10 20 30 40 50 60 70 80 1BY4 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER GENE REGULATION/DNA 22-OCT-98 1BY4
TITLE STRUCTURE AND MECHANISM OF THE HOMODIMERIC ASSEMBLY OF THE TITLE 2 RXR ON DNA
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (RETINOIC ACID RECEPTOR RXR-ALPHA); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'- COMPND 7 D(*C*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3'); COMPND 8 CHAIN: E, G; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'- COMPND 12 D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*A)-3'); COMPND 13 CHAIN: F, H; COMPND 14 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES
KEYWDS RXR, NUCLEAR RECEPTOR, HORMONE RESPONSE ELEMENT, PROTEIN- KEYWDS 2 DNA INTERATIONS, CRYSTAL STRUCTURE, GENE REGULATION/DNA KEYWDS 3 COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR Q.ZHAO,S.A.CHASSE,S.DEVARAKONDA,M.L.SIERK,B.AHVAZI, AUTHOR 2 P.B.SIGLER,F.RASTINEJAD
REVDAT 4 24-FEB-09 1BY4 1 VERSN REVDAT 3 26-SEP-01 1BY4 3 ATOM REVDAT 2 07-MAY-00 1BY4 1 JRNL DBREF SEQADV REVDAT 1 12-JAN-00 1BY4 0
JRNL AUTH Q.ZHAO,S.A.CHASSE,S.DEVARAKONDA,M.L.SIERK,B.AHVAZI, JRNL AUTH 2 F.RASTINEJAD JRNL TITL STRUCTURAL BASIS OF RXR-DNA INTERACTIONS. JRNL REF J.MOL.BIOL. V. 296 509 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10669605 JRNL DOI 10.1006/JMBI.1999.3457
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 72.3 REMARK 3 NUMBER OF REFLECTIONS : 45581 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.19 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3533 REMARK 3 BIN R VALUE (WORKING SET) : 0.3450 REMARK 3 BIN FREE R VALUE : 0.3520 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 : 2587 REMARK 3 NUCLEIC ACID ATOMS : 1238 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 230 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) : 0.019 REMARK 3 BOND ANGLES (DEGREES) : 2.14 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.00 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 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : TIP3P.PARAMETER REMARK 3 PARAMETER FILE 4 : ZINC.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ZINC.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: EXTRA ATOM O2* ON DC 2494 OF CHAIN G REMARK 3 WAS REMOVED.
REMARK 4 REMARK 4 1BY4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUL-99. REMARK 100 THE RCSB ID CODE IS RCSB007010.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-97 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9095 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46828 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 6.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.7 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.3900 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 (%) : 83.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.41900 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: AMORE REMARK 200 STARTING MODEL: 2NUL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 MM TRIS BUFFER (PH 7.5),20% REMARK 280 PEG3350, 5 MM MGCL2, 400MM NH4CL
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 16.82500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H, C, D 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 DC E 1494 REMARK 465 GLY A 1128 REMARK 465 SER A 1129 REMARK 465 PHE A 1130 REMARK 465 GLY C 2128 REMARK 465 SER C 2129 REMARK 465 PHE C 2130 REMARK 465 THR C 2131 REMARK 465 GLY D 2228 REMARK 465 ARG D 2309
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 DT E1495 P OP1 OP2 REMARK 470 THR A1131 OG1 CG2 REMARK 470 LYS A1132 CG CD CE NZ REMARK 470 LYS C2132 CG CD CE NZ REMARK 470 ARG C2209 CG CD NE CZ NH1 NH2
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 3252 O HOH B 3271 2.11 REMARK 500 OP2 DA G 2503 O HIS D 2246 2.18 REMARK 500 NH2 ARG C 2164 O ARG C 2209 2.18 REMARK 500 O HOH E 3312 O HOH F 3051 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 DG F1533 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DC G2494 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DC G2494 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG G2497 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC H2542 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 GLY C2144 N - CA - C ANGL. DEV. = -16.0 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 LYS A1132 -149.29 -61.61 REMARK 500 CYS A1138 -2.50 -153.24 REMARK 500 SER A1143 36.35 -95.57 REMARK 500 HIS A1146 -64.28 -129.79 REMARK 500 ARG A1164 -88.32 -62.86 REMARK 500 LYS A1165 56.47 -67.40 REMARK 500 ASP A1166 110.04 5.03 REMARK 500 THR A1168 59.05 -152.71 REMARK 500 CYS A1171 124.58 -35.68 REMARK 500 ASP A1173 -63.75 -138.72 REMARK 500 ASN A1174 142.05 171.24 REMARK 500 LYS A1175 106.26 -47.43 REMARK 500 ASP A1176 -63.11 -167.96 REMARK 500 CYS A1177 118.21 -2.77 REMARK 500 ILE A1179 107.50 -58.54 REMARK 500 MET A1200 113.29 -28.75 REMARK 500 GLU A1208 101.16 -36.10 REMARK 500 SER B1229 -76.45 -173.26 REMARK 500 LYS B1232 -97.70 -146.33 REMARK 500 ASP B1240 179.82 -51.65 REMARK 500 HIS B1246 -59.21 -121.88 REMARK 500 ASP B1273 -62.71 -147.56 REMARK 500 ASN B1274 -163.43 -176.16 REMARK 500 LYS B1275 -74.86 -61.31 REMARK 500 CYS B1287 70.96 -108.76 REMARK 500 GLN B1288 -25.72 -38.91 REMARK 500 GLU B1308 168.45 -36.49 REMARK 500 CYS C2138 -17.43 -150.32 REMARK 500 HIS C2146 -53.40 -121.23 REMARK 500 ASP C2166 90.56 -37.60 REMARK 500 ASN C2174 -71.70 -174.00 REMARK 500 LYS C2175 10.92 -168.50 REMARK 500 TYR C2189 -71.39 -54.56 REMARK 500 LEU C2196 39.15 -83.79 REMARK 500 ALA C2197 -34.92 -144.53 REMARK 500 LYS D2232 -95.84 -106.25 REMARK 500 TYR D2247 54.43 -161.44 REMARK 500 ASP D2273 -123.24 -121.99 REMARK 500 ASN D2274 -126.58 -120.45 REMARK 500 LYS D2275 -118.01 -58.25 REMARK 500 GLN D2306 -165.74 -115.78 REMARK 500 GLU D2307 -48.28 -143.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DA E1503 0.10 SIDE_CHAIN REMARK 500 DA E1508 0.07 SIDE_CHAIN REMARK 500 DC F1535 0.06 SIDE_CHAIN REMARK 500 DC F1536 0.06 SIDE_CHAIN REMARK 500 DT F1537 0.09 SIDE_CHAIN REMARK 500 DC F1543 0.07 SIDE_CHAIN REMARK 500 DG G2497 0.09 SIDE_CHAIN REMARK 500 DA G2502 0.06 SIDE_CHAIN REMARK 500 DA G2503 0.13 SIDE_CHAIN REMARK 500 DG G2505 0.08 SIDE_CHAIN REMARK 500 PHE C2158 0.08 SIDE_CHAIN REMARK 500 TYR D2247 0.07 SIDE_CHAIN 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 C3066 DISTANCE = 5.29 ANGSTROMS REMARK 525 HOH E3312 DISTANCE = 5.08 ANGSTROMS
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1330 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1135 SG REMARK 620 2 CYS A1138 SG 99.8 REMARK 620 3 CYS A1155 SG 108.7 110.5 REMARK 620 4 CYS A1152 SG 112.7 101.5 121.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1331 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1177 SG REMARK 620 2 CYS A1190 SG 109.2 REMARK 620 3 CYS A1171 SG 115.1 113.3 REMARK 620 4 CYS A1187 SG 105.0 115.0 98.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1335 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1235 SG REMARK 620 2 CYS B1255 SG 103.3 REMARK 620 3 CYS B1238 SG 106.0 108.6 REMARK 620 4 CYS B1252 SG 126.6 103.5 107.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1336 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1290 SG REMARK 620 2 CYS B1271 SG 111.4 REMARK 620 3 CYS B1287 SG 114.0 113.1 REMARK 620 4 CYS B1277 SG 103.6 96.4 116.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C2330 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C2152 SG REMARK 620 2 CYS C2135 SG 117.9 REMARK 620 3 CYS C2138 SG 97.4 101.6 REMARK 620 4 CYS C2155 SG 112.6 107.1 120.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C2331 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C2171 SG REMARK 620 2 CYS C2177 SG 123.1 REMARK 620 3 CYS C2190 SG 109.3 112.1 REMARK 620 4 CYS C2187 SG 109.4 101.2 98.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D2335 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D2235 SG REMARK 620 2 CYS D2252 SG 122.9 REMARK 620 3 CYS D2255 SG 103.4 105.1 REMARK 620 4 CYS D2238 SG 109.1 108.6 106.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D2336 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D2271 SG REMARK 620 2 CYS D2277 SG 96.8 REMARK 620 3 CYS D2290 SG 95.8 108.7 REMARK 620 4 CYS D2287 SG 122.7 116.3 113.6 REMARK 620 N 1 2 3
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1330 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1331 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1335 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1336 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 2330 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 2331 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 2335 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 2336
DBREF 1BY4 A 1128 1209 UNP P19793 RXRA_HUMAN 128 209 DBREF 1BY4 B 1228 1309 UNP P19793 RXRA_HUMAN 128 209 DBREF 1BY4 C 2128 2209 UNP P19793 RXRA_HUMAN 128 209 DBREF 1BY4 D 2228 2309 UNP P19793 RXRA_HUMAN 128 209 DBREF 1BY4 E 1494 1509 PDB 1BY4 1BY4 1494 1509 DBREF 1BY4 F 1531 1545 PDB 1BY4 1BY4 1531 1545 DBREF 1BY4 G 2494 2509 PDB 1BY4 1BY4 2494 2509 DBREF 1BY4 H 2531 2545 PDB 1BY4 1BY4 2531 2545
SEQADV 1BY4 GLY A 1128 UNP P19793 ALA 128 CONFLICT SEQADV 1BY4 GLY B 1228 UNP P19793 ALA 128 CONFLICT SEQADV 1BY4 GLY C 2128 UNP P19793 ALA 128 CONFLICT SEQADV 1BY4 GLY D 2228 UNP P19793 ALA 128 CONFLICT
SEQRES 1 A 82 GLY SER PHE THR LYS HIS ILE CYS ALA ILE CYS GLY ASP SEQRES 2 A 82 ARG SER SER GLY LYS HIS TYR GLY VAL TYR SER CYS GLU SEQRES 3 A 82 GLY CYS LYS GLY PHE PHE LYS ARG THR VAL ARG LYS ASP SEQRES 4 A 82 LEU THR TYR THR CYS ARG ASP ASN LYS ASP CYS LEU ILE SEQRES 5 A 82 ASP LYS ARG GLN ARG ASN ARG CYS GLN TYR CYS ARG TYR SEQRES 6 A 82 GLN LYS CYS LEU ALA MET GLY MET LYS ARG GLU ALA VAL SEQRES 7 A 82 GLN GLU GLU ARG SEQRES 1 B 82 GLY SER PHE THR LYS HIS ILE CYS ALA ILE CYS GLY ASP SEQRES 2 B 82 ARG SER SER GLY LYS HIS TYR GLY VAL TYR SER CYS GLU SEQRES 3 B 82 GLY CYS LYS GLY PHE PHE LYS ARG THR VAL ARG LYS ASP SEQRES 4 B 82 LEU THR TYR THR CYS ARG ASP ASN LYS ASP CYS LEU ILE SEQRES 5 B 82 ASP LYS ARG GLN ARG ASN ARG CYS GLN TYR CYS ARG TYR SEQRES 6 B 82 GLN LYS CYS LEU ALA MET GLY MET LYS ARG GLU ALA VAL SEQRES 7 B 82 GLN GLU GLU ARG SEQRES 1 C 82 GLY SER PHE THR LYS HIS ILE CYS ALA ILE CYS GLY ASP SEQRES 2 C 82 ARG SER SER GLY LYS HIS TYR GLY VAL TYR SER CYS GLU SEQRES 3 C 82 GLY CYS LYS GLY PHE PHE LYS ARG THR VAL ARG LYS ASP SEQRES 4 C 82 LEU THR TYR THR CYS ARG ASP ASN LYS ASP CYS LEU ILE SEQRES 5 C 82 ASP LYS ARG GLN ARG ASN ARG CYS GLN TYR CYS ARG TYR SEQRES 6 C 82 GLN LYS CYS LEU ALA MET GLY MET LYS ARG GLU ALA VAL SEQRES 7 C 82 GLN GLU GLU ARG SEQRES 1 D 82 GLY SER PHE THR LYS HIS ILE CYS ALA ILE CYS GLY ASP SEQRES 2 D 82 ARG SER SER GLY LYS HIS TYR GLY VAL TYR SER CYS GLU SEQRES 3 D 82 GLY CYS LYS GLY PHE PHE LYS ARG THR VAL ARG LYS ASP SEQRES 4 D 82 LEU THR TYR THR CYS ARG ASP ASN LYS ASP CYS LEU ILE SEQRES 5 D 82 ASP LYS ARG GLN ARG ASN ARG CYS GLN TYR CYS ARG TYR SEQRES 6 D 82 GLN LYS CYS LEU ALA MET GLY MET LYS ARG GLU ALA VAL SEQRES 7 D 82 GLN GLU GLU ARG SEQRES 1 E 16 DC DT DA DG DG DT DC DA DA DA DG DG DT SEQRES 2 E 16 DC DA DG SEQRES 1 F 15 DC DT DG DA DC DC DT DT DT DG DA DC DC SEQRES 2 F 15 DT DA SEQRES 1 G 16 DC DT DA DG DG DT DC DA DA DA DG DG DT SEQRES 2 G 16 DC DA DG SEQRES 1 H 15 DC DT DG DA DC DC DT DT DT DG DA DC DC SEQRES 2 H 15 DT DA
HET ZN A1330 1 HET ZN A1331 1 HET ZN B1335 1 HET ZN B1336 1 HET ZN C2330 1 HET ZN C2331 1 HET ZN D2335 1 HET ZN D2336 1
HETNAM ZN ZINC ION
FORMUL 9 ZN 8(ZN 2+) FORMUL 17 HOH *230(H2 O)
HELIX 1 1 GLU A 1153 ARG A 1164 1 12 HELIX 2 2 ARG A 1182 ARG A 1184 5 3 HELIX 3 3 GLN A 1188 LEU A 1196 1 9 HELIX 4 4 ARG A 1202 ALA A 1204 5 3 HELIX 5 5 GLU B 1253 ARG B 1264 1 12 HELIX 6 6 GLN B 1288 ALA B 1297 1 10 HELIX 7 7 ARG B 1302 ALA B 1304 5 3 HELIX 8 8 GLU C 2153 ARG C 2164 1 12 HELIX 9 9 GLN C 2188 MET C 2198 1 11 HELIX 10 10 GLU D 2253 VAL D 2263 1 11 HELIX 11 11 ARG D 2284 ARG D 2286 5 3 HELIX 12 12 GLN D 2288 MET D 2298 1 11 HELIX 13 13 ARG D 2302 ALA D 2304 5 3
SHEET 1 A 2 HIS B1233 ILE B1234 0 SHEET 2 A 2 ARG B1241 SER B1242 -1 O SER B1242 N HIS B1233 SHEET 1 B 2 GLY B1244 LYS B1245 0 SHEET 2 B 2 TYR B1250 SER B1251 -1 N SER B1251 O GLY B1244 SHEET 1 C 2 HIS D2233 ILE D2234 0 SHEET 2 C 2 ARG D2241 SER D2242 -1 N SER D2242 O HIS D2233 SHEET 1 D 2 GLY D2244 LYS D2245 0 SHEET 2 D 2 TYR D2250 SER D2251 -1 N SER D2251 O GLY D2244
LINK ZN ZN A1330 SG CYS A1135 1555 1555 2.43 LINK ZN ZN A1330 SG CYS A1138 1555 1555 2.46 LINK ZN ZN A1330 SG CYS A1155 1555 1555 2.22 LINK ZN ZN A1330 SG CYS A1152 1555 1555 2.31 LINK ZN ZN A1331 SG CYS A1177 1555 1555 2.36 LINK ZN ZN A1331 SG CYS A1190 1555 1555 2.35 LINK ZN ZN A1331 SG CYS A1171 1555 1555 2.44 LINK ZN ZN A1331 SG CYS A1187 1555 1555 2.44 LINK ZN ZN B1335 SG CYS B1235 1555 1555 2.32 LINK ZN ZN B1335 SG CYS B1255 1555 1555 2.41 LINK ZN ZN B1335 SG CYS B1238 1555 1555 2.54 LINK ZN ZN B1335 SG CYS B1252 1555 1555 2.28 LINK ZN ZN B1336 SG CYS B1290 1555 1555 2.33 LINK ZN ZN B1336 SG CYS B1271 1555 1555 2.31 LINK ZN ZN B1336 SG CYS B1287 1555 1555 2.17 LINK ZN ZN B1336 SG CYS B1277 1555 1555 2.43 LINK ZN ZN C2330 SG CYS C2152 1555 1555 2.33 LINK ZN ZN C2330 SG CYS C2135 1555 1555 2.41 LINK ZN ZN C2330 SG CYS C2138 1555 1555 2.44 LINK ZN ZN C2330 SG CYS C2155 1555 1555 2.11 LINK ZN ZN C2331 SG CYS C2171 1555 1555 2.36 LINK ZN ZN C2331 SG CYS C2177 1555 1555 2.32 LINK ZN ZN C2331 SG CYS C2190 1555 1555 2.42 LINK ZN ZN C2331 SG CYS C2187 1555 1555 2.35 LINK ZN ZN D2335 SG CYS D2235 1555 1555 2.33 LINK ZN ZN D2335 SG CYS D2252 1555 1555 2.30 LINK ZN ZN D2335 SG CYS D2255 1555 1555 2.45 LINK ZN ZN D2335 SG CYS D2238 1555 1555 2.47 LINK ZN ZN D2336 SG CYS D2271 1555 1555 2.32 LINK ZN ZN D2336 SG CYS D2277 1555 1555 2.35 LINK ZN ZN D2336 SG CYS D2290 1555 1555 2.45 LINK ZN ZN D2336 SG CYS D2287 1555 1555 2.21
SITE 1 AC1 4 CYS A1135 CYS A1138 CYS A1152 CYS A1155 SITE 1 AC2 4 CYS A1171 CYS A1177 CYS A1187 CYS A1190 SITE 1 AC3 4 CYS B1235 CYS B1238 CYS B1252 CYS B1255 SITE 1 AC4 4 CYS B1271 CYS B1277 CYS B1287 CYS B1290 SITE 1 AC5 4 CYS C2135 CYS C2138 CYS C2152 CYS C2155 SITE 1 AC6 5 CYS C2171 ASP C2176 CYS C2177 CYS C2187 SITE 2 AC6 5 CYS C2190 SITE 1 AC7 4 CYS D2235 CYS D2238 CYS D2252 CYS D2255 SITE 1 AC8 4 CYS D2271 CYS D2277 CYS D2287 CYS D2290
CRYST1 70.930 33.650 101.400 90.00 89.95 90.00 P 1 21 1 8
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 0.014098 0.000000 -0.000012 0.00000
SCALE2 0.000000 0.029718 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009862 0.00000