HEADER PEPTIDE BINDING PROTEIN 03-JUN-14 2RUH TITLE CHEMICAL SHIFT ASSIGNMENTS FOR MIP AND MDM2 IN BOUND STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE MDM2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MIP-MDM2 FUSION, UNP RESIDUES 6-120; COMPND 5 SYNONYM: DOUBLE MINUTE 2 PROTEIN, HDM2, ONCOPROTEIN MDM2, P53-BINDING COMPND 6 PROTEIN MDM2; COMPND 7 EC: 6.3.2.-; 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET15B; SOURCE 9 OTHER_DETAILS: PROTEIN EXPRESSES AS HAT-GB1-(THROMBIN CLEAVAGE SOURCE 10 SITE)-MIP-(TEV CLEAVAGE SITE)-MDM2-T7TAG FUSION. KEYWDS UBIQUITIN LIGASE, PEPTIDE BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.NAGATA,K.SHIRAKAWA,N.KOBAYASHI,H.SHIHEIDO,K.HORISAWA,M.KATAHIRA, AUTHOR 2 N.DOI,H.YANAGAWA REVDAT 2 14-JUN-23 2RUH 1 REMARK SEQADV REVDAT 1 15-OCT-14 2RUH 0 JRNL AUTH T.NAGATA,K.SHIRAKAWA,N.KOBAYASHI,H.SHIHEIDO,N.TABATA, JRNL AUTH 2 Y.SAKUMA-YONEMURA,K.HORISAWA,M.KATAHIRA,N.DOI,H.YANAGAWA JRNL TITL STRUCTURAL BASIS FOR INHIBITION OF THE MDM2:P53 INTERACTION JRNL TITL 2 BY AN OPTIMIZED MDM2-BINDING PEPTIDE SELECTED WITH MRNA JRNL TITL 3 DISPLAY JRNL REF PLOS ONE V. 9 09163 2014 JRNL REFN ESSN 1932-6203 JRNL PMID 25275651 JRNL DOI 10.1371/JOURNAL.PONE.0109163 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 12 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: AMBER12 USING THE AMBER 2003 FORCE REMARK 3 FIELD AND A GENERALIZED BORN MODEL REMARK 4 REMARK 4 2RUH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000150281. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.6 REMARK 210 IONIC STRENGTH : 160 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 650 UM [U-100% 13C; U-100% 15N] REMARK 210 MIP-MDM2 FUSION-1, 20 MM TRIS-2, REMARK 210 300 MM SODIUM CHLORIDE-3, 95% REMARK 210 H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D C(CO)NH; 3D REMARK 210 HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D HN(CO)CA; 3D REMARK 210 H(CCO)NH; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY; 3D REMARK 210 HCCH-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.0.14, KUJIRA 0.984, REMARK 210 NMRVIEW, NMRPIPE, NMRDRAW, REMARK 210 SPARKY, CHIMERA REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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: 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: 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 -2 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 ARG A -2 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 ARG A 71 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 ARG A -2 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 3 ARG A 71 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 ARG A -9 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 ARG A -2 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 ARG A 103 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG A 103 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A -2 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG A -9 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 18 ARG A 103 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 19 ARG A -9 NE - CZ - NH1 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 GLU A 1 41.03 -90.39 REMARK 500 1 ALA A 19 -91.54 57.24 REMARK 500 1 SER A 23 27.31 -149.03 REMARK 500 1 GLU A 29 -6.67 -148.41 REMARK 500 1 GLN A 117 65.65 -119.85 REMARK 500 2 GLN A 10 -47.03 61.64 REMARK 500 2 ALA A 19 -10.53 56.88 REMARK 500 2 THR A 22 18.10 -143.72 REMARK 500 2 GLN A 24 -53.59 -158.89 REMARK 500 2 GLN A 30 47.97 -78.00 REMARK 500 2 GLU A 31 36.85 -79.47 REMARK 500 2 GLN A 50 -21.80 57.47 REMARK 500 2 TYR A 82 69.70 -106.81 REMARK 500 2 ASN A 85 -0.02 59.80 REMARK 500 2 GLU A 101 49.35 -78.38 REMARK 500 2 THR A 113 -31.76 -132.51 REMARK 500 3 SER A 13 118.54 61.76 REMARK 500 3 VAL A 14 128.83 65.22 REMARK 500 3 ASP A 17 -90.74 27.28 REMARK 500 3 SER A 28 -24.16 64.70 REMARK 500 3 ARG A 35 72.36 47.29 REMARK 500 3 GLN A 78 34.12 -73.91 REMARK 500 3 ASN A 85 9.53 57.47 REMARK 500 4 GLU A 5 -33.97 63.47 REMARK 500 4 ALA A 19 43.62 -147.22 REMARK 500 4 GLN A 24 130.10 63.29 REMARK 500 4 SER A 28 8.02 58.87 REMARK 500 4 TYR A 82 68.74 -104.88 REMARK 500 4 ASN A 85 16.01 58.47 REMARK 500 5 GLU A 5 36.13 -79.65 REMARK 500 5 PHE A 9 -0.01 61.61 REMARK 500 5 VAL A 20 -10.17 -140.80 REMARK 500 5 ARG A 35 82.21 48.73 REMARK 500 5 CYS A 83 108.92 -160.38 REMARK 500 5 THR A 113 -34.44 -132.52 REMARK 500 5 MET A 118 -34.16 63.66 REMARK 500 6 LEU A 7 -93.07 50.20 REMARK 500 6 GLN A 10 122.37 67.58 REMARK 500 6 SER A 13 -87.64 -90.52 REMARK 500 6 SER A 23 41.84 -77.98 REMARK 500 6 GLN A 24 45.65 -75.41 REMARK 500 6 CYS A 83 48.69 -156.67 REMARK 500 6 HIS A 102 -85.66 35.08 REMARK 500 6 GLN A 116 39.55 -76.58 REMARK 500 7 LEU A 7 6.59 -150.02 REMARK 500 7 VAL A 14 124.38 64.88 REMARK 500 7 THR A 16 39.94 -74.63 REMARK 500 7 ARG A 35 70.33 51.70 REMARK 500 7 TYR A 82 59.95 -110.50 REMARK 500 7 CYS A 83 48.61 -67.72 REMARK 500 REMARK 500 THIS ENTRY HAS 135 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 11569 RELATED DB: BMRB DBREF 2RUH A 12 108 UNP Q00987 MDM2_HUMAN 6 102 SEQADV 2RUH MET A -11 UNP Q00987 EXPRESSION TAG SEQADV 2RUH PRO A -10 UNP Q00987 EXPRESSION TAG SEQADV 2RUH ARG A -9 UNP Q00987 EXPRESSION TAG SEQADV 2RUH PHE A -8 UNP Q00987 EXPRESSION TAG SEQADV 2RUH TRP A -7 UNP Q00987 EXPRESSION TAG SEQADV 2RUH GLU A -6 UNP Q00987 EXPRESSION TAG SEQADV 2RUH TYR A -5 UNP Q00987 EXPRESSION TAG SEQADV 2RUH TRP A -4 UNP Q00987 EXPRESSION TAG SEQADV 2RUH LEU A -3 UNP Q00987 EXPRESSION TAG SEQADV 2RUH ARG A -2 UNP Q00987 EXPRESSION TAG SEQADV 2RUH LEU A -1 UNP Q00987 EXPRESSION TAG SEQADV 2RUH MET A 0 UNP Q00987 EXPRESSION TAG SEQADV 2RUH GLU A 1 UNP Q00987 EXPRESSION TAG SEQADV 2RUH GLY A 2 UNP Q00987 EXPRESSION TAG SEQADV 2RUH GLY A 3 UNP Q00987 EXPRESSION TAG SEQADV 2RUH GLY A 4 UNP Q00987 EXPRESSION TAG SEQADV 2RUH GLU A 5 UNP Q00987 EXPRESSION TAG SEQADV 2RUH ASN A 6 UNP Q00987 EXPRESSION TAG SEQADV 2RUH LEU A 7 UNP Q00987 EXPRESSION TAG SEQADV 2RUH TYR A 8 UNP Q00987 EXPRESSION TAG SEQADV 2RUH PHE A 9 UNP Q00987 EXPRESSION TAG SEQADV 2RUH GLN A 10 UNP Q00987 EXPRESSION TAG SEQADV 2RUH GLY A 11 UNP Q00987 EXPRESSION TAG SEQADV 2RUH MET A 109 UNP Q00987 EXPRESSION TAG SEQADV 2RUH ALA A 110 UNP Q00987 EXPRESSION TAG SEQADV 2RUH SER A 111 UNP Q00987 EXPRESSION TAG SEQADV 2RUH MET A 112 UNP Q00987 EXPRESSION TAG SEQADV 2RUH THR A 113 UNP Q00987 EXPRESSION TAG SEQADV 2RUH GLY A 114 UNP Q00987 EXPRESSION TAG SEQADV 2RUH GLY A 115 UNP Q00987 EXPRESSION TAG SEQADV 2RUH GLN A 116 UNP Q00987 EXPRESSION TAG SEQADV 2RUH GLN A 117 UNP Q00987 EXPRESSION TAG SEQADV 2RUH MET A 118 UNP Q00987 EXPRESSION TAG SEQADV 2RUH GLY A 119 UNP Q00987 EXPRESSION TAG SEQRES 1 A 131 MET PRO ARG PHE TRP GLU TYR TRP LEU ARG LEU MET GLU SEQRES 2 A 131 GLY GLY GLY GLU ASN LEU TYR PHE GLN GLY MET SER VAL SEQRES 3 A 131 PRO THR ASP GLY ALA VAL THR THR SER GLN ILE PRO ALA SEQRES 4 A 131 SER GLU GLN GLU THR LEU VAL ARG PRO LYS PRO LEU LEU SEQRES 5 A 131 LEU LYS LEU LEU LYS SER VAL GLY ALA GLN LYS ASP THR SEQRES 6 A 131 TYR THR MET LYS GLU VAL LEU PHE TYR LEU GLY GLN TYR SEQRES 7 A 131 ILE MET THR LYS ARG LEU TYR ASP GLU LYS GLN GLN HIS SEQRES 8 A 131 ILE VAL TYR CYS SER ASN ASP LEU LEU GLY ASP LEU PHE SEQRES 9 A 131 GLY VAL PRO SER PHE SER VAL LYS GLU HIS ARG LYS ILE SEQRES 10 A 131 TYR THR MET MET ALA SER MET THR GLY GLY GLN GLN MET SEQRES 11 A 131 GLY HELIX 1 1 ARG A -9 GLU A 1 1 11 HELIX 2 2 GLY A 3 LEU A 7 5 5 HELIX 3 3 LYS A 37 VAL A 47 1 11 HELIX 4 4 MET A 56 ARG A 71 1 16 HELIX 5 5 ASP A 86 GLY A 93 1 8 HELIX 6 6 GLU A 101 THR A 113 1 13 SHEET 1 A 2 LEU A 33 VAL A 34 0 SHEET 2 A 2 TYR A 54 THR A 55 -1 O TYR A 54 N VAL A 34 SHEET 1 B 2 ILE A 80 TYR A 82 0 SHEET 2 B 2 SER A 96 SER A 98 -1 O PHE A 97 N VAL A 81 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