PDB Short entry for 4DQM HEADER TRANSCRIPTION/TRANSFERASE 16-FEB-12 4DQM TITLE REVEALING A MARINE NATURAL PRODUCT AS A NOVEL AGONIST FOR RETINOIC TITLE 2 ACID RECEPTORS WITH A UNIQUE BINDING MODE AND ANTITUMOR ACTIVITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOIC ACID RECEPTOR ALPHA; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN, UNP RESIDUES 182-415; COMPND 5 SYNONYM: RAR-ALPHA, NUCLEAR RECEPTOR SUBFAMILY 1 GROUP B MEMBER 1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NUCLEAR RECEPTOR COACTIVATOR 1; COMPND 9 CHAIN: B, D; COMPND 10 FRAGMENT: LXXLL MOTIF 7, UNP RESIDUES 1432-1441; COMPND 11 SYNONYM: NCOA-1, CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 74, BHLHE74, COMPND 12 PROTEIN HIN-2, RIP160, RENAL CARCINOMA ANTIGEN NY-REN-52, STEROID COMPND 13 RECEPTOR COACTIVATOR 1, SRC-1; COMPND 14 EC: 2.3.1.48; COMPND 15 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: NR1B1, RARA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. KEYWDS NUCLEAR RECEPTOR TRANSCRIPTION FACTOR, LIGAND BINDING DOMAIN, KEYWDS 2 TRANSCRIPTION REGULATION, NUCLEUS, TRANSCRIPTION-TRANSFERASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.WANG,Z.WANG,S.LIN,W.ZHENG,R.WANG,S.JIN,J.CHEN,L.JIN,Y.LI REVDAT 3 15-NOV-17 4DQM 1 REMARK REVDAT 2 16-APR-14 4DQM 1 REMARK REVDAT 1 03-OCT-12 4DQM 0 JRNL AUTH S.WANG,Z.WANG,S.LIN,W.ZHENG,R.WANG,S.JIN,J.CHEN,L.JIN,Y.LI JRNL TITL REVEALING A NATURAL MARINE PRODUCT AS A NOVEL AGONIST FOR JRNL TITL 2 RETINOIC ACID RECEPTORS WITH A UNIQUE BINDING MODE AND JRNL TITL 3 INHIBITORY EFFECTS ON CANCER CELLS. JRNL REF BIOCHEM.J. V. 446 79 2012 JRNL REFN ISSN 0264-6021 JRNL PMID 22642567 JRNL DOI 10.1042/BJ20120726 REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.9 REMARK 3 NUMBER OF REFLECTIONS : 16995 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 + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 922 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1139 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.3210 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.3350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3855 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 31 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.10000 REMARK 3 B22 (A**2) : 0.15000 REMARK 3 B33 (A**2) : -0.05000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.885 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.337 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.263 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.510 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3968 ; 0.014 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5360 ; 1.750 ; 2.018 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 484 ; 6.145 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 162 ;39.109 ;24.815 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 763 ;19.768 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;23.147 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 636 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2863 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 4DQM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070660. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5619 REMARK 200 MONOCHROMATOR : DIAMOND [111] REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17478 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 0.64800 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2% V/V TACSIMATE PH7.0, 5% 2-PROPANOL, REMARK 280 0.1M IMADAZOLE , 8% PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.23000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.74000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.23000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 56.74000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 ASP C 282 N REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 CYS A 333 SG 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 N SER A 287 O3 LUF A 501 1.68 REMARK 500 SG CYS A 235 C23 LUF A 501 1.79 REMARK 500 N SER C 287 O3 LUF C 501 1.87 REMARK 500 SG CYS C 235 C23 LUF C 501 1.91 REMARK 500 OE2 GLU C 412 O SER D 1433 1.96 REMARK 500 NH2 ARG C 364 O HOH C 610 2.12 REMARK 500 CA PHE C 286 O3 LUF C 501 2.14 REMARK 500 CA PHE A 286 O3 LUF A 501 2.16 REMARK 500 C PHE A 286 O3 LUF A 501 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 333 CB CYS A 333 SG -0.344 REMARK 500 HIS A 372 CG HIS A 372 CD2 0.054 REMARK 500 TRP C 225 CE2 TRP C 225 CD2 0.079 REMARK 500 HIS C 372 CG HIS C 372 CD2 0.056 REMARK 500 GLU D1441 CD GLU D1441 OE2 0.068 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 CYS A 333 CA - CB - SG ANGL. DEV. = 17.3 DEGREES REMARK 500 LEU C 378 CB - CG - CD1 ANGL. DEV. = -10.4 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 TYR A 208 126.90 -174.44 REMARK 500 SER A 213 42.22 23.62 REMARK 500 GLU A 215 -64.30 -99.12 REMARK 500 ASP A 322 -165.84 -106.32 REMARK 500 LYS A 390 6.73 -69.97 REMARK 500 PRO A 403 -73.66 -75.75 REMARK 500 LEU B1434 -53.40 -22.43 REMARK 500 PHE C 199 86.37 -154.71 REMARK 500 THR C 209 -151.51 -127.03 REMARK 500 THR C 210 157.08 179.70 REMARK 500 SER C 213 49.27 28.91 REMARK 500 LEU C 220 112.86 -161.87 REMARK 500 ASP C 341 18.69 86.53 REMARK 500 PRO C 403 -81.80 -71.65 REMARK 500 SER D1433 3.16 -53.47 REMARK 500 LEU D1434 -53.64 107.17 REMARK 500 THR D1440 44.80 -93.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 LUF C 501 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LUF A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LUF C 501 DBREF 4DQM A 182 415 UNP P10276 RARA_HUMAN 182 415 DBREF 4DQM B 1432 1441 UNP Q15788 NCOA1_HUMAN 1432 1441 DBREF 4DQM C 182 415 UNP P10276 RARA_HUMAN 182 415 DBREF 4DQM D 1432 1441 UNP Q15788 NCOA1_HUMAN 1432 1441 SEQRES 1 A 234 PRO GLU VAL GLY GLU LEU ILE GLU LYS VAL ARG LYS ALA SEQRES 2 A 234 HIS GLN GLU THR PHE PRO ALA LEU CYS GLN LEU GLY LYS SEQRES 3 A 234 TYR THR THR ASN ASN SER SER GLU GLN ARG VAL SER LEU SEQRES 4 A 234 ASP ILE ASP LEU TRP ASP LYS PHE SER GLU LEU SER THR SEQRES 5 A 234 LYS CYS ILE ILE LYS THR VAL GLU PHE ALA LYS GLN LEU SEQRES 6 A 234 PRO GLY PHE THR THR LEU THR ILE ALA ASP GLN ILE THR SEQRES 7 A 234 LEU LEU LYS ALA ALA CYS LEU ASP ILE LEU ILE LEU ARG SEQRES 8 A 234 ILE CYS THR ARG TYR THR PRO GLU GLN ASP THR MET THR SEQRES 9 A 234 PHE SER ASP GLY LEU THR LEU ASN ARG THR GLN MET HIS SEQRES 10 A 234 ASN ALA GLY PHE GLY PRO LEU THR ASP LEU VAL PHE ALA SEQRES 11 A 234 PHE ALA ASN GLN LEU LEU PRO LEU GLU MET ASP ASP ALA SEQRES 12 A 234 GLU THR GLY LEU LEU SER ALA ILE CYS LEU ILE CYS GLY SEQRES 13 A 234 ASP ARG GLN ASP LEU GLU GLN PRO ASP ARG VAL ASP MET SEQRES 14 A 234 LEU GLN GLU PRO LEU LEU GLU ALA LEU LYS VAL TYR VAL SEQRES 15 A 234 ARG LYS ARG ARG PRO SER ARG PRO HIS MET PHE PRO LYS SEQRES 16 A 234 MET LEU MET LYS ILE THR ASP LEU ARG SER ILE SER ALA SEQRES 17 A 234 LYS GLY ALA GLU ARG VAL ILE THR LEU LYS MET GLU ILE SEQRES 18 A 234 PRO GLY SER MET PRO PRO LEU ILE GLN GLU MET LEU GLU SEQRES 1 B 10 LYS SER LEU LEU GLN GLN LEU LEU THR GLU SEQRES 1 C 234 PRO GLU VAL GLY GLU LEU ILE GLU LYS VAL ARG LYS ALA SEQRES 2 C 234 HIS GLN GLU THR PHE PRO ALA LEU CYS GLN LEU GLY LYS SEQRES 3 C 234 TYR THR THR ASN ASN SER SER GLU GLN ARG VAL SER LEU SEQRES 4 C 234 ASP ILE ASP LEU TRP ASP LYS PHE SER GLU LEU SER THR SEQRES 5 C 234 LYS CYS ILE ILE LYS THR VAL GLU PHE ALA LYS GLN LEU SEQRES 6 C 234 PRO GLY PHE THR THR LEU THR ILE ALA ASP GLN ILE THR SEQRES 7 C 234 LEU LEU LYS ALA ALA CYS LEU ASP ILE LEU ILE LEU ARG SEQRES 8 C 234 ILE CYS THR ARG TYR THR PRO GLU GLN ASP THR MET THR SEQRES 9 C 234 PHE SER ASP GLY LEU THR LEU ASN ARG THR GLN MET HIS SEQRES 10 C 234 ASN ALA GLY PHE GLY PRO LEU THR ASP LEU VAL PHE ALA SEQRES 11 C 234 PHE ALA ASN GLN LEU LEU PRO LEU GLU MET ASP ASP ALA SEQRES 12 C 234 GLU THR GLY LEU LEU SER ALA ILE CYS LEU ILE CYS GLY SEQRES 13 C 234 ASP ARG GLN ASP LEU GLU GLN PRO ASP ARG VAL ASP MET SEQRES 14 C 234 LEU GLN GLU PRO LEU LEU GLU ALA LEU LYS VAL TYR VAL SEQRES 15 C 234 ARG LYS ARG ARG PRO SER ARG PRO HIS MET PHE PRO LYS SEQRES 16 C 234 MET LEU MET LYS ILE THR ASP LEU ARG SER ILE SER ALA SEQRES 17 C 234 LYS GLY ALA GLU ARG VAL ILE THR LEU LYS MET GLU ILE SEQRES 18 C 234 PRO GLY SER MET PRO PRO LEU ILE GLN GLU MET LEU GLU SEQRES 1 D 10 LYS SER LEU LEU GLN GLN LEU LEU THR GLU HET LUF A 501 28 HET LUF C 501 26 HETNAM LUF (5S)-4-[(3E,7E)-4,8-DIMETHYL-10-(2,6,6- HETNAM 2 LUF TRIMETHYLCYCLOHEX-1-EN-1-YL)DECA-3,7-DIEN-1-YL]-5- HETNAM 3 LUF HYDROXYFURAN-2(5H)-ONE HETSYN LUF LUFFARIELLOLIDE FORMUL 5 LUF 2(C25 H38 O3) FORMUL 7 HOH *31(H2 O) HELIX 1 1 PRO A 182 PHE A 199 1 18 HELIX 2 2 ALA A 201 LEU A 205 5 5 HELIX 3 3 ASP A 221 GLN A 245 1 25 HELIX 4 4 GLY A 248 LEU A 252 5 5 HELIX 5 5 THR A 253 THR A 275 1 23 HELIX 6 6 ARG A 294 ALA A 300 1 7 HELIX 7 7 GLY A 301 PRO A 304 5 4 HELIX 8 8 LEU A 305 LEU A 317 1 13 HELIX 9 9 PRO A 318 GLU A 320 5 3 HELIX 10 10 ASP A 322 ILE A 335 1 14 HELIX 11 11 GLN A 344 ARG A 367 1 24 HELIX 12 12 HIS A 372 MET A 379 1 8 HELIX 13 13 MET A 379 LYS A 390 1 12 HELIX 14 14 LYS A 390 ILE A 402 1 13 HELIX 15 15 PRO A 407 GLU A 415 1 9 HELIX 16 16 SER B 1433 GLU B 1441 1 9 HELIX 17 17 GLU C 183 PHE C 199 1 17 HELIX 18 18 ALA C 201 LEU C 205 5 5 HELIX 19 19 ASP C 221 GLN C 245 1 25 HELIX 20 20 GLY C 248 LEU C 252 5 5 HELIX 21 21 THR C 253 THR C 275 1 23 HELIX 22 22 ARG C 294 ALA C 300 1 7 HELIX 23 23 GLY C 301 GLY C 303 5 3 HELIX 24 24 PRO C 304 LEU C 316 1 13 HELIX 25 25 ASP C 322 ILE C 335 1 14 HELIX 26 26 GLN C 344 ARG C 367 1 24 HELIX 27 27 HIS C 372 LYS C 390 1 19 HELIX 28 28 LYS C 390 MET C 400 1 11 HELIX 29 29 PRO C 407 GLU C 415 1 9 HELIX 30 30 LEU D 1435 THR D 1440 1 6 SHEET 1 A 3 TYR A 277 THR A 278 0 SHEET 2 A 3 THR A 283 THR A 285 -1 O THR A 283 N THR A 278 SHEET 3 A 3 THR A 291 ASN A 293 -1 O LEU A 292 N MET A 284 SHEET 1 B 3 TYR C 277 THR C 278 0 SHEET 2 B 3 THR C 283 THR C 285 -1 O THR C 283 N THR C 278 SHEET 3 B 3 THR C 291 ASN C 293 -1 O LEU C 292 N MET C 284 LINK SG CYS A 235 O2 LUF A 501 1555 1555 0.72 LINK SG CYS C 235 O2 LUF C 501 1555 1555 1.55 SITE 1 AC1 13 PHE A 228 LEU A 231 SER A 232 CYS A 235 SITE 2 AC1 13 LEU A 266 LEU A 269 ILE A 273 ARG A 276 SITE 3 AC1 13 PHE A 286 SER A 287 GLY A 301 VAL A 395 SITE 4 AC1 13 LEU A 414 SITE 1 AC2 13 PHE C 228 LEU C 231 SER C 232 CYS C 235 SITE 2 AC2 13 LEU C 266 LEU C 269 ILE C 273 ARG C 276 SITE 3 AC2 13 PHE C 286 SER C 287 PHE C 302 VAL C 395 SITE 4 AC2 13 HOH C 605 CRYST1 54.120 104.460 113.480 90.00 90.00 90.00 P 2 21 21 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 0.018477 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009573 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008812 0.00000