HEADER LIGAND BINDING PROTEIN 28-JUL-06 2HVC TITLE THE CRYSTAL STRUCTURE OF LIGAND-BINDING DOMAIN (LBD) OF HUMAN ANDROGEN TITLE 2 RECEPTOR IN COMPLEX WITH A SELECTIVE MODULATOR LGD2226 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANDROGEN RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGIND-BINDING DOMAIN(RESIDUES 669-918); COMPND 5 SYNONYM: DIHYDROTESTOSTERONE RECEPTOR, AR; 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-KG KEYWDS COMPLEXED WITH LGD2226, DNA-BINDING, STEROID-BINDING, LIGAND BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.WANG,X.-Q.LIU,H.LI,K.-N.LIANG,J.N.MINER,M.HONG,E.A.KALLEL,A.VAN AUTHOR 2 OEVEREN,L.ZHI,T.JIANG REVDAT 3 25-OCT-23 2HVC 1 REMARK REVDAT 2 24-FEB-09 2HVC 1 VERSN REVDAT 1 31-JUL-07 2HVC 0 JRNL AUTH F.WANG,X.-Q.LIU,H.LI,K.-N.LIANG,J.N.MINER,M.HONG,E.A.KALLEL, JRNL AUTH 2 A.VAN OEVEREN,L.ZHI,T.JIANG JRNL TITL STRUCTURE OF THE LIGAND-BINDING DOMAIN (LBD) OF HUMAN JRNL TITL 2 ANDROGEN RECEPTOR IN COMPLEX WITH A SELECTIVE MODULATOR JRNL TITL 3 LGD2226 JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 62 1067 2006 JRNL REFN ESSN 1744-3091 JRNL PMID 17077481 JRNL DOI 10.1107/S1744309106039340 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 16458 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 824 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2043 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 114 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2HVC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1000038806. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 79 REMARK 200 PH : 7.2 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 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 : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16570 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 11.90 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.92 REMARK 200 R MERGE FOR SHELL (I) : 0.28300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: MOLREP REMARK 200 STARTING MODEL: 1XQ3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MIXING THE PROTEIN SOLUTION(5MG/ML) REMARK 280 WITH EQUAL VOLUME OF THE RESERVOIR SOLUTION WITH 0.4M NA2HPO4, REMARK 280 0.4M K2HPO4, AS THE PRIMARY PRECIPITATORS. PH 7.2, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 28.82000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.08500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.69500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.08500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.82000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.69500 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLN A 670 N - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 500 PRO A 849 C - N - CA ANGL. DEV. = 13.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 819 44.69 -99.90 REMARK 500 LYS A 847 -69.20 -126.12 REMARK 500 PRO A 849 -28.15 -34.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LGD A 2226 DBREF 2HVC A 669 918 UNP P10275 ANDR_HUMAN 669 918 SEQRES 1 A 250 CYS GLN PRO ILE PHE LEU ASN VAL LEU GLU ALA ILE GLU SEQRES 2 A 250 PRO GLY VAL VAL CYS ALA GLY HIS ASP ASN ASN GLN PRO SEQRES 3 A 250 ASP SER PHE ALA ALA LEU LEU SER SER LEU ASN GLU LEU SEQRES 4 A 250 GLY GLU ARG GLN LEU VAL HIS VAL VAL LYS TRP ALA LYS SEQRES 5 A 250 ALA LEU PRO GLY PHE ARG ASN LEU HIS VAL ASP ASP GLN SEQRES 6 A 250 MET ALA VAL ILE GLN TYR SER TRP MET GLY LEU MET VAL SEQRES 7 A 250 PHE ALA MET GLY TRP ARG SER PHE THR ASN VAL ASN SER SEQRES 8 A 250 ARG MET LEU TYR PHE ALA PRO ASP LEU VAL PHE ASN GLU SEQRES 9 A 250 TYR ARG MET HIS LYS SER ARG MET TYR SER GLN CYS VAL SEQRES 10 A 250 ARG MET ARG HIS LEU SER GLN GLU PHE GLY TRP LEU GLN SEQRES 11 A 250 ILE THR PRO GLN GLU PHE LEU CYS MET LYS ALA LEU LEU SEQRES 12 A 250 LEU PHE SER ILE ILE PRO VAL ASP GLY LEU LYS ASN GLN SEQRES 13 A 250 LYS PHE PHE ASP GLU LEU ARG MET ASN TYR ILE LYS GLU SEQRES 14 A 250 LEU ASP ARG ILE ILE ALA CYS LYS ARG LYS ASN PRO THR SEQRES 15 A 250 SER CYS SER ARG ARG PHE TYR GLN LEU THR LYS LEU LEU SEQRES 16 A 250 ASP SER VAL GLN PRO ILE ALA ARG GLU LEU HIS GLN PHE SEQRES 17 A 250 THR PHE ASP LEU LEU ILE LYS SER HIS MET VAL SER VAL SEQRES 18 A 250 ASP PHE PRO GLU MET MET ALA GLU ILE ILE SER VAL GLN SEQRES 19 A 250 VAL PRO LYS ILE LEU SER GLY LYS VAL LYS PRO ILE TYR SEQRES 20 A 250 PHE HIS THR HET LGD A2226 26 HETNAM LGD 6-[BIS(2,2,2-TRIFLUOROETHYL)AMINO]-4-(TRIFLUOROMETHYL) HETNAM 2 LGD QUINOLIN-2(1H)-ONE HETSYN LGD 1,2-DIHYDRO-6-N,N-BIS(2,2,2-TRIFLUOROETHYL)AMINO-4- HETSYN 2 LGD TRIFLUOROMETHYL-2-QUINOLINONE FORMUL 2 LGD C14 H9 F9 N2 O FORMUL 3 HOH *114(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 PHE A 813 1 14 HELIX 8 8 ASN A 823 CYS A 844 1 22 HELIX 9 9 ASN A 848 SER A 884 1 37 HELIX 10 10 HIS A 885 SER A 888 5 4 HELIX 11 11 PRO A 892 GLN A 902 1 11 HELIX 12 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 18 HOH A 36 LEU A 701 LEU A 704 ASN A 705 SITE 2 AC1 18 GLY A 708 GLN A 711 TRP A 741 MET A 742 SITE 3 AC1 18 MET A 745 VAL A 746 MET A 749 ARG A 752 SITE 4 AC1 18 PHE A 764 MET A 780 MET A 787 LEU A 873 SITE 5 AC1 18 PHE A 876 THR A 877 CRYST1 57.640 65.390 72.170 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 0.017349 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015293 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013856 0.00000