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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ER-ALPHA LIGAND-BINDING DOMAIN (Y537S) IN COMPLEX WITH AN N-TRIFLUOROETHYL 4-CHLOROBENZYL OBHS-N DERIVATIVE
 
Authors :  J. C. Nwachukwu, S. Srinivasan, N. E. Bruno, V. Dharmarajan, D. Goswami I. Kastrati, S. Novick, J. Nowak, H. B. Zhou, N. Boonmuen, Y. Zhao, J. Mi J. Frasor, B. S. Katzenellenbogen, P. R. Griffin, J. A. Katzenellenbo K. W. Nettles
Date :  07 Jun 16  (Deposition) - 16 Nov 16  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Nuclear Receptor, Transcription Factor, Ligand Binding, Protein- Ligand Complex, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Srinivasan, J. C. Nwachukwu, N. E. Bruno, V. Dharmarajan, D. Goswami, I. Kastrati, S. Novick, J. Nowak, V. Cavett, H. B. Zhou, N. Boonmuen, Y. Zhao, J. Min, J. Frasor, B. S. Katzenellenbogen, P. R. Griffin, J. A. Katzenellenbogen, K. W. Nettles
Full Antagonism Of The Estrogen Receptor Without A Prototypical Ligand Side Chain.
Nat. Chem. Biol. V. 13 111 2017
PubMed-ID: 27870835  |  Reference-DOI: 10.1038/NCHEMBIO.2236

(-) Compounds

Molecule 1 - ESTROGEN RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: LIGAND-BINDING DOMAIN
    Gene: ESR1, ESR, NR3A1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ER,ER-ALPHA,ESTRADIOL RECEPTOR,NUCLEAR RECEPTOR SUBFAMILY 3 GROUP A MEMBER 1
 
Molecule 2 - NCOA2
    Chains: C, D
    Engineered: YES
    Fragment: NUCLEAR RECEPTOR-INTERACTING PEPTIDE
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1OBT2Ligand/Ion(1S,2R,4S)-N-(4-CHLOROPHENYL)-5,6-BIS(4-HYDROXYPHENYL)-N-(2,2,2-TRIFLUOROETHYL)-7-OXABICYCLO[2.2.1]HEPT-5-ENE-2-SULFONAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1OBT1Ligand/Ion(1S,2R,4S)-N-(4-CHLOROPHENYL)-5,6-BIS(4-HYDROXYPHENYL)-N-(2,2,2-TRIFLUOROETHYL)-7-OXABICYCLO[2.2.1]HEPT-5-ENE-2-SULFONAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1OBT1Ligand/Ion(1S,2R,4S)-N-(4-CHLOROPHENYL)-5,6-BIS(4-HYDROXYPHENYL)-N-(2,2,2-TRIFLUOROETHYL)-7-OXABICYCLO[2.2.1]HEPT-5-ENE-2-SULFONAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:347 , ALA A:350 , GLU A:353 , LEU A:387 , MET A:388 , ARG A:394 , MET A:421 , ILE A:424 , GLY A:521 , HIS A:524 , LEU A:525 , LEU A:540 , HOH A:723binding site for residue OBT A 601
2AC2SOFTWAREMET B:343 , LEU B:346 , THR B:347 , ALA B:350 , GLU B:353 , TRP B:383 , LEU B:387 , MET B:388 , ARG B:394 , MET B:421 , ILE B:424 , GLY B:521 , LEU B:525 , LEU B:540binding site for residue OBT B 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KD9)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asp A:332 -Pro A:333
2Arg A:335 -Pro A:336
3Glu A:419 -Gly A:420

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KD9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KD9)

(-) Exons   (0, 0)

(no "Exon" information available for 5KD9)

(-) 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:235
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.hhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh......eeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kd9 A 305 SLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLSDLLLEMLDAHR 548
                                   314       324       334       344       354       364       374       384       394       404       414       424       434       444       454      |473       483       493       503       513       523       533       543     
                                                                                                                                                                                      461|                                                                             
                                                                                                                                                                                       471                                                                             


Chain B from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee..eee.........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5kd9 B 305 SLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSVPLSDLLLEMLDAH 547
                                   314       324       334       344       354       364       374       384       394       404       414       424       434       444       454     ||473       483       493       503       513       523   ||  539        
                                                                                                                                                                                     460|                                                      527|             
                                                                                                                                                                                      470                                                       534             


Chain C 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
                 5kd9 C 687 HKILHRLLQD 696
                                   696


Chain D from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author .hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 5kd9 D 688 KILHRLLQD 696
   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 5KD9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KD9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KD9)

(-) Gene Ontology  (138, 152)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ESR1_HUMAN | P03372: 1a52 1akf 1ere 1err 1g50 1gwq 1gwr 1hcp 1hcq 1l2i 1pcg 1qkt 1qku 1r5k 1sj0 1uom 1x7e 1x7r 1xp1 1xp6 1xp9 1xpc 1xqc 1yim 1yin 1zky 2ayr 2b1v 2b1z 2b23 2bj4 2fai 2g44 2g5o 2i0j 2iog 2iok 2jf9 2jfa 2llo 2llq 2ocf 2ouz 2p15 2pog 2q6j 2q70 2qa6 2qa8 2qab 2qe4 2qgt 2qgw 2qh6 2qr9 2qse 2qxm 2qxs 2qzo 2r6w 2r6y 2yat 2yja 3cbm 3cbo 3cbp 3dt3 3erd 3ert 3hlv 3hm1 3l03 3os8 3os9 3osa 3q95 3q97 3uu7 3uua 3uuc 3uud 4aa6 4dma 4iu7 4iui 4iv2 4iv4 4ivw 4ivy 4iw6 4iw8 4iwc 4iwf 4jc3 4jdd 4mg5 4mg6 4mg7 4mg8 4mg9 4mga 4mgb 4mgc 4mgd 4o6f 4pp6 4ppp 4pps 4pxm 4q13 4q50 4tuz 4tv1 4xi3 4zn7 4zn9 4znh 4zns 4znt 4znu 4znv 4znw 5aau 5aav 5acc 5ak2 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 5egv 5ehj 5ei1 5eit 5fqp 5fqr 5fqs 5fqt 5fqv 5hyr 5jmm 5kcc 5kcd 5kce 5kcf 5kct 5kcu 5kcw 5kr9 5kra 5krc 5krf 5krh 5kri 5krj 5krk 5krl 5krm 5kro 5n10 5t0x 5t92 5t97 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 5tn9 5tnb 5u2b 5u2d
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(-) Related Entries Specified in the PDB File

5kcc 5kcd 5kcf 5kct 5kcu 5kcw