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 THE GLUCOCORTICOID RECEPTOR LIGAND BINDING DOMAIN BOUND TO A DIBENZOXAPINE SULFONAMIDE
 
Authors :  M. Carson, J. G. Luz, D. Clawson, M. Coghlan
Date :  22 Jul 13  (Deposition) - 29 Jan 14  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Nuclear Hormone Receptor, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. W. Carson, J. G. Luz, C. Suen, C. Montrose, R. Zink, X. Ruan, C. Cheng, H. Cole, M. D. Adrian, D. T. Kohlman, T. Mabry, N. Snyder, B. Condon, M. Maletic, D. Clawson, A. Pustilnik, M. J. Coghlan
Glucocorticoid Receptor Modulators Informed By Crystallography Lead To A New Rationale For Receptor Selectivity, Function, And Implications For Structure-Based Design.
J. Med. Chem. V. 57 849 2014
PubMed-ID: 24446728  |  Reference-DOI: 10.1021/JM401616G

(-) Compounds

Molecule 1 - GLUCOCORTICOID RECEPTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: STEROID-BINDING REGION, RESIDUES 522-777
    Gene: NR3C1, GRL
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GR, NUCLEAR RECEPTOR SUBFAMILY 3 GROUP C MEMBER 1
 
Molecule 2 - D30 PEPTIDE
    Chains: B
    Engineered: YES
    Other Details: D30 SYNTHETIC PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1LSJ2Ligand/IonN-{3-[(1Z)-1-(10-METHOXYDIBENZO[B,E]OXEPIN-11(6H)-YLIDENE)PROPYL]PHENYL}METHANESULFONAMIDE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1LSJ4Ligand/IonN-{3-[(1Z)-1-(10-METHOXYDIBENZO[B,E]OXEPIN-11(6H)-YLIDENE)PROPYL]PHENYL}METHANESULFONAMIDE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1LSJ2Ligand/IonN-{3-[(1Z)-1-(10-METHOXYDIBENZO[B,E]OXEPIN-11(6H)-YLIDENE)PROPYL]PHENYL}METHANESULFONAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:563 , ASN A:564 , GLN A:570 , MET A:601 , MET A:604 , LEU A:608 , PHE A:623 , MET A:639 , LEU A:732 , TYR A:735 , CYS A:736 , THR A:739 , PHE A:749BINDING SITE FOR RESIDUE LSJ A 801
2AC2SOFTWARELEU A:532 , PRO A:582 , ASN A:586 , LEU A:685 , THR A:692 , TRP A:712 , TYR A:716BINDING SITE FOR RESIDUE LSJ A 802

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:776 -Lys A:777

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LSJ)

(-) 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:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee..eeee.hhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.eee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lsj A 526 PQLTPTLVSLLEVIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMYLMAFALGWRSYRQSSANLLCFAPDLIINEQRMTLPGMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLKSQELFDEIRMTYIKELGKAIVNWQRFYQLTKLLDSMHEVVENLLNYCFQTFLDKTMSIEFPEMLAEIITNQIPKYSNGNIKKLLFHQK 777
                                   535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695      |713       723       733       743       753       763       773    
                                                                                                                                                                                                          702|                                                                  
                                                                                                                                                                                                           711                                                                  


Chain B from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4lsj B   0 SSRLWELLME   9
                                     9
   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 4LSJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (37, 37)

Asymmetric Unit(hide GO term definitions)

 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
    LSJ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln A:776 - Lys A:777   [ 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 | 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
  4lsj
    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
 
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)

 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 4mdd 4p6w 4p6x 4udc 4udd 5cbx 5cby 5cbz 5cc1 5e69 5e6a 5e6b 5e6c 5e6d 5emc 5emp 5emq 5g3j 5g5w

(-) Related Entries Specified in the PDB File

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