HEADER LIGASE 04-NOV-22 8F12 TITLE STRUCTURE OF THE MDM2 P53 BINDING DOMAIN IN COMPLEX WITH H103, 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: H103; 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 3 15-NOV-23 8F12 1 REMARK REVDAT 2 25-OCT-23 8F12 1 REMARK REVDAT 1 15-FEB-23 8F12 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. 1.86 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 13668 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 661 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 49.1100 - 3.1800 1.00 2762 132 0.1985 0.2026 REMARK 3 2 3.1800 - 2.5200 1.00 2595 134 0.2282 0.2570 REMARK 3 3 2.5200 - 2.2100 1.00 2582 133 0.2245 0.3047 REMARK 3 4 2.2100 - 2.0000 1.00 2534 141 0.2358 0.2989 REMARK 3 5 2.0000 - 1.8600 0.99 2534 121 0.2569 0.2942 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.13 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 : 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 8F12 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_1000269793. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-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 : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03317 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 : 13715 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 49.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 25.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 23.70 REMARK 200 R MERGE FOR SHELL (I) : 1.57700 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: 3G03 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.2 M AMMONIUM SULFATE, 0.1 M CITRATE REMARK 280 PH 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 42.29500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.15500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.15500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 63.44250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.15500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.15500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.14750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.15500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.15500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 63.44250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.15500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.15500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.14750 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 42.29500 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: 1980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 ACE B 0 REMARK 465 DAS B 1 REMARK 465 NH2 B 18 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 16.18 -146.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 364 DISTANCE = 7.72 ANGSTROMS DBREF 8F12 A 17 111 UNP Q00987 MDM2_HUMAN 17 111 DBREF 8F12 B 0 18 PDB 8F12 8F12 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 DTY DGL DCY DNE DGL DAL DAL DNE SEQRES 2 B 19 DNE DCY DGN DGN DVA NH2 HET DPR B 2 7 HET DAL B 3 5 HET DTR B 4 14 HET DTY B 5 12 HET DGL B 6 9 HET DCY B 7 6 HET DNE B 8 8 HET DGL B 9 9 HET DAL B 10 5 HET DAL B 11 5 HET DNE B 12 8 HET DNE B 13 8 HET DCY B 14 6 HET DGN B 15 9 HET DGN B 16 9 HET DVA B 17 7 HET SO4 A 201 5 HET SO4 A 202 5 HET CL A 203 1 HET WHL B 101 14 HETNAM DPR D-PROLINE HETNAM DAL D-ALANINE HETNAM DTR D-TRYPTOPHAN HETNAM DTY D-TYROSINE HETNAM DGL D-GLUTAMIC ACID HETNAM DCY D-CYSTEINE HETNAM DNE D-NORLEUCINE HETNAM DGN D-GLUTAMINE HETNAM DVA D-VALINE HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETNAM WHL N,N'-(1,4-PHENYLENE)DIACETAMIDE FORMUL 2 DPR C5 H9 N O2 FORMUL 2 DAL 3(C3 H7 N O2) FORMUL 2 DTR C11 H12 N2 O2 FORMUL 2 DTY C9 H11 N O3 FORMUL 2 DGL 2(C5 H9 N O4) FORMUL 2 DCY 2(C3 H7 N O2 S) FORMUL 2 DNE 3(C6 H13 N O2) FORMUL 2 DGN 2(C5 H10 N2 O3) FORMUL 2 DVA C5 H11 N O2 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 CL CL 1- FORMUL 6 WHL C10 H12 N2 O2 FORMUL 7 HOH *77(H2 O) HELIX 1 AA1 PRO A 20 GLN A 24 5 5 HELIX 2 AA2 LYS A 31 VAL A 41 1 11 HELIX 3 AA3 MET A 50 ARG A 65 1 16 HELIX 4 AA4 ASP A 80 GLY A 87 1 8 HELIX 5 AA5 GLU A 95 ARG A 105 1 11 HELIX 6 AA6 DTY 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 DPR B 2 N DAL B 3 1555 1555 1.32 LINK C DAL B 3 N DTR B 4 1555 1555 1.32 LINK C DTR B 4 N DTY B 5 1555 1555 1.33 LINK C DTY B 5 N DGL B 6 1555 1555 1.33 LINK C DGL B 6 N DCY B 7 1555 1555 1.33 LINK C DCY B 7 N DNE B 8 1555 1555 1.32 LINK SG DCY B 7 CH WHL B 101 1555 1555 1.90 LINK C DNE B 8 N DGL B 9 1555 1555 1.33 LINK C DGL 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 DNE B 12 1555 1555 1.32 LINK C DNE B 12 N DNE B 13 1555 1555 1.33 LINK C DNE B 13 N DCY B 14 1555 1555 1.33 LINK C DCY B 14 N DGN B 15 1555 1555 1.33 LINK SG DCY B 14 CK WHL B 101 1555 1555 1.71 LINK C DGN B 15 N DGN B 16 1555 1555 1.33 LINK C DGN B 16 N DVA B 17 1555 1555 1.33 CRYST1 60.310 60.310 84.590 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 0.016581 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016581 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011822 0.00000