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

(-) Description

Title :  GR IN COMPLEX WITH DEXAMETHASONE
 
Authors :  K. Edman, A. Hogner, A. Hussein, M. Bjursell, A. Aagaard, S. Backstrom, L. Wissler, T. Jellesmark-Jensen, A. Cavallin, U. Karlsson, E. Nilss D. Lecina, R. Takahashi, C. Grebner, M. Lepisto, V. Guallar
Date :  09 Dec 14  (Deposition) - 25 Nov 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Signaling Protein, Nuclear Hormone Receptor, Ligand Complex, Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Edman, A. Hosseini, M. K. Bjursell, A. Aagaard, L. Wissler, A. Gunnarsson, T. Kaminski, C. Kohler, S. Backstrom, T. J. Jensen, A. Cavallin, U. Karlsson, E. Nilsson, D. Lecina, R. Takahashi, C. Grebner, S. Geschwindner, M. Lepisto, A. C. Hogner, V. Guallar
Ligand Binding Mechanism In Steroid Receptors: From Conserved Plasticity To Differential Evolutionary Constraints.
Structure V. 23 2280 2015
PubMed-ID: 26602186  |  Reference-DOI: 10.1016/J.STR.2015.09.012

(-) Compounds

Molecule 1 - GLUCOCORTICOID RECEPTOR
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HIGH FIVE CELLS
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PFASTBAC1
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: LIGAND BINDING DOMAIN, UNP RESIDUES 500-777
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GR, NUCLEAR RECEPTOR SUBFAMILY 3 GROUP C MEMBER 1
 
Molecule 2 - NUCLEAR RECEPTOR COACTIVATOR 2
    Chains: B
    Fragment: RESIDUES 740-753
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NCOA-2, CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 75, BHLHE75, TRANSCRIPTIONAL INTERMEDIARY FACTOR 2, HTIF2, NCOA2
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CPS1Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
2DEX1Ligand/IonDEXAMETHASONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:557 , TRP A:610 , ASP A:638 , TYR A:660 , TYR A:735 , GLN A:738 , MET A:745 , GLN A:776BINDING SITE FOR RESIDUE CPS A1777
2AC2SOFTWAREMET A:560 , LEU A:563 , ASN A:564 , GLY A:567 , GLN A:570 , MET A:604 , ARG A:611 , PHE A:623 , GLN A:642 , TYR A:735 , CYS A:736 , THR A:739 , ILE A:747 , PHE A:749BINDING SITE FOR RESIDUE DEX A1778

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:705 -Gly A:706
2Asn A:707 -Ser A:708

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UDC)

(-) 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:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee..eee..hhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.ee......hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4udc A 529 TPTLVSLLEVIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLIINEQRMTLPDMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVVENLLNYCFQTFLDKTMSIEFPEMLAEIITNQIPKYSNGNIKKLLFHQ 776
                                   538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768        


Chain B from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 4udc B 741 ENALLRYLLDKDD 753
                                   750
   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 4UDC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (83, 91)

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
    CPS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DEX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:707 - Ser A:708   [ RasMol ]  
    Glu A:705 - Gly A:706   [ RasMol ]  
 

(-) 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 | Asym./Biol. Unit - sites 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
  4udc
    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
  GCR_HUMAN | P04150
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  NCOA2_HUMAN | Q15596
    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
  GCR_HUMAN | P04150
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  NCOA2_HUMAN | Q15596
    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
        GCR_HUMAN | P04150: 1m2z 1nhz 1p93 3bqd 3cld 3e7c 3h52 3k22 3k23 4csj 4hn5 4hn6 4lsj 4mdd 4p6w 4p6x 4udd 5cbx 5cby 5cbz 5cc1 5e69 5e6a 5e6b 5e6c 5e6d 5emc 5emp 5emq 5g3j 5g5w
        NCOA2_HUMAN | Q15596: 1gwq 1gwr 1m2z 1mv9 1mvc 1mzn 1p93 1t63 1t65 1uhl 1yok 1zdt 1zdu 1zky 2ao6 2b1v 2b1z 2b23 2fai 2g44 2g5o 2ldc 2p15 2p1t 2p1u 2p1v 2q7j 2q7l 2yjd 2zxz 2zy0 3a9e 3cld 3dzu 3dzy 3e00 3e7c 3e94 3erd 3fug 3gn8 3k22 3k23 3kwy 3kyt 3l0e 3l0j 3l0l 3o1d 3o1e 3oap 3ozj 3pcu 3plz 3q95 3q97 3r5m 3up0 3up3 4csj 4dos 4e2j 4fhh 4fhi 4ia1 4ia2 4ia3 4ia7 4iqr 4iu7 4iui 4iv2 4iv4 4ivw 4ivy 4iw6 4iw8 4iwc 4iwf 4k4j 4k6i 4m8e 4m8h 4nie 4nqa 4oc7 4p6w 4p6x 4pld 4ple 4poh 4poj 4pp3 4pp5 4pp6 4ppp 4pps 4pxm 4q0a 4qe6 4qe8 4rfw 4rmc 4rmd 4rme 4ruo 4udd 4wg0 4zn7 4zn9 4znh 4zns 4znt 4znu 4znv 4znw 4zo1 4zsh 5aph 5apj 5di7 5did 5die 5dig 5dk9 5dkb 5dke 5dkg 5dks 5dl4 5dlr 5dmc 5dmf 5dp0 5drj 5drm 5dtv 5du5 5due 5dug 5duh 5dvs 5dvv 5dwe 5dwg 5dwi 5dwj 5dx3 5dxb 5dxe 5dxg 5dxk 5dxm 5dxp 5dxq 5dxr 5dy8 5dyb 5dyd 5dz0 5dz1 5dz3 5dzh 5dzi 5e0w 5e0x 5e14 5e15 5e19 5e1c 5ec9 5egv 5ehj 5ei1 5eit 5g3j 5g42 5g43 5g44 5g45 5g46 5g5w 5h1e 5hyr 5i4v 5iaw 5ick 5kcc 5kcd 5kce 5kcf 5kct 5kcu 5kcw 5kd9 5kr9 5kra 5krc 5krf 5krh 5kri 5krj 5krk 5krl 5krm 5kro 5l11 5lga 5syz 5tld 5tlf 5tlg 5tll 5tlm 5tlo 5tlp 5tlt 5tlu 5tlv 5tlx 5tly 5tm1 5tm2 5tm3 5tm4 5tm5 5tm6 5tm7 5tm8 5tm9 5tml 5tmm 5tmo 5tmq 5tmr 5tms 5tmt 5tmu 5tmv 5tmw 5tmz 5tn1 5tn3 5tn4 5tn5 5tn6 5tn7 5tn8 5u2d

(-) Related Entries Specified in the PDB File

4uda MR IN COMPLEX WITH DEXAMETHASONE
4udb MR IN COMPLEX WITH DESISOBUTYRYLCICLESONIDE
4udd GR IN COMPLEX WITH DESISOBUTYRYLCICLESONIDE