HEADER PROTEIN BINDING 29-SEP-11 3U15 TITLE STRUCTURE OF HDMX WITH DIMER INDUCING INDOLYL HYDANTOIN RO-2443 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN MDM4; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: UNP RESIDUES 14-111; COMPND 5 SYNONYM: DOUBLE MINUTE 4 PROTEIN, MDM2-LIKE P53-BINDING PROTEIN, COMPND 6 PROTEIN MDMX, P53-BINDING PROTEIN MDM4; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MDM4, MDMX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS CELL CYCLE, UBIQUITIN LIGASE, MDM2, MDMX, P53, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR C.M.LUKACS,C.A.JANSON,B.J.GRAVES REVDAT 5 13-SEP-23 3U15 1 REMARK SEQADV REVDAT 4 08-NOV-17 3U15 1 REMARK REVDAT 3 01-AUG-12 3U15 1 JRNL REVDAT 2 25-JUL-12 3U15 1 JRNL REVDAT 1 27-JUN-12 3U15 0 JRNL AUTH B.GRAVES,T.THOMPSON,M.XIA,C.JANSON,C.LUKACS,D.DEO, JRNL AUTH 2 P.DI LELLO,D.FRY,C.GARVIE,K.S.HUANG,L.GAO,C.TOVAR,A.LOVEY, JRNL AUTH 3 J.WANNER,L.T.VASSILEV JRNL TITL ACTIVATION OF THE P53 PATHWAY BY SMALL-MOLECULE-INDUCED MDM2 JRNL TITL 2 AND MDMX DIMERIZATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 11788 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22745160 JRNL DOI 10.1073/PNAS.1203789109 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 35945 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1951 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2653 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.1850 REMARK 3 BIN FREE R VALUE SET COUNT : 114 REMARK 3 BIN FREE R VALUE : 0.3960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2625 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 122 REMARK 3 SOLVENT ATOMS : 149 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.09000 REMARK 3 B22 (A**2) : 1.09000 REMARK 3 B33 (A**2) : -2.17000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.026 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.580 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2813 ; 0.016 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3802 ; 2.685 ; 2.051 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 323 ;10.676 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 120 ;42.521 ;24.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 515 ;25.305 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;17.230 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 392 ; 0.142 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2116 ; 0.010 ; 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 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 4 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.256 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : -K, -H, -L REMARK 3 TWIN FRACTION : 0.249 REMARK 3 TWIN DOMAIN : 3 REMARK 3 TWIN OPERATOR : -H,-K,L REMARK 3 TWIN FRACTION : 0.247 REMARK 3 TWIN DOMAIN : 4 REMARK 3 TWIN OPERATOR : K, H, -L REMARK 3 TWIN FRACTION : 0.248 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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: NULL REMARK 4 REMARK 4 3U15 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068174. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41300 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 36.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.650 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.66 REMARK 200 R MERGE FOR SHELL (I) : 0.40100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3FEA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4-2.0M AMMONIUM SULFATE 1.4-2.0M REMARK 280 NACL, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.92467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.84933 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: 1810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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: 1810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 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 GLY A 12 REMARK 465 PRO A 13 REMARK 465 ASP A 14 REMARK 465 SER A 15 REMARK 465 ALA A 16 REMARK 465 SER A 17 REMARK 465 ARG A 18 REMARK 465 ILE A 19 REMARK 465 SER A 20 REMARK 465 PRO A 21 REMARK 465 GLY A 22 REMARK 465 GLN A 23 REMARK 465 ILE A 24 REMARK 465 ASN A 25 REMARK 465 THR A 108 REMARK 465 LEU A 109 REMARK 465 ALA A 110 REMARK 465 THR A 111 REMARK 465 GLY B 12 REMARK 465 PRO B 13 REMARK 465 ASP B 14 REMARK 465 SER B 15 REMARK 465 ALA B 16 REMARK 465 SER B 17 REMARK 465 ARG B 18 REMARK 465 ILE B 19 REMARK 465 SER B 20 REMARK 465 PRO B 21 REMARK 465 GLY B 22 REMARK 465 GLN B 23 REMARK 465 ILE B 24 REMARK 465 ASN B 25 REMARK 465 THR B 108 REMARK 465 LEU B 109 REMARK 465 ALA B 110 REMARK 465 THR B 111 REMARK 465 GLY C 12 REMARK 465 PRO C 13 REMARK 465 ASP C 14 REMARK 465 SER C 15 REMARK 465 ALA C 16 REMARK 465 SER C 17 REMARK 465 ARG C 18 REMARK 465 ILE C 19 REMARK 465 SER C 20 REMARK 465 PRO C 21 REMARK 465 GLY C 22 REMARK 465 GLN C 23 REMARK 465 ILE C 24 REMARK 465 ASN C 25 REMARK 465 THR C 108 REMARK 465 LEU C 109 REMARK 465 ALA C 110 REMARK 465 THR C 111 REMARK 465 GLY D 12 REMARK 465 PRO D 13 REMARK 465 ASP D 14 REMARK 465 SER D 15 REMARK 465 ALA D 16 REMARK 465 SER D 17 REMARK 465 ARG D 18 REMARK 465 ILE D 19 REMARK 465 SER D 20 REMARK 465 PRO D 21 REMARK 465 GLY D 22 REMARK 465 GLN D 23 REMARK 465 ILE D 24 REMARK 465 ASN D 25 REMARK 465 VAL D 107 REMARK 465 THR D 108 REMARK 465 LEU D 109 REMARK 465 ALA D 110 REMARK 465 THR D 111 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 LEU B 31 N LYS B 35 2.05 REMARK 500 NZ LYS C 63 O HOH C 121 2.14 REMARK 500 O TYR C 99 N ARG C 103 2.14 REMARK 500 OD2 ASP D 100 O HOH D 137 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 HIS D 72 CG HIS D 72 CD2 0.060 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 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 LEU A 34 CA - CB - CG ANGL. DEV. = 19.0 DEGREES REMARK 500 ARG D 103 NE - CZ - NH2 ANGL. DEV. = 3.1 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 GLU A 70 67.34 -118.15 REMARK 500 SER A 96 -56.09 -29.47 REMARK 500 LEU B 80 -50.47 -29.67 REMARK 500 LEU C 31 -67.07 -22.75 REMARK 500 PRO C 32 -71.54 -41.24 REMARK 500 MET C 53 -35.65 -33.82 REMARK 500 LYS C 63 9.20 -67.46 REMARK 500 LEU C 65 1.37 -64.33 REMARK 500 GLU C 70 81.22 178.33 REMARK 500 LEU C 80 -68.62 -24.68 REMARK 500 ASN C 105 31.24 -82.45 REMARK 500 PRO D 29 156.40 -43.70 REMARK 500 LEU D 31 -45.37 -16.80 REMARK 500 PRO D 32 -84.41 -55.72 REMARK 500 LEU D 33 -44.00 -25.38 REMARK 500 TYR D 59 -76.68 -39.87 REMARK 500 GLN D 64 49.74 39.48 REMARK 500 GLN D 68 -71.35 -61.70 REMARK 500 CYS D 76 -7.02 178.95 REMARK 500 ASN D 105 75.14 -108.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU B 106 VAL B 107 35.18 REMARK 500 LYS C 93 ASP C 94 146.72 REMARK 500 LYS D 93 ASP D 94 148.42 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 03M A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 112 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 03M B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 03M C 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 03M D 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FEA RELATED DB: PDB REMARK 900 STARTING MODEL FOR MOLECULAR REPLACEMENT. REMARK 900 RELATED ID: 3VBG RELATED DB: PDB DBREF 3U15 A 14 111 UNP O15151 MDM4_HUMAN 14 111 DBREF 3U15 B 14 111 UNP O15151 MDM4_HUMAN 14 111 DBREF 3U15 C 14 111 UNP O15151 MDM4_HUMAN 14 111 DBREF 3U15 D 14 111 UNP O15151 MDM4_HUMAN 14 111 SEQADV 3U15 GLY A 12 UNP O15151 EXPRESSION TAG SEQADV 3U15 PRO A 13 UNP O15151 EXPRESSION TAG SEQADV 3U15 SER A 17 UNP O15151 CYS 17 ENGINEERED MUTATION SEQADV 3U15 GLY B 12 UNP O15151 EXPRESSION TAG SEQADV 3U15 PRO B 13 UNP O15151 EXPRESSION TAG SEQADV 3U15 SER B 17 UNP O15151 CYS 17 ENGINEERED MUTATION SEQADV 3U15 GLY C 12 UNP O15151 EXPRESSION TAG SEQADV 3U15 PRO C 13 UNP O15151 EXPRESSION TAG SEQADV 3U15 SER C 17 UNP O15151 CYS 17 ENGINEERED MUTATION SEQADV 3U15 GLY D 12 UNP O15151 EXPRESSION TAG SEQADV 3U15 PRO D 13 UNP O15151 EXPRESSION TAG SEQADV 3U15 SER D 17 UNP O15151 CYS 17 ENGINEERED MUTATION SEQRES 1 A 100 GLY PRO ASP SER ALA SER ARG ILE SER PRO GLY GLN ILE SEQRES 2 A 100 ASN GLN VAL ARG PRO LYS LEU PRO LEU LEU LYS ILE LEU SEQRES 3 A 100 HIS ALA ALA GLY ALA GLN GLY GLU MET PHE THR VAL LYS SEQRES 4 A 100 GLU VAL MET HIS TYR LEU GLY GLN TYR ILE MET VAL LYS SEQRES 5 A 100 GLN LEU TYR ASP GLN GLN GLU GLN HIS MET VAL TYR CYS SEQRES 6 A 100 GLY GLY ASP LEU LEU GLY GLU LEU LEU GLY ARG GLN SER SEQRES 7 A 100 PHE SER VAL LYS ASP PRO SER PRO LEU TYR ASP MET LEU SEQRES 8 A 100 ARG LYS ASN LEU VAL THR LEU ALA THR SEQRES 1 B 100 GLY PRO ASP SER ALA SER ARG ILE SER PRO GLY GLN ILE SEQRES 2 B 100 ASN GLN VAL ARG PRO LYS LEU PRO LEU LEU LYS ILE LEU SEQRES 3 B 100 HIS ALA ALA GLY ALA GLN GLY GLU MET PHE THR VAL LYS SEQRES 4 B 100 GLU VAL MET HIS TYR LEU GLY GLN TYR ILE MET VAL LYS SEQRES 5 B 100 GLN LEU TYR ASP GLN GLN GLU GLN HIS MET VAL TYR CYS SEQRES 6 B 100 GLY GLY ASP LEU LEU GLY GLU LEU LEU GLY ARG GLN SER SEQRES 7 B 100 PHE SER VAL LYS ASP PRO SER PRO LEU TYR ASP MET LEU SEQRES 8 B 100 ARG LYS ASN LEU VAL THR LEU ALA THR SEQRES 1 C 100 GLY PRO ASP SER ALA SER ARG ILE SER PRO GLY GLN ILE SEQRES 2 C 100 ASN GLN VAL ARG PRO LYS LEU PRO LEU LEU LYS ILE LEU SEQRES 3 C 100 HIS ALA ALA GLY ALA GLN GLY GLU MET PHE THR VAL LYS SEQRES 4 C 100 GLU VAL MET HIS TYR LEU GLY GLN TYR ILE MET VAL LYS SEQRES 5 C 100 GLN LEU TYR ASP GLN GLN GLU GLN HIS MET VAL TYR CYS SEQRES 6 C 100 GLY GLY ASP LEU LEU GLY GLU LEU LEU GLY ARG GLN SER SEQRES 7 C 100 PHE SER VAL LYS ASP PRO SER PRO LEU TYR ASP MET LEU SEQRES 8 C 100 ARG LYS ASN LEU VAL THR LEU ALA THR SEQRES 1 D 100 GLY PRO ASP SER ALA SER ARG ILE SER PRO GLY GLN ILE SEQRES 2 D 100 ASN GLN VAL ARG PRO LYS LEU PRO LEU LEU LYS ILE LEU SEQRES 3 D 100 HIS ALA ALA GLY ALA GLN GLY GLU MET PHE THR VAL LYS SEQRES 4 D 100 GLU VAL MET HIS TYR LEU GLY GLN TYR ILE MET VAL LYS SEQRES 5 D 100 GLN LEU TYR ASP GLN GLN GLU GLN HIS MET VAL TYR CYS SEQRES 6 D 100 GLY GLY ASP LEU LEU GLY GLU LEU LEU GLY ARG GLN SER SEQRES 7 D 100 PHE SER VAL LYS ASP PRO SER PRO LEU TYR ASP MET LEU SEQRES 8 D 100 ARG LYS ASN LEU VAL THR LEU ALA THR HET 03M A 1 28 HET SO4 A 112 5 HET 03M B 1 28 HET 03M C 1 28 HET 03M D 1 28 HET SO4 D 2 5 HETNAM 03M (5Z)-5-[(6-CHLORO-7-METHYL-1H-INDOL-3-YL)METHYLIDENE]- HETNAM 2 03M 3-(3,4-DIFLUOROBENZYL)IMIDAZOLIDINE-2,4-DIONE HETNAM SO4 SULFATE ION FORMUL 5 03M 4(C20 H14 CL F2 N3 O2) FORMUL 6 SO4 2(O4 S 2-) FORMUL 11 HOH *149(H2 O) HELIX 1 1 LYS A 30 ALA A 39 1 10 HELIX 2 2 THR A 48 LYS A 63 1 16 HELIX 3 3 ASP A 79 GLY A 86 1 8 HELIX 4 4 PRO A 95 ASN A 105 1 11 HELIX 5 5 LYS B 30 ALA B 40 1 11 HELIX 6 6 THR B 48 GLN B 64 1 17 HELIX 7 7 ASP B 79 LEU B 85 1 7 HELIX 8 8 PRO B 95 LEU B 106 1 12 HELIX 9 9 LYS C 30 GLY C 41 1 12 HELIX 10 10 THR C 48 LYS C 63 1 16 HELIX 11 11 ASP C 79 GLY C 86 1 8 HELIX 12 12 PRO C 95 ARG C 103 1 9 HELIX 13 13 LYS D 30 ALA D 40 1 11 HELIX 14 14 THR D 48 LYS D 63 1 16 HELIX 15 15 LEU D 81 GLY D 86 1 6 HELIX 16 16 PRO D 95 ASN D 105 1 11 SHEET 1 A 2 ARG A 28 PRO A 29 0 SHEET 2 A 2 LEU A 106 VAL A 107 -1 O VAL A 107 N ARG A 28 SHEET 1 B 2 MET A 73 TYR A 75 0 SHEET 2 B 2 SER A 89 SER A 91 -1 O PHE A 90 N VAL A 74 SHEET 1 C 2 ARG C 28 PRO C 29 0 SHEET 2 C 2 LEU C 106 VAL C 107 -1 O VAL C 107 N ARG C 28 SHEET 1 D 3 TYR C 66 ASP C 67 0 SHEET 2 D 3 GLU C 70 TYR C 75 -1 O GLU C 70 N ASP C 67 SHEET 3 D 3 SER C 89 SER C 91 -1 O PHE C 90 N VAL C 74 SHEET 1 E 2 MET D 73 TYR D 75 0 SHEET 2 E 2 SER D 89 SER D 91 -1 O PHE D 90 N VAL D 74 SITE 1 AC1 15 GLY A 57 ILE A 60 MET A 61 TYR A 66 SITE 2 AC1 15 GLN A 71 VAL A 92 HOH A 118 HOH A 121 SITE 3 AC1 15 03M B 1 MET B 53 GLY B 57 ILE B 60 SITE 4 AC1 15 PHE B 90 VAL B 92 LEU B 98 SITE 1 AC2 7 GLN A 71 HIS A 72 LYS A 93 GLU B 70 SITE 2 AC2 7 GLN B 71 HIS B 72 LYS B 93 SITE 1 AC3 12 03M A 1 MET A 53 LEU A 56 GLY A 57 SITE 2 AC3 12 PHE A 90 VAL A 92 LEU A 98 GLY B 57 SITE 3 AC3 12 ILE B 60 MET B 61 TYR B 66 GLN B 71 SITE 1 AC4 14 ILE C 60 MET C 61 TYR C 66 GLN C 71 SITE 2 AC4 14 VAL C 92 HOH C 118 HOH C 136 03M D 1 SITE 3 AC4 14 MET D 53 LEU D 56 GLY D 57 ILE D 60 SITE 4 AC4 14 VAL D 92 LEU D 98 SITE 1 AC5 17 03M C 1 MET C 53 LEU C 56 GLY C 57 SITE 2 AC5 17 ILE C 60 GLN C 71 PHE C 90 VAL C 92 SITE 3 AC5 17 LEU C 98 GLY D 57 ILE D 60 MET D 61 SITE 4 AC5 17 TYR D 66 GLN D 68 GLN D 71 HOH D 119 SITE 5 AC5 17 HOH D 139 SITE 1 AC6 5 GLN C 71 HIS C 72 GLU D 70 GLN D 71 SITE 2 AC6 5 HIS D 72 CRYST1 73.031 73.031 68.774 90.00 90.00 120.00 P 31 12 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 0.013693 0.007906 0.000000 0.00000 SCALE2 0.000000 0.015811 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014540 0.00000