKGADPNTSDSDGRTPLDLAREHGNEEIVKLLEKQ 158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       


Chain B from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains d4hb5b_ B: automated matches                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hb5 B   2 SELGKRLIEAAENGNKDRVKDLLENGADPNASDSDGRTPLHYAAENGHKEIVKLLLSKGADPNAKDSDGRTPLHYAAENGHKEIVKLLLSKGADPNAKDSDGRTPLHYAAENGHKEIVKLLLSKGADPNTSDSDGRTPLDLAREHGNEEIVKLLEKQGGWLE 163
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HB5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HB5)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4HB5)

 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 4hb5)
 
  Sites
(no "Sites" information available for 4hb5)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4hb5)
 
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
  4hb5
    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 4HB5)

(-) Related Entries Specified in the PDB File

4gmr RELATED ID: NESG-OR267 RELATED DB: TARGETTRACK
4gpm