HEADER TRANSCRIPTION 19-APR-11 3RLJ TITLE CRYSTAL STRUCTURE OF THE ANDROGEN RECEPTOR LIGAND BINDING DOMAIN IN TITLE 2 COMPLEX WITH SARM S-22 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANDROGEN RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND-BINDING DOMAIN RESIDUES 671-917; COMPND 5 SYNONYM: DIHYDROTESTOSTERONE RECEPTOR, NUCLEAR RECEPTOR SUBFAMILY 3 COMPND 6 GROUP C MEMBER 4; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: AR, DHTR, NR3C4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS STEROID RECEPTOR, DHT, TESTOSTERONE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR C.E.BOHL,C.B.DUKE,A.JONES,J.T.DALTON,D.D.MILLER REVDAT 2 15-JUN-11 3RLJ 1 JRNL REVDAT 1 04-MAY-11 3RLJ 0 JRNL AUTH C.B.DUKE,A.JONES,C.E.BOHL,J.T.DALTON,D.D.MILLER JRNL TITL UNEXPECTED BINDING ORIENTATION OF BULKY-B-RING JRNL TITL 2 ANTI-ANDROGENS AND IMPLICATIONS FOR FUTURE DRUG TARGETS. JRNL REF J.MED.CHEM. V. 54 3973 2011 JRNL REFN ISSN 0022-2623 JRNL PMID 21506597 JRNL DOI 10.1021/JM2000097 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 308831.160 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 20617 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2031 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3037 REMARK 3 BIN R VALUE (WORKING SET) : 0.3440 REMARK 3 BIN FREE R VALUE : 0.3740 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 343 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2015 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 182 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.55000 REMARK 3 B22 (A**2) : 2.44000 REMARK 3 B33 (A**2) : -0.89000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.33 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.39 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.74 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.310 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.980 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.240 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.180 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 51.76 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : S22.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : S22.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3RLJ COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-APR-11. REMARK 100 THE RCSB ID CODE IS RCSB065080. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20682 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 23.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 2AXA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M SODIUM CITRATE, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 27.37100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.68700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.39750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.68700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.37100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.39750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 847 CG CD CE NZ REMARK 470 ASN A 848 CG OD1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 813 43.10 -109.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 133 DISTANCE = 5.34 ANGSTROMS REMARK 525 HOH A 232 DISTANCE = 5.72 ANGSTROMS REMARK 525 HOH A 240 DISTANCE = 7.26 ANGSTROMS REMARK 525 HOH A 278 DISTANCE = 5.44 ANGSTROMS REMARK 525 HOH A 279 DISTANCE = 6.60 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RLJ A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RLL RELATED DB: PDB DBREF 3RLJ A 671 917 UNP P10275 ANDR_HUMAN 671 917 SEQRES 1 A 247 PRO ILE PHE LEU ASN VAL LEU GLU ALA ILE GLU PRO GLY SEQRES 2 A 247 VAL VAL CYS ALA GLY HIS ASP ASN ASN GLN PRO ASP SER SEQRES 3 A 247 PHE ALA ALA LEU LEU SER SER LEU ASN GLU LEU GLY GLU SEQRES 4 A 247 ARG GLN LEU VAL HIS VAL VAL LYS TRP ALA LYS ALA LEU SEQRES 5 A 247 PRO GLY PHE ARG ASN LEU HIS VAL ASP ASP GLN MET ALA SEQRES 6 A 247 VAL ILE GLN TYR SER TRP MET GLY LEU MET VAL PHE ALA SEQRES 7 A 247 MET GLY TRP ARG SER PHE THR ASN VAL ASN SER ARG MET SEQRES 8 A 247 LEU TYR PHE ALA PRO ASP LEU VAL PHE ASN GLU TYR ARG SEQRES 9 A 247 MET HIS LYS SER ARG MET TYR SER GLN CYS VAL ARG MET SEQRES 10 A 247 ARG HIS LEU SER GLN GLU PHE GLY TRP LEU GLN ILE THR SEQRES 11 A 247 PRO GLN GLU PHE LEU CYS MET LYS ALA LEU LEU LEU PHE SEQRES 12 A 247 SER ILE ILE PRO VAL ASP GLY LEU LYS ASN GLN LYS PHE SEQRES 13 A 247 PHE ASP GLU LEU ARG MET ASN TYR ILE LYS GLU LEU ASP SEQRES 14 A 247 ARG ILE ILE ALA CYS LYS ARG LYS ASN PRO THR SER CYS SEQRES 15 A 247 SER ARG ARG PHE TYR GLN LEU THR LYS LEU LEU ASP SER SEQRES 16 A 247 VAL GLN PRO ILE ALA ARG GLU LEU HIS GLN PHE THR PHE SEQRES 17 A 247 ASP LEU LEU ILE LYS SER HIS MET VAL SER VAL ASP PHE SEQRES 18 A 247 PRO GLU MET MET ALA GLU ILE ILE SER VAL GLN VAL PRO SEQRES 19 A 247 LYS ILE LEU SER GLY LYS VAL LYS PRO ILE TYR PHE HIS HET RLJ A 1 28 HETNAM RLJ (2S)-3-(4-CYANOPHENOXY)-N-[4-CYANO-3-(TRIFLUOROMETHYL) HETNAM 2 RLJ PHENYL]-2-HYDROXY-2-METHYLPROPANAMIDE FORMUL 2 RLJ C19 H14 F3 N3 O3 FORMUL 3 HOH *182(H2 O) HELIX 1 1 PRO A 671 GLU A 681 1 11 HELIX 2 2 SER A 696 LYS A 720 1 25 HELIX 3 3 GLY A 724 LEU A 728 5 5 HELIX 4 4 HIS A 729 ASN A 758 1 30 HELIX 5 5 ASN A 771 SER A 778 1 8 HELIX 6 6 MET A 780 LEU A 797 1 18 HELIX 7 7 THR A 800 LEU A 812 1 13 HELIX 8 8 ASN A 823 CYS A 844 1 22 HELIX 9 10 LYS A 883 SER A 888 1 6 HELIX 10 11 PRO A 892 GLN A 902 1 11 HELIX 11 12 GLN A 902 SER A 908 1 7 SHEET 1 A 2 LEU A 762 ALA A 765 0 SHEET 2 A 2 LEU A 768 PHE A 770 -1 O PHE A 770 N LEU A 762 SHEET 1 B 2 ILE A 815 PRO A 817 0 SHEET 2 B 2 VAL A 911 PRO A 913 -1 O LYS A 912 N ILE A 816 SITE 1 AC1 19 HOH A 101 HOH A 108 LEU A 704 ASN A 705 SITE 2 AC1 19 GLY A 708 GLN A 711 GLN A 738 TRP A 741 SITE 3 AC1 19 MET A 742 MET A 745 VAL A 746 MET A 749 SITE 4 AC1 19 ARG A 752 PHE A 764 LEU A 873 THR A 877 SITE 5 AC1 19 MET A 895 ILE A 899 VAL A 903 CRYST1 54.742 66.795 69.374 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.018268 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014971 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014415 0.00000 MASTER 267 0 1 11 4 0 5 6 0 0 0 19 END