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(-) Description

Title :  CRYSTAL STRUCTURE OF VDR-LBD COMPLEXED WITH 2-METHYLIDENE-26,27-DIPHENYL-19-NOR-1,25-DIHYDROXYVITAMIN D3
 
Authors :  A. Kato, T. Itoh, K. Yamamoto
Date :  02 May 16  (Deposition) - 29 Jun 16  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,C,D,F
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  D,F  (1x)
Keywords :  Transcription, Vitamin D3, Vdr, Vdre, Rxr, Co-Factors, Antagonist (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kato, T. Itoh, Y. Anami, D. Egawa, K. Yamamoto
Helix12-Stabilization Antagonist Of Vitamin D Receptor
Bioconjug. Chem. V. 27 1750 2016
PubMed-ID: 27294600  |  Reference-DOI: 10.1021/ACS.BIOCONJCHEM.6B00246

(-) Compounds

Molecule 1 - VITAMIN D3 RECEPTOR
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 116-164, 212-423
    Gene: VDR, NR1I1
    Mutation: YES
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: VDR,1,25-DIHYDROXYVITAMIN D3 RECEPTOR,NUCLEAR RECEPTOR SUBFAMILY 1 GROUP I MEMBER 1
 
Molecule 2 - MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 1
    Chains: C, F
    Engineered: YES
    Fragment: UNP RESIDUES 640-652
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ACDF
Biological Unit 1 (1x): AC  
Biological Unit 2 (1x):   DF

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1AKX2Ligand/Ion(1R,3R)-5-[(2E)-2-[(1R,3AS,7AR)-7A-METHYL-1-[(2R)-6-OXIDANYL-7-PHENYL-6-(PHENYLMETHYL)HEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLIDENE]-2-METHYLIDENE-CYCLOHEXANE-1,3-DIOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1AKX1Ligand/Ion(1R,3R)-5-[(2E)-2-[(1R,3AS,7AR)-7A-METHYL-1-[(2R)-6-OXIDANYL-7-PHENYL-6-(PHENYLMETHYL)HEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLIDENE]-2-METHYLIDENE-CYCLOHEXANE-1,3-DIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1AKX1Ligand/Ion(1R,3R)-5-[(2E)-2-[(1R,3AS,7AR)-7A-METHYL-1-[(2R)-6-OXIDANYL-7-PHENYL-6-(PHENYLMETHYL)HEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLIDENE]-2-METHYLIDENE-CYCLOHEXANE-1,3-DIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:143 , LEU A:223 , VAL A:230 , SER A:233 , ARG A:270 , SER A:271 , SER A:274 , TRP A:282 , CYS A:284 , ASP A:295 , VAL A:296 , ALA A:299 , HIS A:393 , GLN A:396binding site for residue AKX A 501
2AC2SOFTWARETYR D:143 , LEU D:223 , LEU D:226 , VAL D:230 , SER D:233 , ARG D:270 , SER D:271 , SER D:274 , TRP D:282 , CYS D:284 , ASP D:295 , VAL D:296 , ALA D:299 , HIS D:393 , GLN D:396binding site for residue AKX D 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B5B)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:369 -Pro A:370
2Pro D:369 -Pro D:370

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B5B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B5B)

(-) Exons   (0, 0)

(no "Exon" information available for 5B5B)

(-) 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:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eee......eehhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b5b A 114 SPLKDSLRPKLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMSPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGN 420
                                   123       133       143       153     ||221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411         
                                                                       159|                                                                                                                                                                                                          
                                                                        218                                                                                                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:11
                                           
               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
                 5b5b C 625 KNHPMLMNLLK 635
                                   634 


Chain D from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...hhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eee......eehhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5b5b D 123 KLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMSPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGN 420
                                   132       142       152      |220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420
                                                              159|                                                                                                                                                                                                          
                                                               218                                                                                                                                                                                                          


Chain F from PDB  Type:PROTEIN  Length:11
                                           
               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
                 5b5b F 625 KNHPMLMNLLK 635
                                   634
   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 5B5B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B5B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B5B)

(-) Gene Ontology  (126, 133)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MED1_HUMAN | Q15648: 1rjk 1rk3 1rkg 1rkh 2o4j 2o4r 2zfx 3a2h 3aun 3vjs 3vjt 3vrt 3vru 3vrv 3vrw 3w0g 3w0h 3w0i 3w0j 3w5p 3w5q 3w5r 3w5t 3wt5 3wt6 3wt7 3wtq 4ynk 5awj 5awk 5b41 5gic 5gid 5gie
        VDR_RAT | P13053: 1rjk 1rk3 1rkg 1rkh 2o4j 2o4r 2zfx 2zl9 2zla 2zlc 2zmh 2zmi 2zmj 2zxm 2zxn 3a2h 3afr 3aun 3vjs 3vjt 3vrt 3vru 3vrv 3vrw 3vt3 3vt4 3vt5 3vt6 3vt7 3vt8 3vt9 3vtb 3vtc 3vtd 3w0g 3w0h 3w0i 3w0j 3w5p 3w5q 3w5r 3w5t 3wt5 3wt6 3wt7 3wtq 4ynk 5awj 5awk 5b41 5gic 5gid 5gie 5h1e

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