HEADER APOPTOSIS 18-DEC-18 6Q9U TITLE HDMX (14-111; C17S) COMPLEXED WITH COMPOUND 12 AT 2.4A; STRUCTURAL TITLE 2 STATES OF HDM2 AND HDMX: X-RAY ELUCIDATION OF ADAPTATIONS AND BINDING TITLE 3 INTERACTIONS FOR DIFFERENT CHEMICAL COMPOUND CLASSES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN MDM4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, P53 BINDING DOMAIN; 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 BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-DERIVED VECTOR KEYWDS HDMX, MDM4, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR J.KALLEN REVDAT 4 24-JAN-24 6Q9U 1 REMARK REVDAT 3 23-OCT-19 6Q9U 1 REMARK REVDAT 2 24-JUL-19 6Q9U 1 JRNL REVDAT 1 15-MAY-19 6Q9U 0 JRNL AUTH J.KALLEN,A.IZAAC,S.CHAU,E.WIRTH,J.SCHOEPFER,R.MAH, JRNL AUTH 2 A.SCHLAPBACH,S.STUTZ,A.VAUPEL,V.GUAGNANO,K.MASUYA, JRNL AUTH 3 T.M.STACHYRA,B.SALEM,P.CHENE,F.GESSIER,P.HOLZER,P.FURET JRNL TITL STRUCTURAL STATES OF HDM2 AND HDMX: X-RAY ELUCIDATION OF JRNL TITL 2 ADAPTATIONS AND BINDING INTERACTIONS FOR DIFFERENT CHEMICAL JRNL TITL 3 COMPOUND CLASSES. JRNL REF CHEMMEDCHEM V. 14 1305 2019 JRNL REFN ESSN 1860-7187 JRNL PMID 31066983 JRNL DOI 10.1002/CMDC.201900201 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 4260 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) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 225 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 689 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 46 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.09000 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): 0.429 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.280 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.201 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6Q9U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1200013525. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-12 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 : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99983 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4485 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 19.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.14100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.34700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 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: 6Q9Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.3M AMSO4, 2% W/V 18-CROWN-ETHER, REMARK 280 0.1M HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 27.91250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 13.95625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 41.86875 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL 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 GLY A 13 REMARK 465 PRO A 14 REMARK 465 ASP A 15 REMARK 465 SER A 16 REMARK 465 ALA A 17 REMARK 465 SER A 18 REMARK 465 ARG A 19 REMARK 465 ILE A 20 REMARK 465 SER A 21 REMARK 465 PRO A 22 REMARK 465 GLY A 23 REMARK 465 GLN A 24 REMARK 465 ALA A 111 REMARK 465 THR A 112 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 GLN A 65 56.76 38.69 REMARK 500 GLU A 71 88.46 -150.79 REMARK 500 PRO A 96 59.16 -103.85 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 HRE A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue O4B A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6Q96 RELATED DB: PDB DBREF 6Q9U A 15 112 UNP O15151 MDM4_HUMAN 14 111 SEQADV 6Q9U GLY A 13 UNP O15151 EXPRESSION TAG SEQADV 6Q9U PRO A 14 UNP O15151 EXPRESSION TAG SEQADV 6Q9U SER A 18 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 HET HRE A 201 39 HET O4B A 202 18 HET CL A 203 1 HETNAM HRE 4-[(4~{S})-5-(5-CHLORANYL-2-OXIDANYLIDENE-1~{H}- HETNAM 2 HRE PYRIDIN-3-YL)-2-[2-(DIMETHYLAMINO)-4-METHOXY- HETNAM 3 HRE PYRIMIDIN-5-YL]-6-OXIDANYLIDENE-3-PROPAN-2-YL-4~{H}- HETNAM 4 HRE PYRROLO[3,4-C]PYRAZOL-4-YL]BENZENECARBONITRILE HETNAM O4B 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE HETNAM CL CHLORIDE ION FORMUL 2 HRE C27 H25 CL N8 O3 FORMUL 3 O4B C12 H24 O6 FORMUL 4 CL CL 1- FORMUL 5 HOH *46(H2 O) HELIX 1 AA1 LYS A 31 ALA A 41 1 11 HELIX 2 AA2 VAL A 50 LYS A 64 1 15 HELIX 3 AA3 ASP A 80 GLY A 87 1 8 HELIX 4 AA4 PRO A 96 ASN A 106 1 11 SHEET 1 AA1 3 PHE A 48 THR A 49 0 SHEET 2 AA1 3 GLN A 27 PRO A 30 -1 N VAL A 28 O PHE A 48 SHEET 3 AA1 3 LEU A 107 THR A 109 -1 O VAL A 108 N ARG A 29 SHEET 1 AA2 3 TYR A 67 ASP A 68 0 SHEET 2 AA2 3 GLU A 71 TYR A 76 -1 O MET A 74 N ASP A 68 SHEET 3 AA2 3 SER A 90 SER A 92 -1 O PHE A 91 N VAL A 75 SITE 1 AC1 11 MET A 54 HIS A 55 GLY A 58 GLN A 59 SITE 2 AC1 11 ILE A 61 TYR A 67 GLN A 72 VAL A 93 SITE 3 AC1 11 PRO A 96 LEU A 99 TYR A 100 SITE 1 AC2 7 ILE A 25 VAL A 28 ALA A 40 VAL A 50 SITE 2 AC2 7 VAL A 63 LYS A 64 THR A 109 SITE 1 AC3 2 TYR A 56 GLN A 59 CRYST1 45.403 45.403 55.825 90.00 90.00 90.00 P 41 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 0.022025 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022025 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017913 0.00000