HEADER LIGASE 13-JUL-22 8AEU TITLE STRUCTURE OF HMDM2 IN COMPLEX WITH NUTLIN-3A-AA COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE MDM2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DOUBLE MINUTE 2 PROTEIN,HDM2,ONCOPROTEIN MDM2,RING-TYPE E3 COMPND 5 UBIQUITIN TRANSFERASE MDM2,P53-BINDING PROTEIN MDM2; COMPND 6 EC: 2.3.2.27 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS BIOLOGICAL ACTIVITY, DRUG DESIGN, INHIBITORS, PROTEIN-PROTEIN KEYWDS 2 INTERACTIONS, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR B.LABUZEK,P.GOLIK,K.MAGIERA-MULARZ,T.BERG REVDAT 5 07-FEB-24 8AEU 1 REMARK REVDAT 4 29-MAR-23 8AEU 1 JRNL REVDAT 3 22-MAR-23 8AEU 1 JRNL REVDAT 2 01-MAR-23 8AEU 1 JRNL REVDAT 1 18-JAN-23 8AEU 0 JRNL AUTH F.NIETZOLD,S.RUBNER,B.LABUZEK,P.GOLIK,E.SURMIAK,X.DEL CORTE, JRNL AUTH 2 R.KITEL,C.PROTZEL,R.REPPICH-SACHER,J.STICHEL, JRNL AUTH 3 K.MAGIERA-MULARZ,T.A.HOLAK,T.BERG JRNL TITL NUTLIN-3A-AA: IMPROVING THE BIOACTIVITY OF A P53/MDM2 JRNL TITL 2 INTERACTION INHIBITOR BY INTRODUCING A SOLVENT-EXPOSED JRNL TITL 3 METHYLENE GROUP. JRNL REF CHEMBIOCHEM V. 24 00006 2023 JRNL REFN ESSN 1439-7633 JRNL PMID 36602436 JRNL DOI 10.1002/CBIC.202300006 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 617 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.500 REMARK 3 FREE R VALUE TEST SET COUNT : 820 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 2.0520 - 2.0000 1.00 554 60 0.2740 0.3630 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 1.00 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.122 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.33000 REMARK 3 B22 (A**2) : 1.33000 REMARK 3 B33 (A**2) : -2.67000 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|ALL } REMARK 3 ORIGIN FOR THE GROUP (A): 29.0080 14.2270 18.2490 REMARK 3 T TENSOR REMARK 3 T11: 0.0378 T22: 0.0308 REMARK 3 T33: 0.0526 T12: 0.0255 REMARK 3 T13: 0.0219 T23: 0.0107 REMARK 3 L TENSOR REMARK 3 L11: 3.8483 L22: 2.2426 REMARK 3 L33: 1.3335 L12: 2.4040 REMARK 3 L13: -0.7490 L23: -0.8578 REMARK 3 S TENSOR REMARK 3 S11: -0.0331 S12: -0.0490 S13: 0.1029 REMARK 3 S21: -0.0364 S22: 0.0267 S23: 0.1369 REMARK 3 S31: -0.0736 S32: -0.1569 S33: 0.0063 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES : WITH TLS ADDED HYDROGENS REMARK 3 HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 8AEU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1292124179. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8645 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 45.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 24.70 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHASER REMARK 200 STARTING MODEL: 4ZFI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.05 M TRIS HYDROCHLORIDE PH 7.6, 1.6 M AMMONIUM SULFATE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 37.68800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.11650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.11650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 56.53200 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.11650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.11650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 18.84400 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.11650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.11650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 56.53200 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.11650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.11650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 18.84400 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 37.68800 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 56.23300 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 56.23300 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 37.68800 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 MET A 1 REMARK 465 GLN A 2 REMARK 465 ILE A 3 REMARK 465 PRO A 4 REMARK 465 ALA A 5 REMARK 465 SER A 6 REMARK 465 GLU A 7 REMARK 465 GLN A 8 REMARK 465 GLN A 96 REMARK 465 GLN A 97 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 CYS A 61 30.18 -93.73 REMARK 500 REMARK 500 REMARK: NULL DBREF 8AEU A 2 97 UNP Q00987 MDM2_HUMAN 18 113 SEQADV 8AEU MET A 1 UNP Q00987 INITIATING METHIONINE SEQRES 1 A 97 MET GLN ILE PRO ALA SER GLU GLN GLU THR LEU VAL ARG SEQRES 2 A 97 PRO LYS PRO LEU LEU LEU LYS LEU LEU LYS SER VAL GLY SEQRES 3 A 97 ALA GLN LYS ASP THR TYR THR MET LYS GLU VAL LEU PHE SEQRES 4 A 97 TYR LEU GLY GLN TYR ILE MET THR LYS ARG LEU TYR ASP SEQRES 5 A 97 GLU LYS GLN GLN HIS ILE VAL TYR CYS SER ASN ASP LEU SEQRES 6 A 97 LEU GLY ASP LEU PHE GLY VAL PRO SER PHE SER VAL LYS SEQRES 7 A 97 GLU HIS ARG LYS ILE TYR THR MET ILE TYR ARG ASN LEU SEQRES 8 A 97 VAL VAL VAL ASN GLN GLN HET BME A 301 4 HET M0L A 302 41 HETNAM BME BETA-MERCAPTOETHANOL HETNAM M0L 4-[[(4~{S},5~{R})-4,5-BIS(4-CHLOROPHENYL)-2-(4-METHOXY- HETNAM 2 M0L 2-PROPAN-2-YLOXY-PHENYL)-4,5-DIHYDROIMIDAZOL-1- HETNAM 3 M0L YL]CARBONYL]-3-METHYLIDENE-PIPERAZIN-2-ONE HETSYN M0L NUTLIN-3A ANALOGUE; 4-[[(4S,5R)-4,5-BIS(4- HETSYN 2 M0L CHLOROPHENYL)-2-(4-METHOXY-2-PROPAN-2-YLOXY-PHENYL)-4, HETSYN 3 M0L 5-DIHYDROIMIDAZOL-1-YL]CARBONYL]-3-METHYLIDENE- HETSYN 4 M0L PIPERAZIN-2-ONE FORMUL 2 BME C2 H6 O S FORMUL 3 M0L C31 H30 CL2 N4 O4 FORMUL 4 HOH *12(H2 O) HELIX 1 AA1 LYS A 15 VAL A 25 1 11 HELIX 2 AA2 THR A 33 LYS A 48 1 16 HELIX 3 AA3 ASN A 63 GLY A 71 1 9 HELIX 4 AA4 GLU A 79 ASN A 90 1 12 CRYST1 56.233 56.233 75.376 90.00 90.00 90.00 P 43 21 2 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 0.017783 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017783 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013267 0.00000