HEADER LIGASE 04-NOV-22 8F10 TITLE STRUCTURE OF THE MDM2 P53 BINDING DOMAIN IN COMPLEX WITH H102, AN ALL- TITLE 2 D HELICON POLYPEPTIDE 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; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: H102; COMPND 10 CHAIN: B; COMPND 11 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; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS E3 LIGASE, D-PEPTIDE, STAPLED PEPTIDE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR K.LI,A.J.CALLAHAN,T.L.TRAVALINE,O.S.TOKAREVA,J.-M.SWIECICKI, AUTHOR 2 G.L.VERDINE,B.L.PENTELUTE,J.H.MCGEE REVDAT 4 16-OCT-24 8F10 1 REMARK REVDAT 3 15-NOV-23 8F10 1 REMARK REVDAT 2 25-OCT-23 8F10 1 REMARK REVDAT 1 15-FEB-23 8F10 0 JRNL AUTH A.J.CALLAHAN,S.GANDHESIRI,T.L.TRAVALINE,L.LOZANO SALAZAR, JRNL AUTH 2 S.HANNA,Y.-C.LEE,K.LI,O.S.TOKAREVA,J.-M.SWIECICKI,A.LOAS, JRNL AUTH 3 G.L.VERDINE,J.H.MCGEE,B.L.PENTELUTE JRNL TITL SINGLE-SHOT FLOW SYNTHESIS OF D-PROTEINS FOR MIRROR-IMAGE JRNL TITL 2 PHAGE DISPLAY JRNL REF CHEMRXIV 2023 JRNL REFN ISSN 2573-2293 JRNL DOI 10.26434/CHEMRXIV-2023-X86XP REMARK 2 REMARK 2 RESOLUTION. 1.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.1 REMARK 3 NUMBER OF REFLECTIONS : 20092 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 968 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 28.0200 - 2.4500 0.97 3279 170 0.1434 0.1556 REMARK 3 2 2.4500 - 1.9400 0.97 3207 162 0.1465 0.1450 REMARK 3 3 1.9400 - 1.7000 0.97 3200 138 0.1590 0.1587 REMARK 3 4 1.7000 - 1.5400 0.96 3175 153 0.1671 0.2109 REMARK 3 5 1.5400 - 1.4300 0.92 2964 178 0.1707 0.2087 REMARK 3 6 1.4300 - 1.3500 0.66 2152 109 0.2061 0.2314 REMARK 3 7 1.3500 - 1.2800 0.35 1147 58 0.2321 0.2216 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.46 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 : 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: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -0.7968 5.4555 -11.0623 REMARK 3 T TENSOR REMARK 3 T11: 0.0810 T22: 0.0851 REMARK 3 T33: 0.0713 T12: -0.0081 REMARK 3 T13: 0.0074 T23: -0.0004 REMARK 3 L TENSOR REMARK 3 L11: 1.0151 L22: 1.7322 REMARK 3 L33: 1.2706 L12: -0.4525 REMARK 3 L13: 0.0735 L23: -0.1206 REMARK 3 S TENSOR REMARK 3 S11: -0.0080 S12: 0.0206 S13: -0.0076 REMARK 3 S21: 0.0395 S22: 0.0177 S23: 0.0603 REMARK 3 S31: -0.0259 S32: -0.0651 S33: -0.0132 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 8F10 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1000269628. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-21 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 : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20614 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.280 REMARK 200 RESOLUTION RANGE LOW (A) : 42.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.3 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.30 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: 3G03 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M TRI-SODIUM CITRATE, 33 % W/V REMARK 280 PEG 6000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 19.96000 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 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 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 465 ACE B 0 REMARK 465 DAS B 1 REMARK 465 DPR B 2 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 77 12.88 -143.55 REMARK 500 REMARK 500 REMARK: NULL DBREF 8F10 A 17 111 UNP Q00987 MDM2_HUMAN 17 111 DBREF 8F10 B 0 18 PDB 8F10 8F10 0 18 SEQRES 1 A 95 SER GLN ILE PRO ALA SER GLU GLN GLU THR LEU VAL ARG SEQRES 2 A 95 PRO LYS PRO LEU LEU LEU LYS LEU LEU LYS SER VAL GLY SEQRES 3 A 95 ALA GLN LYS ASP THR TYR THR MET LYS GLU VAL LEU PHE SEQRES 4 A 95 TYR LEU GLY GLN TYR ILE MET THR LYS ARG LEU TYR ASP SEQRES 5 A 95 GLU LYS GLN GLN HIS ILE VAL TYR CYS SER ASN ASP LEU SEQRES 6 A 95 LEU GLY ASP LEU PHE GLY VAL PRO SER PHE SER VAL LYS SEQRES 7 A 95 GLU HIS ARG LYS ILE TYR THR MET ILE TYR ARG ASN LEU SEQRES 8 A 95 VAL VAL VAL ASN SEQRES 1 B 19 ACE DAS DPR DAL DTR DSG DHI DCY DGL DTY DAL DAL DPN SEQRES 2 B 19 DVA DCY DSN DGL DVA NH2 HET DAL B 3 10 HET DTR B 4 24 HET DSG B 5 14 HET DHI B 6 18 HET DCY B 7 10 HET DGL B 8 15 HET DTY B 9 21 HET DAL B 10 10 HET DAL B 11 10 HET DPN B 12 20 HET DVA B 13 16 HET DCY B 14 10 HET DSN B 15 11 HET DGL B 16 15 HET DVA B 17 16 HET NH2 B 18 1 HET EDO A 201 10 HET EDO A 202 10 HET CL A 203 1 HET GOL A 204 12 HET GOL A 205 14 HET EDO A 206 10 HET WHL B 101 14 HET EDO B 102 10 HET IMD B 103 10 HETNAM DAL D-ALANINE HETNAM DTR D-TRYPTOPHAN HETNAM DSG D-ASPARAGINE HETNAM DHI D-HISTIDINE HETNAM DCY D-CYSTEINE HETNAM DGL D-GLUTAMIC ACID HETNAM DTY D-TYROSINE HETNAM DPN D-PHENYLALANINE HETNAM DVA D-VALINE HETNAM DSN D-SERINE HETNAM NH2 AMINO GROUP HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM WHL N,N'-(1,4-PHENYLENE)DIACETAMIDE HETNAM IMD IMIDAZOLE HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DAL 3(C3 H7 N O2) FORMUL 2 DTR C11 H12 N2 O2 FORMUL 2 DSG C4 H8 N2 O3 FORMUL 2 DHI C6 H10 N3 O2 1+ FORMUL 2 DCY 2(C3 H7 N O2 S) FORMUL 2 DGL 2(C5 H9 N O4) FORMUL 2 DTY C9 H11 N O3 FORMUL 2 DPN C9 H11 N O2 FORMUL 2 DVA 2(C5 H11 N O2) FORMUL 2 DSN C3 H7 N O3 FORMUL 2 NH2 H2 N FORMUL 3 EDO 4(C2 H6 O2) FORMUL 5 CL CL 1- FORMUL 6 GOL 2(C3 H8 O3) FORMUL 9 WHL C10 H12 N2 O2 FORMUL 11 IMD C3 H5 N2 1+ FORMUL 12 HOH *105(H2 O) HELIX 1 AA1 LYS A 31 VAL A 41 1 11 HELIX 2 AA2 MET A 50 ARG A 65 1 16 HELIX 3 AA3 ASP A 80 GLY A 87 1 8 HELIX 4 AA4 GLU A 95 ASN A 106 1 12 HELIX 5 AA5 DSG B 5 DVA B 17 1 13 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 109 -1 O VAL A 108 N ARG A 29 SHEET 1 AA2 2 ILE A 74 TYR A 76 0 SHEET 2 AA2 2 SER A 90 SER A 92 -1 O PHE A 91 N VAL A 75 LINK C DAL B 3 N DTR B 4 1555 1555 1.32 LINK C DTR B 4 N DSG B 5 1555 1555 1.32 LINK C DSG B 5 N DHI B 6 1555 1555 1.33 LINK C DHI B 6 N DCY B 7 1555 1555 1.33 LINK C DCY B 7 N DGL B 8 1555 1555 1.32 LINK SG DCY B 7 CH WHL B 101 1555 1555 1.78 LINK C DGL B 8 N DTY B 9 1555 1555 1.34 LINK C DTY B 9 N DAL B 10 1555 1555 1.33 LINK C DAL B 10 N DAL B 11 1555 1555 1.33 LINK C DAL B 11 N DPN B 12 1555 1555 1.32 LINK C DPN B 12 N DVA B 13 1555 1555 1.32 LINK C DVA B 13 N DCY B 14 1555 1555 1.32 LINK C DCY B 14 N DSN B 15 1555 1555 1.32 LINK SG DCY B 14 CK WHL B 101 1555 1555 1.77 LINK C DSN B 15 N DGL B 16 1555 1555 1.31 LINK C DGL B 16 N DVA B 17 1555 1555 1.33 LINK C DVA B 17 N NH2 B 18 1555 1555 1.42 CRYST1 28.150 39.920 42.360 90.00 95.44 90.00 P 1 21 1 2 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 0.035524 0.000000 0.003386 0.00000 SCALE2 0.000000 0.025050 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023714 0.00000