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 :  11B-HYDROXYSTEROID DEHYDROGENASE TYPE I IN COMPLEX WITH INHIBITOR
 
Authors :  G. Branden, C. Boden, D. Ogg
Date :  24 Mar 15  (Deposition) - 03 Feb 16  (Release) - 03 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dehydrogenase Inhibitor, Bhsd, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. R. Robb, S. Boyd, C. D. Davies, A. G. Dossiter, F. W. Goldberg, P. D. Kemmitt, J. S. Scott, J. G. Swales
Design Of Pyrozolo-Pyrimidines As 11Beta-Hsd1 Inhibitors Through Optimisation Of Molecular Electrostatic Potential.
Medchemcomm V. 6 926 2016
PubMed: search  |  Reference-DOI: 10.1039/C5MD00043B

(-) Compounds

Molecule 1 - CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1
    Chains: A, B
    EC Number: 1.1.1.146
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Taxid: 866768
    Fragment: UNP RESIDUES 26-284
    Gene: HSD11B1, HSD11, HSD11L
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 11-BETA-HYDROXYSTEROID DEHYDROGENASE 1,11-BETA-HSD1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
14JX2Ligand/IonN-[(1R,2S,3S,5S,7S)-5-HYDROXYTRICYCLO[3.3.1.1~3,7~]DEC-2-YL]-5,7-DIMETHYLPYRAZOLO[1,5-A]PYRIMIDINE-3-CARBOXAMIDE
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:41 , ALA A:42 , SER A:43 , LYS A:44 , GLY A:45 , ILE A:46 , ALA A:65 , ARG A:66 , SER A:67 , THR A:92 , MET A:93 , ASN A:119 , ILE A:121 , VAL A:168 , SER A:169 , SER A:170 , TYR A:183 , LYS A:187 , LEU A:215 , GLY A:216 , LEU A:217 , ILE A:218 , THR A:220 , THR A:222 , ALA A:223 , 4JX A:302binding site for residue NAP A 301
2AC2SOFTWAREILE A:121 , SER A:170 , LEU A:171 , TYR A:177 , TYR A:183 , LEU A:215 , LEU A:217 , ALA A:226 , NAP A:301binding site for residue 4JX A 302
3AC3SOFTWAREGLY B:41 , ALA B:42 , SER B:43 , LYS B:44 , GLY B:45 , ILE B:46 , ALA B:65 , ARG B:66 , SER B:67 , GLY B:91 , THR B:92 , MET B:93 , ASN B:119 , HIS B:120 , ILE B:121 , VAL B:168 , SER B:169 , SER B:170 , TYR B:183 , LYS B:187 , LEU B:215 , GLY B:216 , LEU B:217 , ILE B:218 , THR B:220 , THR B:222 , ALA B:223 , 4JX B:302binding site for residue NAP B 301
4AC4SOFTWARETHR B:124 , SER B:170 , LEU B:171 , TYR B:183 , LEU B:215 , GLY B:216 , LEU B:217 , ALA B:223 , ALA B:226 , ILE B:230 , NAP B:301binding site for residue 4JX B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val B:231 -His B:232

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YYZ)

(-) 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:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..eeeee...hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yyz A  26 EFRPEMLQGKKVIVTGASKGIGREMAYHLAKMGAHVVVTARSKETLQKVVSHCLELGAASAHYIAGTMEDMTFAEQFVAQAGKLMGGLDMLILNHITNTSLNLFHDDIHHVRKSMEVNFLSYVVLTVAALPMLKQSNGSIVVVSSLAGKVAYPLVAAYSASKFALDGFFSSIRKEYSVSRVNVSITLCVLGLIDTETAMKAVSGIVHMQAAPKEECALEIIKGGALRQEEVYYDSSRWTTLLIRNPSRKILEELYSTSY 284
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275         


Chain B from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhh..eeeee...hhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhh.........hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yyz B  26 EFRPEMLQGKKVIVTGASKGIGREMAYHLAKMGAHVVVTARSKETLQKVVSHCLELGAASAHYIAGTMEDMTFAEQFVAQAGKLMGGLDMLILNHITNTSLNLFHDDIHHVRKSMEVNFLSYVVLTVAALPMLKQSNGSIVVVSSLAGKVAYPLVAAYSASKFALDGFFSSIRKEYSVSRVNVSITLCVLGLIDTETAMKAVSGIVHMQAAPKEECALEIIKGGALRQEEVYYDSSRWTTLLIRNPSRKILEELYSTS 283
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275
   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 4YYZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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
    4JX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Val B:231 - His B:232   [ 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
  4yyz
    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
  DHI1_HUMAN | P28845
    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)
  1.1.1.146
    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
  DHI1_HUMAN | P28845
    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
        DHI1_HUMAN | P28845: 1xu7 1xu9 2bel 2ilt 2irw 2rbe 3byz 3bzu 3ch6 3czr 3d3e 3d4n 3d5q 3ey4 3fco 3frj 3h6k 3hfg 3oq1 3pdj 3qqp 3tfq 4bb5 4bb6 4c7j 4c7k 4hfr 4hx5 4iju 4ijv 4ijw 4k1l 4p38

(-) Related Entries Specified in the PDB File

4c7j 11B-HYDROXYSTEROID DEHYDROGENASE TYPE I IN COMPLEX WITH INHIBITOR
4c7k 11B-HYDROXYSTEROID DEHYDROGENASE TYPE I IN COMPLEX WITH INHIBITOR