HEADER TRANSCRIPTION 27-OCT-07 3B67 TITLE CRYSTAL STRUCTURE OF THE ANDROGEN RECEPTOR LIGAND BINDING DOMAIN IN TITLE 2 COMPLEX WITH SARM C-23 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANDROGEN RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 671-919; COMPND 5 SYNONYM: DIHYDROTESTOSTERONE RECEPTOR; COMPND 6 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 ANDROGEN RECEPTOR, SARM, DISEASE MUTATION, DNA-BINDING, LIPID- KEYWDS 2 BINDING, METAL-BINDING, NUCLEUS, POLYMORPHISM, STEROID-BINDING, KEYWDS 3 TRANSCRIPTION, TRANSCRIPTION REGULATION, TRIPLET REPEAT EXPANSION, KEYWDS 4 UBL CONJUGATION, ZINC, ZINC-FINGER EXPDTA X-RAY DIFFRACTION AUTHOR C.E.BOHL,D.D.MILLER,J.T.DALTON REVDAT 4 30-AUG-23 3B67 1 REMARK REVDAT 3 24-FEB-09 3B67 1 VERSN REVDAT 2 04-NOV-08 3B67 1 JRNL REVDAT 1 09-SEP-08 3B67 0 JRNL AUTH C.E.BOHL,Z.WU,J.CHEN,M.L.MOHLER,J.YANG,D.J.HWANG,S.MUSTAFA, JRNL AUTH 2 D.D.MILLER,C.E.BELL,J.T.DALTON JRNL TITL EFFECT OF B-RING SUBSTITUTION PATTERN ON BINDING MODE OF JRNL TITL 2 PROPIONAMIDE SELECTIVE ANDROGEN RECEPTOR MODULATORS JRNL REF BIOORG.MED.CHEM.LETT. V. 18 5567 2008 JRNL REFN ISSN 0960-894X JRNL PMID 18805694 JRNL DOI 10.1016/J.BMCL.2008.09.002 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) : 29.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 108104.750 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 20474 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) : 0.226 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2009 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) (%) : 97.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2978 REMARK 3 BIN R VALUE (WORKING SET) : 0.3750 REMARK 3 BIN FREE R VALUE : 0.3930 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 320 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2014 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 179 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.59000 REMARK 3 B22 (A**2) : 0.88000 REMARK 3 B33 (A**2) : -1.48000 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) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.37 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) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.43 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.780 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) : 1.300 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.990 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.260 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.170 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 64.92 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 : F5.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 : F5.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 3B67 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000045128. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-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 : MIRRORS 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 : 20501 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 29.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.930 REMARK 200 R MERGE (I) : 0.14100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2000 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: PDB ENTRY 2AXA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 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 27.43250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.87050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.10050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.87050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.43250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.10050 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 THR A 918 REMARK 465 GLN A 919 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 ND2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B67 A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AXA RELATED DB: PDB REMARK 900 RELATED ID: 3B5R RELATED DB: PDB REMARK 900 RELATED ID: 3B65 RELATED DB: PDB REMARK 900 RELATED ID: 3B66 RELATED DB: PDB REMARK 900 RELATED ID: 3B68 RELATED DB: PDB DBREF 3B67 A 671 919 UNP P10275 ANDR_HUMAN 671 919 SEQRES 1 A 249 PRO ILE PHE LEU ASN VAL LEU GLU ALA ILE GLU PRO GLY SEQRES 2 A 249 VAL VAL CYS ALA GLY HIS ASP ASN ASN GLN PRO ASP SER SEQRES 3 A 249 PHE ALA ALA LEU LEU SER SER LEU ASN GLU LEU GLY GLU SEQRES 4 A 249 ARG GLN LEU VAL HIS VAL VAL LYS TRP ALA LYS ALA LEU SEQRES 5 A 249 PRO GLY PHE ARG ASN LEU HIS VAL ASP ASP GLN MET ALA SEQRES 6 A 249 VAL ILE GLN TYR SER TRP MET GLY LEU MET VAL PHE ALA SEQRES 7 A 249 MET GLY TRP ARG SER PHE THR ASN VAL ASN SER ARG MET SEQRES 8 A 249 LEU TYR PHE ALA PRO ASP LEU VAL PHE ASN GLU TYR ARG SEQRES 9 A 249 MET HIS LYS SER ARG MET TYR SER GLN CYS VAL ARG MET SEQRES 10 A 249 ARG HIS LEU SER GLN GLU PHE GLY TRP LEU GLN ILE THR SEQRES 11 A 249 PRO GLN GLU PHE LEU CYS MET LYS ALA LEU LEU LEU PHE SEQRES 12 A 249 SER ILE ILE PRO VAL ASP GLY LEU LYS ASN GLN LYS PHE SEQRES 13 A 249 PHE ASP GLU LEU ARG MET ASN TYR ILE LYS GLU LEU ASP SEQRES 14 A 249 ARG ILE ILE ALA CYS LYS ARG LYS ASN PRO THR SER CYS SEQRES 15 A 249 SER ARG ARG PHE TYR GLN LEU THR LYS LEU LEU ASP SER SEQRES 16 A 249 VAL GLN PRO ILE ALA ARG GLU LEU HIS GLN PHE THR PHE SEQRES 17 A 249 ASP LEU LEU ILE LYS SER HIS MET VAL SER VAL ASP PHE SEQRES 18 A 249 PRO GLU MET MET ALA GLU ILE ILE SER VAL GLN VAL PRO SEQRES 19 A 249 LYS ILE LEU SER GLY LYS VAL LYS PRO ILE TYR PHE HIS SEQRES 20 A 249 THR GLN HET B67 A 1 32 HETNAM B67 (2S)-2-HYDROXY-2-METHYL-N-[4-NITRO-3-(TRIFLUOROMETHYL) HETNAM 2 B67 PHENYL]-3-(PENTAFLUOROPHENOXY)PROPANAMIDE FORMUL 2 B67 C17 H10 F8 N2 O5 FORMUL 3 HOH *179(H2 O) HELIX 1 1 PRO A 671 GLU A 681 1 11 HELIX 2 2 SER A 696 ALA A 721 1 26 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 SER A 884 VAL A 887 5 4 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 14 LEU A 704 ASN A 705 LEU A 707 GLN A 711 SITE 2 AC1 14 TRP A 741 MET A 742 MET A 745 MET A 749 SITE 3 AC1 14 ARG A 752 PHE A 764 LEU A 873 THR A 877 SITE 4 AC1 14 MET A 895 ILE A 899 CRYST1 54.865 66.201 69.741 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 0.018227 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015106 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014339 0.00000