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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ENGINEERED PROTEIN. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET OR266.
 
Authors :  S. Vorobiev, M. Su, F. Parmeggiani, J. Seetharaman, P. -S. Huang, M. Mao D. Lee, J. K. Everett, T. B. Acton, D. Baker, G. T. Montelione, L. Tong, J Northeast Structural Genomics Consortium (Nesg)
Date :  16 Aug 12  (Deposition) - 29 Aug 12  (Release) - 12 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  De Novo Protein, Psi-Biology, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Or266 (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 - OR266 DE NOVO PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21, OR266-21.1-NC5A
    Expression System Strain: BL21(DE3)+ MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: SYNTHETIC CONSTRUCT
    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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NO31Ligand/IonNITRATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NO31Ligand/IonNITRATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NO3-1Ligand/IonNITRATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:16 , LYS A:17 , ASP A:18BINDING SITE FOR RESIDUE NO3 A 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GMR)

(-) 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:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gmr A   2 SELGKRLIEAAENGNKDRVKDLLENGADVNASDSDGKTPLHLAAENGHKEVVKLLLSQGADPNAKDSDGKTPLHLAAENGHKEVVKLLLSQGADPNAKDSDGKTPLHLAAENGHKEVVKLLLSQGADPNTSDSDGRTPLDLAREHGNEEVVKLLEKQGGWLEHHHHH 168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       


Chain B from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhh.............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gmr B   2 SELGKRLIEAAENGNKDRVKDLLENGADVNASDSDGKTPLHLAAENGHKEVVKLLLSQGADPNAKDSDGKTPLHLAAENGHKEVVKLLLSQGADPNAKDSDGKTPLHLAAENGHKEVVKLLLSQGADPNTSDSDGRTPLDLAREHGNEEVVKLLEKQGGWLE 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  (0, 0)

(no "SCOP Domain" information available for 4GMR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

 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
    NO3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4gmr)
 
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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  4gmr
    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 4GMR)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4GMR)