HEADER LIGASE 18-DEC-18 6Q9O TITLE HDM2 (17-111, WILDTYPE) COMPLEXED WITH COMPOUND 10 AT 1.21A; TITLE 2 STRUCTURAL STATES OF HDM2 AND HDMX: X-RAY ELUCIDATION OF ADAPTATIONS TITLE 3 AND BINDING INTERACTIONS FOR DIFFERENT CHEMICAL COMPOUND CLASSES COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE MDM2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, P53 BINDING DOMAIN; COMPND 5 SYNONYM: DOUBLE MINUTE 2 PROTEIN,HDM2,ONCOPROTEIN MDM2,RING-TYPE E3 COMPND 6 UBIQUITIN TRANSFERASE MDM2,P53-BINDING PROTEIN MDM2; COMPND 7 EC: 2.3.2.27; COMPND 8 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 BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-DERIVED VECTOR KEYWDS PPI WITH P53, INHIBITOR COMPLEX, CELL CYCLE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR J.KALLEN REVDAT 3 24-JAN-24 6Q9O 1 REMARK REVDAT 2 24-JUL-19 6Q9O 1 JRNL REVDAT 1 15-MAY-19 6Q9O 0 JRNL AUTH J.KALLEN,A.IZAAC,S.CHAU,E.WIRTH,J.SCHOEPFER,R.MAH, JRNL AUTH 2 A.SCHLAPBACH,S.STUTZ,A.VAUPEL,V.GUAGNANO,K.MASUYA, JRNL AUTH 3 T.M.STACHYRA,B.SALEM,P.CHENE,F.GESSIER,P.HOLZER,P.FURET JRNL TITL STRUCTURAL STATES OF HDM2 AND HDMX: X-RAY ELUCIDATION OF JRNL TITL 2 ADAPTATIONS AND BINDING INTERACTIONS FOR DIFFERENT CHEMICAL JRNL TITL 3 COMPOUND CLASSES. JRNL REF CHEMMEDCHEM V. 14 1305 2019 JRNL REFN ESSN 1860-7187 JRNL PMID 31066983 JRNL DOI 10.1002/CMDC.201900201 REMARK 2 REMARK 2 RESOLUTION. 1.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 48324 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1542 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 186 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08000 REMARK 3 B22 (A**2) : -0.27000 REMARK 3 B33 (A**2) : 0.15000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.043 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.037 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.020 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.966 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6Q9O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1200013517. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50939 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.210 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.26200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.540 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: 4OQ3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4M AMSO4, 0.1M NACITRATE, 0.2M NACL, REMARK 280 0.1M TRIS, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K 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 29.48800 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY A 16 REMARK 465 ASN A 111 REMARK 465 GLY B 16 REMARK 465 ASN B 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 GLN B 44 38.99 -147.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HU8 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HU8 B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OQ3 RELATED DB: PDB DBREF 6Q9O A 17 111 UNP Q00987 MDM2_HUMAN 17 111 DBREF 6Q9O B 17 111 UNP Q00987 MDM2_HUMAN 17 111 SEQADV 6Q9O GLY A 16 UNP Q00987 EXPRESSION TAG SEQADV 6Q9O GLY B 16 UNP Q00987 EXPRESSION TAG SEQRES 1 A 96 GLY SER GLN ILE PRO ALA SER GLU GLN GLU THR LEU VAL SEQRES 2 A 96 ARG PRO LYS PRO LEU LEU LEU LYS LEU LEU LYS SER VAL SEQRES 3 A 96 GLY ALA GLN LYS ASP THR TYR THR MET LYS GLU VAL LEU SEQRES 4 A 96 PHE TYR LEU GLY GLN TYR ILE MET THR LYS ARG LEU TYR SEQRES 5 A 96 ASP GLU LYS GLN GLN HIS ILE VAL TYR CYS SER ASN ASP SEQRES 6 A 96 LEU LEU GLY ASP LEU PHE GLY VAL PRO SER PHE SER VAL SEQRES 7 A 96 LYS GLU HIS ARG LYS ILE TYR THR MET ILE TYR ARG ASN SEQRES 8 A 96 LEU VAL VAL VAL ASN SEQRES 1 B 96 GLY SER GLN ILE PRO ALA SER GLU GLN GLU THR LEU VAL SEQRES 2 B 96 ARG PRO LYS PRO LEU LEU LEU LYS LEU LEU LYS SER VAL SEQRES 3 B 96 GLY ALA GLN LYS ASP THR TYR THR MET LYS GLU VAL LEU SEQRES 4 B 96 PHE TYR LEU GLY GLN TYR ILE MET THR LYS ARG LEU TYR SEQRES 5 B 96 ASP GLU LYS GLN GLN HIS ILE VAL TYR CYS SER ASN ASP SEQRES 6 B 96 LEU LEU GLY ASP LEU PHE GLY VAL PRO SER PHE SER VAL SEQRES 7 B 96 LYS GLU HIS ARG LYS ILE TYR THR MET ILE TYR ARG ASN SEQRES 8 B 96 LEU VAL VAL VAL ASN HET HU8 A 201 39 HET HU8 B 201 39 HETNAM HU8 ~{N}-~{TERT}-BUTYL-2-[4-CHLORANYL-2-[5-(3-CHLORANYL-4- HETNAM 2 HU8 FLUORANYL-PHENYL)-2-CYCLOHEXYL-4-(1~{H}-1,2,3,4- HETNAM 3 HU8 TETRAZOL-5-YL)IMIDAZOL-1-YL]PHENYL]ETHANAMIDE FORMUL 3 HU8 2(C28 H30 CL2 F N7 O) FORMUL 5 HOH *186(H2 O) HELIX 1 AA1 PRO A 20 GLU A 25 1 6 HELIX 2 AA2 LYS A 31 VAL A 41 1 11 HELIX 3 AA3 MET A 50 LYS A 64 1 15 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 PRO B 20 GLU B 25 1 6 HELIX 7 AA7 LYS B 31 VAL B 41 1 11 HELIX 8 AA8 MET B 50 LYS B 64 1 15 HELIX 9 AA9 ASP B 80 GLY B 87 1 8 HELIX 10 AB1 GLU B 95 ARG B 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 SHEET 1 AA3 3 TYR B 48 THR B 49 0 SHEET 2 AA3 3 LEU B 27 PRO B 30 -1 N VAL B 28 O TYR B 48 SHEET 3 AA3 3 LEU B 107 VAL B 109 -1 O VAL B 108 N ARG B 29 SHEET 1 AA4 2 ILE B 74 TYR B 76 0 SHEET 2 AA4 2 SER B 90 SER B 92 -1 O PHE B 91 N VAL B 75 SITE 1 AC1 16 LEU A 54 PHE A 55 GLY A 58 ILE A 61 SITE 2 AC1 16 MET A 62 VAL A 93 LYS A 94 HIS A 96 SITE 3 AC1 16 ILE A 99 HOH A 322 HOH A 333 HOH A 347 SITE 4 AC1 16 HOH A 353 HOH A 365 HOH B 345 HOH B 374 SITE 1 AC2 15 LEU B 54 GLY B 58 ILE B 61 MET B 62 SITE 2 AC2 15 TYR B 67 GLN B 72 VAL B 93 HIS B 96 SITE 3 AC2 15 TYR B 100 HOH B 316 HOH B 338 HOH B 339 SITE 4 AC2 15 HOH B 340 HOH B 356 HOH B 363 CRYST1 37.929 58.976 39.880 90.00 106.82 90.00 P 1 21 1 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 0.026365 0.000000 0.007971 0.00000 SCALE2 0.000000 0.016956 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026196 0.00000