PDB Short entry for 1TTV HEADER LIGASE 23-JUN-04 1TTV TITLE NMR STRUCTURE OF A COMPLEX BETWEEN MDM2 AND A SMALL MOLECULE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-PROTEIN LIGASE E3 MDM2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIUDES 13-119; COMPND 5 SYNONYM: P53-BINDING PROTEIN MDM2, DOUBLE MINUTE 2 PROTEIN, XDM2; COMPND 6 EC: 6.3.2.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 4 ORGANISM_TAXID: 8355; SOURCE 5 GENE: MDM2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PUBS 520 KEYWDS MDM2, PROTEIN-PROTEIN INTERACTION, LIGASE EXPDTA SOLUTION NMR NUMMDL 18 AUTHOR D.C.FRY,S.D.EMERSON,S.PALME,B.T.VU,C.M.LIU,F.PODLASKI REVDAT 3 27-OCT-21 1TTV 1 REMARK SEQADV REVDAT 2 24-FEB-09 1TTV 1 VERSN REVDAT 1 04-JAN-05 1TTV 0 JRNL AUTH D.C.FRY,S.D.EMERSON,S.PALME,B.T.VU,C.M.LIU,F.PODLASKI JRNL TITL NMR STRUCTURE OF A COMPLEX BETWEEN MDM2 AND A SMALL MOLECULE JRNL TITL 2 INHIBITOR. JRNL REF J.BIOMOL.NMR V. 30 163 2004 JRNL REFN ISSN 0925-2738 JRNL PMID 15557803 JRNL DOI 10.1023/B:JNMR.0000048856.84603.9B REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 2000, CNX 2000.1 REMARK 3 AUTHORS : HARE ET AL. (FELIX), BRUNGER ET AL. (CNX) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE CALCULATIONS UTILIZED 1169 REMARK 3 NOE-BASED DISTANCE CONSTRAINTS, OF WHICH 54 WERE INTERMOLECULAR; REMARK 3 176 DIHEDRAL ANGLE CONSTRAINTS; AND 48 HYDROGEN BOND REMARK 3 CONSTRAINTS. THE PIPERAZINYL MOIETY OF THE INHIBITOR GAVE NO REMARK 3 NOES, HENCE THE POSITIONS OF ITS ATOMS ARE NOT KNOWN AND THE REMARK 3 STEREOCHEMISTRY IS NOT RIGOROUSLY ESTABLISHED. REMARK 4 REMARK 4 1TTV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000022895. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 50MM D13-MES; 150MM KCL; 50MM REMARK 210 D10-DTT; 1.5MM NAN3 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6MM 13C/15N-MDM2; 3.5MM REMARK 210 INHIBITOR; 50MM D13-MES; 150MM REMARK 210 KCL; 50MM D10-DTT; 1.5MM NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 2D 13C/15N- REMARK 210 FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW 5.0.3, CNX 2000.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 42 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 18 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 4 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: 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 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 HB3 HIS A 69 H301 IMY A 120 1.25 REMARK 500 O VAL A 24 H PHE A 44 1.58 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 SER A 16 -74.65 -173.05 REMARK 500 1 THR A 17 -58.95 -165.12 REMARK 500 1 ASP A 19 26.99 -158.29 REMARK 500 1 LYS A 41 179.85 -51.77 REMARK 500 1 GLN A 61 63.16 71.87 REMARK 500 1 LYS A 66 -78.52 -46.49 REMARK 500 1 GLU A 86 129.57 179.35 REMARK 500 2 ILE A 15 -42.96 -148.22 REMARK 500 2 SER A 16 -66.23 70.08 REMARK 500 2 GLU A 21 -166.12 -106.85 REMARK 500 2 GLN A 61 62.18 69.77 REMARK 500 2 ASN A 102 32.23 -96.12 REMARK 500 2 GLU A 110 163.88 60.83 REMARK 500 3 SER A 16 -75.06 -166.72 REMARK 500 3 THR A 17 -67.47 -163.60 REMARK 500 3 GLU A 21 -163.37 -117.39 REMARK 500 3 THR A 27 158.94 -48.65 REMARK 500 3 LYS A 41 177.52 -52.19 REMARK 500 3 GLN A 61 60.25 72.01 REMARK 500 3 ASN A 102 37.96 -95.63 REMARK 500 3 VAL A 104 -82.83 -53.35 REMARK 500 4 ILE A 15 -77.05 64.57 REMARK 500 4 SER A 16 -80.66 61.52 REMARK 500 4 ASP A 19 135.28 63.83 REMARK 500 4 GLU A 21 -81.75 -145.38 REMARK 500 4 THR A 27 162.07 -49.20 REMARK 500 4 LYS A 41 176.15 -49.15 REMARK 500 4 GLN A 61 69.19 69.67 REMARK 500 4 ASN A 102 43.32 -96.67 REMARK 500 5 ILE A 15 -68.24 68.64 REMARK 500 5 SER A 16 -179.68 57.10 REMARK 500 5 THR A 17 167.96 60.12 REMARK 500 5 GLN A 40 -58.16 -125.47 REMARK 500 5 GLN A 61 60.98 75.08 REMARK 500 5 ASN A 102 37.39 -95.92 REMARK 500 5 VAL A 104 -81.87 -52.01 REMARK 500 6 HIS A 14 94.37 -68.43 REMARK 500 6 THR A 17 -73.60 65.61 REMARK 500 6 GLN A 61 67.51 67.56 REMARK 500 6 ASN A 102 33.23 -97.24 REMARK 500 6 ASN A 107 100.52 -57.64 REMARK 500 6 GLU A 110 162.31 173.38 REMARK 500 7 ILE A 15 164.14 58.82 REMARK 500 7 THR A 17 -78.12 64.09 REMARK 500 7 ASP A 19 -79.86 -178.68 REMARK 500 7 LYS A 41 179.25 -54.35 REMARK 500 7 MET A 46 -33.16 -39.17 REMARK 500 7 GLN A 61 65.17 68.74 REMARK 500 7 ASN A 107 101.86 -58.02 REMARK 500 7 PHE A 116 30.84 -98.54 REMARK 500 REMARK 500 THIS ENTRY HAS 119 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 AUTHOR NOTED THAT THE PIPERIZINYL MOIETY PRODUCED NO NOES, REMARK 600 SO THE POSITIONS OF ITS ATOMS COULD NOT BE DETERMINED REMARK 600 EXPERIMENTALLY AND ARE NOT INCLUDED IN THE COORDINATES. REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1 IMY A 120 REMARK 610 2 IMY A 120 REMARK 610 3 IMY A 120 REMARK 610 4 IMY A 120 REMARK 610 5 IMY A 120 REMARK 610 6 IMY A 120 REMARK 610 7 IMY A 120 REMARK 610 8 IMY A 120 REMARK 610 9 IMY A 120 REMARK 610 10 IMY A 120 REMARK 610 11 IMY A 120 REMARK 610 12 IMY A 120 REMARK 610 13 IMY A 120 REMARK 610 14 IMY A 120 REMARK 610 15 IMY A 120 REMARK 610 16 IMY A 120 REMARK 610 17 IMY A 120 REMARK 610 18 IMY A 120 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMY A 120 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YCQ RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF MDM2 WITH A P53 PEPTIDE BY KUSSIE ET AL. REMARK 900 RELATED ID: 1RV1 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF MDM2 WITH AN IMIDAZOLINE INHIBITOR BY LUKACS, REMARK 900 KAMMLOTT, AND GRAVES DBREF 1TTV A 13 119 UNP P56273 MDM2_XENLA 13 119 SEQADV 1TTV LEU A 50 UNP P56273 ILE 50 ENGINEERED MUTATION SEQADV 1TTV HIS A 92 UNP P56273 PRO 92 ENGINEERED MUTATION SEQADV 1TTV ILE A 95 UNP P56273 LEU 95 ENGINEERED MUTATION SEQRES 1 A 107 ASN HIS ILE SER THR SER ASP GLN GLU LYS LEU VAL GLN SEQRES 2 A 107 PRO THR PRO LEU LEU LEU SER LEU LEU LYS SER ALA GLY SEQRES 3 A 107 ALA GLN LYS GLU THR PHE THR MET LYS GLU VAL LEU TYR SEQRES 4 A 107 HIS LEU GLY GLN TYR ILE MET ALA LYS GLN LEU TYR ASP SEQRES 5 A 107 GLU LYS GLN GLN HIS ILE VAL HIS CYS SER ASN ASP PRO SEQRES 6 A 107 LEU GLY GLU LEU PHE GLY VAL GLN GLU PHE SER VAL LYS SEQRES 7 A 107 GLU HIS ARG ARG ILE TYR ALA MET ILE SER ARG ASN LEU SEQRES 8 A 107 VAL SER ALA ASN VAL LYS GLU SER SER GLU ASP ILE PHE SEQRES 9 A 107 GLY ASN VAL HET IMY A 120 54 HETNAM IMY 1-{[4,5-BIS(4-CHLOROPHENYL)-2-(2-ISOPROPOXY-4- HETNAM 2 IMY METHOXYPHENYL)-4,5-DIHYDRO-1H-IMIDAZOL-1- HETNAM 3 IMY YL]CARBONYL}PIPERAZINE HETSYN IMY CIS-[4,5-BIS-(4-CHLOROPHENYL)-2-(2-ISOPROPOXY-4- HETSYN 2 IMY METHOXYPHENYL)-4,5-DIHYD ROIMIDAZOL-1-YL]-PIPERAZIN-1- HETSYN 3 IMY YL-METHANONE FORMUL 2 IMY C30 H32 CL2 N4 O3 HELIX 1 1 THR A 27 ALA A 37 1 11 HELIX 2 2 THR A 45 GLN A 61 1 17 HELIX 3 3 ASP A 76 GLY A 83 1 8 HELIX 4 4 GLU A 91 ARG A 101 1 11 SHEET 1 A 2 VAL A 24 PRO A 26 0 SHEET 2 A 2 LEU A 103 ALA A 106 -1 O SER A 105 N GLN A 25 SHEET 1 B 2 ILE A 70 VAL A 71 0 SHEET 2 B 2 PHE A 87 SER A 88 -1 O PHE A 87 N VAL A 71 SITE 1 AC1 8 LEU A 50 LEU A 53 GLY A 54 ILE A 57 SITE 2 AC1 8 GLN A 68 HIS A 69 VAL A 89 HIS A 92 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