HEADER LIGASE 28-APR-23 8J81 TITLE MDM2 BOUND WITH A PEPTOID 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; COMPND 7 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: MDM2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, COMPLEX, PEPTOID, P53-BINDING PROTEIN, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR M.YOKOMINE,Y.FUKUDA,H.AGO,H.MATSUURA,G.UENO,S.NAGATOISHI,M.YAMAMOTO, AUTHOR 2 K.TSUMOTO,M.JUMPEI,S.SANDO REVDAT 1 01-MAY-24 8J81 0 JRNL AUTH M.YOKOMINE,M.JUMPEI,Y.FUKUDA,T.UEDA,K.TAKEUCHI,K.SUZUKI, JRNL AUTH 2 S.MAEDA,H.AGO,H.MATSUURA,G.UENO,M.YAMAMOTO,A.SENOO, JRNL AUTH 3 S.NAGATOISHI,K.TSUMOTO,S.SANDO JRNL TITL A STRUCTURAL AND PHYSICOCHEMICAL STUDY OF HOW A PEPTOID JRNL TITL 2 BINDS TO A PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 49049 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.870 REMARK 3 FREE R VALUE TEST SET COUNT : 3372 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 37.2100 - 3.8900 1.00 1919 142 0.1553 0.1940 REMARK 3 2 3.8900 - 3.0900 1.00 1894 144 0.1523 0.1818 REMARK 3 3 3.0900 - 2.7000 1.00 1894 144 0.1738 0.1808 REMARK 3 4 2.7000 - 2.4500 1.00 1905 144 0.1813 0.1735 REMARK 3 5 2.4500 - 2.2800 1.00 1907 141 0.1689 0.2102 REMARK 3 6 2.2800 - 2.1400 1.00 1907 142 0.1577 0.1821 REMARK 3 7 2.1400 - 2.0400 1.00 1909 139 0.1599 0.1812 REMARK 3 8 2.0400 - 1.9500 1.00 1921 140 0.1596 0.1562 REMARK 3 9 1.9500 - 1.8700 1.00 1889 136 0.1673 0.1895 REMARK 3 10 1.8700 - 1.8100 1.00 1928 143 0.1689 0.1818 REMARK 3 11 1.8100 - 1.7500 1.00 1905 140 0.1630 0.1929 REMARK 3 12 1.7500 - 1.7000 1.00 1905 139 0.1528 0.1875 REMARK 3 13 1.7000 - 1.6600 1.00 1912 138 0.1676 0.1570 REMARK 3 14 1.6600 - 1.6200 1.00 1923 142 0.1693 0.1549 REMARK 3 15 1.6200 - 1.5800 1.00 1884 139 0.1815 0.2249 REMARK 3 16 1.5800 - 1.5500 1.00 1915 144 0.1823 0.2032 REMARK 3 17 1.5500 - 1.5100 1.00 1866 136 0.1933 0.2227 REMARK 3 18 1.5100 - 1.4900 1.00 1935 147 0.1881 0.2207 REMARK 3 19 1.4900 - 1.4600 1.00 1923 138 0.1917 0.1930 REMARK 3 20 1.4600 - 1.4300 1.00 1891 142 0.1967 0.2303 REMARK 3 21 1.4300 - 1.4100 1.00 1892 135 0.2272 0.2266 REMARK 3 22 1.4100 - 1.3900 1.00 1933 139 0.2619 0.2779 REMARK 3 23 1.3900 - 1.3700 1.00 1893 141 0.2955 0.2684 REMARK 3 24 1.3700 - 1.3500 0.97 1827 137 0.3504 0.3642 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.251 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.95 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 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 : 0.005 876 REMARK 3 ANGLE : 0.897 1202 REMARK 3 CHIRALITY : 0.070 133 REMARK 3 PLANARITY : 0.007 150 REMARK 3 DIHEDRAL : 25.886 356 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8J81 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1300037122. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54705 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 REMARK 200 RESOLUTION RANGE LOW (A) : 37.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 6.010 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.86 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M SODIUM ACETATE TRIHYDRATE PH4.5, REMARK 280 3.0 M SODIUM CHROLIDE. PEPTOID DISSOLVED IN DMSO WAS INCLUDED. REMARK 280 THE FINAL DMSO CONCENTRATION WAS 2.4%, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 19.76050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.89500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.90750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.89500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.76050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.90750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 12 REMARK 465 PRO A 13 REMARK 465 LEU A 14 REMARK 465 GLY A 15 REMARK 465 SER A 16 REMARK 465 SER A 17 REMARK 465 GLN A 18 REMARK 465 ILE A 19 REMARK 465 PRO A 20 REMARK 465 ALA A 21 REMARK 465 SER A 22 REMARK 465 GLU A 23 REMARK 465 GLN A 24 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 ARG A 65 NE CZ NH1 NH2 REMARK 470 GLU A 69 CG CD OE1 OE2 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 71 89.21 -160.30 REMARK 500 CYS A 77 19.52 -141.07 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 UAC A 201 DBREF 8J81 A 17 111 UNP Q00987 MDM2_HUMAN 17 111 SEQADV 8J81 GLY A 12 UNP Q00987 EXPRESSION TAG SEQADV 8J81 PRO A 13 UNP Q00987 EXPRESSION TAG SEQADV 8J81 LEU A 14 UNP Q00987 EXPRESSION TAG SEQADV 8J81 GLY A 15 UNP Q00987 EXPRESSION TAG SEQADV 8J81 SER A 16 UNP Q00987 EXPRESSION TAG SEQRES 1 A 100 GLY PRO LEU GLY SER SER GLN ILE PRO ALA SER GLU GLN SEQRES 2 A 100 GLU THR LEU VAL ARG PRO LYS PRO LEU LEU LEU LYS LEU SEQRES 3 A 100 LEU LYS SER VAL GLY ALA GLN LYS ASP THR TYR THR MET SEQRES 4 A 100 LYS GLU VAL LEU PHE TYR LEU GLY GLN TYR ILE MET THR SEQRES 5 A 100 LYS ARG LEU TYR ASP GLU LYS GLN GLN HIS ILE VAL TYR SEQRES 6 A 100 CYS SER ASN ASP LEU LEU GLY ASP LEU PHE GLY VAL PRO SEQRES 7 A 100 SER PHE SER VAL LYS GLU HIS ARG LYS ILE TYR THR MET SEQRES 8 A 100 ILE TYR ARG ASN LEU VAL VAL VAL ASN HET UAC A 201 54 HET CL A 202 1 HET CL A 203 1 HET CL A 204 1 HET CL A 205 1 HET CL A 206 2 HET CL A 207 2 HET CL A 208 2 HETNAM UAC (2S)-2-[[(2S)-2-[(6-CHLORANYL-1H-INDOL-3-YL)METHYL- HETNAM 2 UAC [(2S)-2-[[(2S)-2-[ETHANOYL-(PHENYLMETHYL) HETNAM 3 UAC AMINO]PROPANOYL]-METHYL- HETNAM 4 UAC AMINO]PROPANOYL]AMINO]PROPANOYL]-METHYL-AMINO]-N-(3,3- HETNAM 5 UAC DIMETHYLBUTYL)-N-[(2S)-1-OXIDANYLIDENE-1-PIPERAZIN-1- HETNAM 6 UAC YL-PROPAN-2-YL]PROPANAMIDE HETNAM CL CHLORIDE ION FORMUL 2 UAC C45 H65 CL N8 O6 FORMUL 3 CL 7(CL 1-) FORMUL 10 HOH *82(H2 O) HELIX 1 AA1 LYS A 31 VAL A 41 1 11 HELIX 2 AA2 MET A 50 LYS A 64 1 15 HELIX 3 AA3 ASP A 80 GLY A 87 1 8 HELIX 4 AA4 GLU A 95 ARG A 105 1 11 SHEET 1 AA1 3 TYR A 48 THR A 49 0 SHEET 2 AA1 3 LEU A 27 PRO A 30 -1 N VAL A 28 O TYR A 48 SHEET 3 AA1 3 LEU A 107 VAL A 110 -1 O VAL A 108 N ARG A 29 SHEET 1 AA2 3 TYR A 67 ASP A 68 0 SHEET 2 AA2 3 GLN A 71 TYR A 76 -1 O ILE 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 CRYST1 39.521 45.815 63.790 90.00 90.00 90.00 P 21 21 21 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 0.025303 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021827 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015676 0.00000