Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  N-TERMINAL MOTIF DIMERIZATION OF EGFR TRANSMEMBRANE DOMAIN IN BICELLAR ENVIRONMENT
 
Authors :  P. Bragin, E. Bocharov, K. Mineev, O. Bocharova, A. Arseniev
Date :  12 Sep 16  (Deposition) - 05 Apr 17  (Release) - 05 Apr 17  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Epidermal Growth Factor Receptor, Bicelles, Activation Mechanism, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. V. Bocharov, P. E. Bragin, K. V. Pavlov, O. V. Bocharova, K. S. Mineev A. A. Polyansky, P. E. Volynsky, R. G. Efremov, A. S. Arseniev
The Conformation Of The Epidermal Growth Factor Receptor Transmembrane Domain Dimer Dynamically Adapts To The Local Membrane Environment.
Biochemistry V. 56 1697 2017
PubMed-ID: 28291355  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B01085

(-) Compounds

Molecule 1 - EPIDERMAL GROWTH FACTOR RECEPTOR
    Chains: A, B
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: EGFR, ERBB, ERBB1, HER1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTO-ONCOGENE C-ERBB-1,RECEPTOR TYROSINE-PROTEIN KINASE ERBB-1

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x): AB
NMR Structure * (1x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5LV6)

(-) Sites  (0, 0)

(no "Site" information available for 5LV6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LV6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LV6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LV6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LV6)

(-) Exons   (0, 0)

(no "Exon" information available for 5LV6)

(-) Sequences/Alignments

NMR Structure
   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:44
                                                                            
               SCOP domains -------------------------------------------- SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                 5lv6 A 634 EGCPTNGPKIPSIATGMVGALLLLLVVALGIGLFMRRRHIVRKR 677
                                   643       653       663       673    


Chain B from PDB  Type:PROTEIN  Length:44
                                                                            
               SCOP domains -------------------------------------------- SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                 5lv6 B 634 EGCPTNGPKIPSIATGMVGALLLLLVVALGIGLFMRRRHIVRKR 677
                                   643       653       663       673
   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 5LV6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LV6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LV6)

(-) Gene Ontology  (111, 111)

NMR Structure(hide GO term definitions)

 Visualization

(-) Interactive Views

NMR Structure
  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 5lv6)
 
  Sites
(no "Sites" information available for 5lv6)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5lv6)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models 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
  5lv6
    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
  EGFR_HUMAN | P00533
    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)
  2.7.10.1
    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
  EGFR_HUMAN | P00533
    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
        EGFR_HUMAN | P00533: 1dnq 1dnr 1ivo 1m14 1m17 1mox 1nql 1xkk 1yy9 1z9i 2eb2 2eb3 2exp 2exq 2gs2 2gs6 2gs7 2itn 2ito 2itp 2itq 2itt 2itu 2itv 2itw 2itx 2ity 2itz 2j5e 2j5f 2j6m 2jit 2jiu 2jiv 2ks1 2m0b 2m20 2n5s 2rf9 2rfd 2rfe 2rgp 3b2u 3b2v 3bel 3buo 3c09 3g5v 3g5y 3gop 3gt8 3ika 3lzb 3njp 3ob2 3op0 3p0y 3pfv 3poz 3qwq 3ug1 3ug2 3vjn 3vjo 3vrp 3vrr 3w2o 3w2p 3w2q 3w2r 3w2s 3w32 3w33 4g5j 4g5p 4hjo 4i1z 4i20 4i21 4i22 4i23 4i24 4jq7 4jq8 4jr3 4jrv 4krl 4krm 4kro 4krp 4li5 4ll0 4lqm 4lrm 4r3p 4r3r 4r5s 4riw 4rix 4riy 4rj4 4rj5 4rj6 4rj7 4rj8 4tks 4uip 4uv7 4wd5 4wkq 4wrg 4zau 4zjv 4zse 5c8k 5c8m 5c8n 5cal 5can 5cao 5cap 5caq 5cas 5cau 5cav 5cnn 5cno 5czh 5czi 5d41 5edp 5edq 5edr 5em5 5em6 5em7 5em8 5fed 5fee 5feq 5gmp 5gnk 5hcx 5hcy 5hcz 5hg5 5hg7 5hg8 5hg9 5hib 5hic 5j9y 5j9z 5jeb 5sx4 5sx5 5u8l 5ug8 5ug9 5uga 5ugb 5ugc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LV6)