HEADER LIGASE 29-NOV-21 7QDQ TITLE CRYSTAL STRUCTURE OF HDM2 IN COMPLEX WITH CAYLIN-1 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,P53-BINDING COMPND 5 PROTEIN MDM2; COMPND 6 EC: 6.3.2.-; 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 NMR MOLECULAR REPLACEMENT, COMPLEX STRUCTURE, DRUG DESIGN, NMR KEYWDS 2 SPECTROSCOPY, STRUCTURE ELUCIDATION, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR A.D.FINKE,M.A.WALTI,M.E.MARSH,J.ORTS REVDAT 3 07-FEB-24 7QDQ 1 REMARK REVDAT 2 19-APR-23 7QDQ 1 JRNL REVDAT 1 05-OCT-22 7QDQ 0 JRNL AUTH V.MERTENS,M.J.ABI SAAD,N.COUDEVYLLE,M.A.WALTI,A.FINKE, JRNL AUTH 2 M.MARSH,J.ORTS JRNL TITL ELUCIDATION OF A NUTLIN-DERIVATIVE-HDM2 COMPLEX STRUCTURE AT JRNL TITL 2 THE INTERACTION SITE BY NMR MOLECULAR REPLACEMENT: A JRNL TITL 3 STRAIGHTFORWARD DERIVATION JRNL REF J MAGN RESON OPEN V.0-11 00032 2022 JRNL DOI 10.1016/J.JMRO.2022.100032 REMARK 2 REMARK 2 RESOLUTION. 1.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 25497 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.630 REMARK 3 FREE R VALUE TEST SET COUNT : 1946 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 33.8000 - 3.0500 1.00 1900 156 0.1559 0.1694 REMARK 3 2 3.0400 - 2.4200 1.00 1788 151 0.1583 0.1987 REMARK 3 3 2.4200 - 2.1100 1.00 1791 142 0.1418 0.1771 REMARK 3 4 2.1100 - 1.9200 0.99 1758 143 0.1490 0.2022 REMARK 3 5 1.9200 - 1.7800 0.99 1731 151 0.1676 0.1973 REMARK 3 6 1.7800 - 1.6800 0.99 1726 138 0.1739 0.1910 REMARK 3 7 1.6800 - 1.5900 0.98 1737 142 0.1967 0.2311 REMARK 3 8 1.5900 - 1.5200 0.97 1691 142 0.2143 0.3240 REMARK 3 9 1.5200 - 1.4600 0.97 1680 146 0.2405 0.3127 REMARK 3 10 1.4600 - 1.4100 0.95 1664 130 0.2792 0.3294 REMARK 3 11 1.4100 - 1.3700 0.94 1628 139 0.3139 0.3504 REMARK 3 12 1.3700 - 1.3300 0.92 1601 135 0.3329 0.3635 REMARK 3 13 1.3300 - 1.3000 0.92 1594 129 0.3538 0.3741 REMARK 3 14 1.3000 - 1.2600 0.73 1262 102 0.4113 0.4554 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.32 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 7QDQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1292119316. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA 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 PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26125 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.260 REMARK 200 RESOLUTION RANGE LOW (A) : 43.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 1.53900 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: 5C5A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.8M AMMONIUM SULFATE, 100MM MES, PH REMARK 280 6.0, VAPOR DIFFUSION, SITTING 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 20.82050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.67550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.83750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.67550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.82050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.83750 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 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 ASN A 111 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 LEU A 66 47.21 -86.34 REMARK 500 GLN A 71 75.16 -150.32 REMARK 500 GLN A 71 75.16 -156.68 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 402 DISTANCE = 5.83 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 63 OG1 REMARK 620 2 VAL A 109 O 92.9 REMARK 620 3 HOH A 309 O 84.6 8.6 REMARK 620 4 HOH A 326 O 92.7 8.8 10.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 204 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 68 OD2 REMARK 620 2 TYR A 76 OH 125.4 REMARK 620 3 THR A 101 O 129.1 35.1 REMARK 620 N 1 2 DBREF 7QDQ A 20 111 UNP Q00987 MDM2_HUMAN 20 111 SEQRES 1 A 92 PRO ALA SER GLU GLN GLU THR LEU VAL ARG PRO LYS PRO SEQRES 2 A 92 LEU LEU LEU LYS LEU LEU LYS SER VAL GLY ALA GLN LYS SEQRES 3 A 92 ASP THR TYR THR MET LYS GLU VAL LEU PHE TYR LEU GLY SEQRES 4 A 92 GLN TYR ILE MET THR LYS ARG LEU TYR ASP GLU LYS GLN SEQRES 5 A 92 GLN HIS ILE VAL TYR CYS SER ASN ASP LEU LEU GLY ASP SEQRES 6 A 92 LEU PHE GLY VAL PRO SER PHE SER VAL LYS GLU HIS ARG SEQRES 7 A 92 LYS ILE TYR THR MET ILE TYR ARG ASN LEU VAL VAL VAL SEQRES 8 A 92 ASN HET CL A 201 1 HET CL A 202 1 HET CL A 203 1 HET NA A 204 1 HET NA A 205 1 HET SO4 A 206 5 HET AU0 A 207 140 HET DMS A 208 10 HET DMS A 209 10 HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETNAM SO4 SULFATE ION HETNAM AU0 CAYLIN-1 HETNAM DMS DIMETHYL SULFOXIDE HETSYN AU0 4-[[(4~{S},5~{R})-4,5-BIS(3,4-DICHLOROPHENYL)-2-(4- HETSYN 2 AU0 METHOXY-2-PROPAN-2-YLOXY-PHENYL)-4,5-DIHYDROIMIDAZOL- HETSYN 3 AU0 1-YL]CARBONYL]PIPERAZIN-2-ONE FORMUL 2 CL 3(CL 1-) FORMUL 5 NA 2(NA 1+) FORMUL 7 SO4 O4 S 2- FORMUL 8 AU0 C30 H28 CL4 N4 O4 FORMUL 9 DMS 2(C2 H6 O S) FORMUL 11 HOH *102(H2 O) HELIX 1 AA1 LYS A 31 GLY A 42 1 12 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 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 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 LINK OG1ATHR A 63 NA NA A 205 1555 4455 3.19 LINK OD2 ASP A 68 NA NA A 204 1555 1555 2.64 LINK OH BTYR A 76 NA NA A 204 1555 1555 2.34 LINK O THR A 101 NA NA A 204 1555 3544 3.01 LINK O VAL A 109 NA NA A 205 1555 1555 2.89 LINK NA NA A 205 O HOH A 309 1555 4555 2.77 LINK NA NA A 205 O HOH A 326 1555 4555 2.96 CRYST1 41.641 43.675 53.351 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 0.024015 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022896 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018744 0.00000