HEADER PROTEIN BINDING/SIGNALING PROTEIN 07-MAY-13 2M86 TITLE SOLUTION STRUCTURE OF HDM2 WITH ENGINEERED CYCLOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MCO-PMI; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE MDM2; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: UNP RESIDUES 17-125; COMPND 9 SYNONYM: DOUBLE MINUTE 2 PROTEIN, HDM2, ONCOPROTEIN MDM2, P53-BINDING COMPND 10 PROTEIN MDM2; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PTXB1; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: MDM2; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS HDM2 ONCOPROTEIN, MCOTI-I CYCLOTIDE, P53 TUMOR SUPPRESSOR, PROTEIN KEYWDS 2 BINDING-SIGNALING PROTEIN COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR S.MAJUMDER,Y.JI,M.MILLARD,R.BORRA,T.BI,A.Y.ELNAGAR,N.NEAMATI, AUTHOR 2 J.A.CAMARERO REVDAT 4 06-NOV-24 2M86 1 REMARK REVDAT 3 14-JUN-23 2M86 1 REMARK SEQADV LINK REVDAT 2 21-AUG-13 2M86 1 JRNL REVDAT 1 31-JUL-13 2M86 0 JRNL AUTH Y.JI,S.MAJUMDER,M.MILLARD,R.BORRA,T.BI,A.Y.ELNAGAR, JRNL AUTH 2 N.NEAMATI,A.SHEKHTMAN,J.A.CAMARERO JRNL TITL IN VIVO ACTIVATION OF THE P53 TUMOR SUPPRESSOR PATHWAY BY AN JRNL TITL 2 ENGINEERED CYCLOTIDE. JRNL REF J.AM.CHEM.SOC. V. 135 11623 2013 JRNL REFN ISSN 0002-7863 JRNL PMID 23848581 JRNL DOI 10.1021/JA405108P REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CHRMM 36 REMARK 3 AUTHORS : KARPLUS, M. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M86 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000103330. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.133 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.2 MM MCO-PMI, 0.2 MM [U-99% REMARK 210 13C; U-99% 15N] HDM2, 90% H2O/10% REMARK 210 D2O; 0.2 MM [U-99% 15N] MO-PMI, REMARK 210 0.2 MM HDM2, 90% H2O/10% D2O; REMARK 210 0.2 MM MCO-PMI, 0.2 MM HDM2, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D 1H-15N NOESY; 3D 1H-15N TOCSY; REMARK 210 2D 1H-1H NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D HNCA; 3D HN(CO)CA; REMARK 210 3D HNCACB; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY B 62 REMARK 465 SER B 63 REMARK 465 SER B 64 REMARK 465 HIS B 65 REMARK 465 HIS B 66 REMARK 465 HIS B 67 REMARK 465 HIS B 68 REMARK 465 HIS B 69 REMARK 465 HIS B 70 REMARK 465 SER B 71 REMARK 465 SER B 72 REMARK 465 GLY B 73 REMARK 465 LEU B 74 REMARK 465 VAL B 75 REMARK 465 PRO B 76 REMARK 465 ARG B 77 REMARK 465 GLY B 78 REMARK 465 SER B 79 REMARK 465 HIS B 80 REMARK 465 MET B 81 REMARK 465 SER B 82 REMARK 465 GLN B 83 REMARK 465 ILE B 84 REMARK 465 PRO B 85 REMARK 465 ALA B 86 REMARK 465 SER B 87 REMARK 465 GLU B 88 REMARK 465 GLN B 89 REMARK 465 GLU B 90 REMARK 465 THR B 91 REMARK 465 VAL B 175 REMARK 465 ASN B 176 REMARK 465 GLN B 177 REMARK 465 GLN B 178 REMARK 465 GLU B 179 REMARK 465 SER B 180 REMARK 465 SER B 181 REMARK 465 ASP B 182 REMARK 465 SER B 183 REMARK 465 GLY B 184 REMARK 465 THR B 185 REMARK 465 SER B 186 REMARK 465 VAL B 187 REMARK 465 SER B 188 REMARK 465 GLU B 189 REMARK 465 ASN B 190 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP B 133 HZ1 LYS B 135 1.50 REMARK 500 N SER A 1 O GLY A 51 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG A 33 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 ARG A 34 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 9 ARG A 33 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 10 ARG A 33 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 1 ALA A 8 87.22 175.16 REMARK 500 1 ALA A 21 94.59 -58.34 REMARK 500 1 ALA A 41 25.59 -161.30 REMARK 500 1 ARG B 130 49.27 75.15 REMARK 500 1 GLN B 136 58.67 -140.22 REMARK 500 2 ALA A 8 85.21 -173.97 REMARK 500 2 ALA A 41 21.53 -157.39 REMARK 500 2 ARG B 130 59.04 74.91 REMARK 500 2 GLN B 136 63.30 -111.84 REMARK 500 3 SER A 6 3.99 -68.65 REMARK 500 3 ALA A 8 84.79 -167.58 REMARK 500 3 ALA A 21 93.71 -51.70 REMARK 500 3 ALA A 41 29.91 -160.17 REMARK 500 3 ARG B 130 53.67 71.98 REMARK 500 4 ALA A 8 87.32 -178.60 REMARK 500 4 ALA A 21 93.32 -48.86 REMARK 500 4 ALA A 41 6.65 -151.69 REMARK 500 4 ARG B 130 53.51 72.04 REMARK 500 4 GLN B 136 57.12 -107.67 REMARK 500 5 ALA A 8 85.96 -150.52 REMARK 500 5 ALA A 21 85.25 -62.60 REMARK 500 5 LEU A 29 33.76 -88.95 REMARK 500 5 CYS A 32 -161.29 -107.30 REMARK 500 5 ARG A 33 -37.38 -150.45 REMARK 500 5 ALA A 41 24.88 -156.44 REMARK 500 5 ARG B 130 50.92 77.34 REMARK 500 5 GLN B 136 63.36 -108.81 REMARK 500 5 ASN B 144 -27.11 76.55 REMARK 500 6 ALA A 8 89.17 -175.78 REMARK 500 6 THR A 10 -60.40 -127.38 REMARK 500 6 ALA A 21 89.16 -69.72 REMARK 500 6 ALA A 41 40.61 -161.35 REMARK 500 6 ARG B 130 41.53 76.02 REMARK 500 6 GLN B 136 53.79 -109.67 REMARK 500 6 ASN B 144 -36.06 76.24 REMARK 500 6 GLU B 160 46.70 -91.18 REMARK 500 7 ALA A 8 89.13 -166.83 REMARK 500 7 ALA A 21 93.49 -45.61 REMARK 500 7 LYS A 27 78.77 79.82 REMARK 500 7 TYR B 113 -166.83 -128.40 REMARK 500 7 ARG B 130 49.30 72.29 REMARK 500 7 GLN B 136 56.59 -115.34 REMARK 500 7 GLN B 137 5.46 -60.92 REMARK 500 7 TYR B 141 78.60 -105.90 REMARK 500 7 CYS B 142 37.81 -86.34 REMARK 500 7 ASN B 144 43.93 70.08 REMARK 500 8 ALA A 8 89.60 174.53 REMARK 500 8 ALA A 21 92.60 -64.87 REMARK 500 8 ALA A 41 24.82 -168.23 REMARK 500 8 ASP B 111 -9.42 -54.44 REMARK 500 REMARK 500 THIS ENTRY HAS 66 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG B 130 0.11 SIDE CHAIN REMARK 500 3 TYR A 15 0.07 SIDE CHAIN REMARK 500 4 TYR A 15 0.07 SIDE CHAIN REMARK 500 4 ARG B 130 0.08 SIDE CHAIN REMARK 500 5 TYR A 15 0.07 SIDE CHAIN REMARK 500 5 ARG A 34 0.08 SIDE CHAIN REMARK 500 5 ARG A 45 0.14 SIDE CHAIN REMARK 500 6 ARG A 34 0.09 SIDE CHAIN REMARK 500 8 ARG A 34 0.08 SIDE CHAIN REMARK 500 8 TYR B 121 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19230 RELATED DB: BMRB DBREF 2M86 B 82 190 UNP Q00987 MDM2_HUMAN 17 125 DBREF 2M86 A 1 51 PDB 2M86 2M86 1 51 SEQADV 2M86 GLY B 62 UNP Q00987 EXPRESSION TAG SEQADV 2M86 SER B 63 UNP Q00987 EXPRESSION TAG SEQADV 2M86 SER B 64 UNP Q00987 EXPRESSION TAG SEQADV 2M86 HIS B 65 UNP Q00987 EXPRESSION TAG SEQADV 2M86 HIS B 66 UNP Q00987 EXPRESSION TAG SEQADV 2M86 HIS B 67 UNP Q00987 EXPRESSION TAG SEQADV 2M86 HIS B 68 UNP Q00987 EXPRESSION TAG SEQADV 2M86 HIS B 69 UNP Q00987 EXPRESSION TAG SEQADV 2M86 HIS B 70 UNP Q00987 EXPRESSION TAG SEQADV 2M86 SER B 71 UNP Q00987 EXPRESSION TAG SEQADV 2M86 SER B 72 UNP Q00987 EXPRESSION TAG SEQADV 2M86 GLY B 73 UNP Q00987 EXPRESSION TAG SEQADV 2M86 LEU B 74 UNP Q00987 EXPRESSION TAG SEQADV 2M86 VAL B 75 UNP Q00987 EXPRESSION TAG SEQADV 2M86 PRO B 76 UNP Q00987 EXPRESSION TAG SEQADV 2M86 ARG B 77 UNP Q00987 EXPRESSION TAG SEQADV 2M86 GLY B 78 UNP Q00987 EXPRESSION TAG SEQADV 2M86 SER B 79 UNP Q00987 EXPRESSION TAG SEQADV 2M86 HIS B 80 UNP Q00987 EXPRESSION TAG SEQADV 2M86 MET B 81 UNP Q00987 EXPRESSION TAG SEQRES 1 A 51 SER GLY SER GLY ALA SER LYS ALA PRO THR SER PHE ALA SEQRES 2 A 51 GLU TYR TRP ASN LEU LEU SER ALA GLY GLY VAL CYS PRO SEQRES 3 A 51 LYS ILE LEU GLN ARG CYS ARG ARG ASP SER ASP CYS PRO SEQRES 4 A 51 GLY ALA CYS ILE CYS ARG GLY ASN GLY TYR CYS GLY SEQRES 1 B 129 GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY LEU SEQRES 2 B 129 VAL PRO ARG GLY SER HIS MET SER GLN ILE PRO ALA SER SEQRES 3 B 129 GLU GLN GLU THR LEU VAL ARG PRO LYS PRO LEU LEU LEU SEQRES 4 B 129 LYS LEU LEU LYS SER VAL GLY ALA GLN LYS ASP THR TYR SEQRES 5 B 129 THR MET LYS GLU VAL LEU PHE TYR LEU GLY GLN TYR ILE SEQRES 6 B 129 MET THR LYS ARG LEU TYR ASP GLU LYS GLN GLN HIS ILE SEQRES 7 B 129 VAL TYR CYS SER ASN ASP LEU LEU GLY ASP LEU PHE GLY SEQRES 8 B 129 VAL PRO SER PHE SER VAL LYS GLU HIS ARG LYS ILE TYR SEQRES 9 B 129 THR MET ILE TYR ARG ASN LEU VAL VAL VAL ASN GLN GLN SEQRES 10 B 129 GLU SER SER ASP SER GLY THR SER VAL SER GLU ASN HELIX 1 1 SER A 11 LEU A 19 1 9 HELIX 2 2 LYS B 96 LYS B 104 1 9 HELIX 3 3 THR B 114 ARG B 130 1 17 HELIX 4 4 ASP B 145 GLY B 152 1 8 HELIX 5 5 GLU B 160 ARG B 170 1 11 SHEET 1 A 2 ILE B 139 TYR B 141 0 SHEET 2 A 2 SER B 155 SER B 157 -1 O PHE B 156 N VAL B 140 SSBOND 1 CYS A 25 CYS A 42 1555 1555 2.03 SSBOND 2 CYS A 32 CYS A 44 1555 1555 2.03 SSBOND 3 CYS A 38 CYS A 50 1555 1555 2.02 LINK N SER A 1 C GLY A 51 1555 1555 1.37 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1