HEADER LYASE 08-DEC-14 4UD7 TITLE STRUCTURE OF THE STAPLED PEPTIDE YS-02 BOUND TO MDM2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MDM2; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: P53 BINDING DOMAIN, UNP RESIDUES 17-125; COMPND 5 EC: 6.3.2.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: YS-02; COMPND 10 CHAIN: F, G, H, I; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: STAPLED PEPTIDE, COVALENT BOND BETWEEN THE SIDE CHAINS COMPND 13 OF RESIDUES 20 AND 24. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX6P-1; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS LYASE, MDM2, STAPLED PEPTIDE, P53 EXPDTA X-RAY DIFFRACTION AUTHOR Y.S.TAN,J.REEKS,C.J.BROWN,C.E.JENNINGS,R.S.EAPEN,Q.S.TNG,D.THEAN, AUTHOR 2 Y.T.YING,F.J.F.GAGO,D.P.LANE,M.E.M.NOBLE,C.VERMA REVDAT 5 20-DEC-23 4UD7 1 REMARK REVDAT 4 15-NOV-23 4UD7 1 LINK ATOM REVDAT 3 27-SEP-23 4UD7 1 LINK REVDAT 2 18-JAN-17 4UD7 1 JRNL REVDAT 1 13-JAN-16 4UD7 0 JRNL AUTH Y.S.TAN,J.REEKS,C.J.BROWN,D.THEAN,F.J.FERRER GAGO,T.Y.YUEN, JRNL AUTH 2 E.T.GOH,X.E.LEE,C.E.JENNINGS,T.L.JOSEPH,R.LAKSHMINARAYANAN, JRNL AUTH 3 D.P.LANE,M.E.NOBLE,C.S.VERMA JRNL TITL BENZENE PROBES IN MOLECULAR DYNAMICS SIMULATIONS REVEAL JRNL TITL 2 NOVEL BINDING SITES FOR LIGAND DESIGN. JRNL REF J PHYS CHEM LETT V. 7 3452 2016 JRNL REFN ESSN 1948-7185 JRNL PMID 27532490 JRNL DOI 10.1021/ACS.JPCLETT.6B01525 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 76.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 59304 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) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3198 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4258 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.14 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE SET COUNT : 221 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3577 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 262 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.06000 REMARK 3 B22 (A**2) : 0.36000 REMARK 3 B33 (A**2) : 0.64000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.094 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.076 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.054 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.544 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3831 ; 0.011 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5203 ; 1.478 ; 2.001 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 455 ; 5.572 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 158 ;44.536 ;24.051 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 694 ;14.163 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;17.334 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 594 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2792 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1828 ; 2.690 ; 1.842 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2281 ; 3.327 ; 2.750 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2003 ; 4.523 ; 2.373 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6017 ; 5.314 ;17.118 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3831 ; 3.655 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 116 ;27.879 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3892 ;15.140 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 6 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 16 110 B 16 110 117 0.11 0.05 REMARK 3 2 A 17 110 C 17 110 104 0.22 0.05 REMARK 3 3 A 17 110 D 17 110 92 0.20 0.05 REMARK 3 4 B 17 110 C 17 110 110 0.24 0.05 REMARK 3 5 B 17 110 D 17 110 97 0.23 0.05 REMARK 3 6 C 17 112 D 17 112 112 0.14 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4UD7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1290062296. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62522 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 52.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.900 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.69000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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: PDB ENTRY 1YCR REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE PH 4.0 AND 15 % REMARK 280 PEG8000 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 34.76900 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, 3, 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, H 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, I 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: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, G 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: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, F 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 12 REMARK 465 PRO A 13 REMARK 465 LEU A 14 REMARK 465 GLN A 112 REMARK 465 GLN A 113 REMARK 465 GLU A 114 REMARK 465 SER A 115 REMARK 465 SER A 116 REMARK 465 ASP A 117 REMARK 465 SER A 118 REMARK 465 GLY A 119 REMARK 465 THR A 120 REMARK 465 SER A 121 REMARK 465 VAL A 122 REMARK 465 SER A 123 REMARK 465 GLU A 124 REMARK 465 ASN A 125 REMARK 465 GLY B 12 REMARK 465 PRO B 13 REMARK 465 LEU B 14 REMARK 465 GLY B 15 REMARK 465 GLN B 112 REMARK 465 GLN B 113 REMARK 465 GLU B 114 REMARK 465 SER B 115 REMARK 465 SER B 116 REMARK 465 ASP B 117 REMARK 465 SER B 118 REMARK 465 GLY B 119 REMARK 465 THR B 120 REMARK 465 SER B 121 REMARK 465 VAL B 122 REMARK 465 SER B 123 REMARK 465 GLU B 124 REMARK 465 ASN B 125 REMARK 465 GLY C 12 REMARK 465 PRO C 13 REMARK 465 LEU C 14 REMARK 465 GLY C 15 REMARK 465 SER C 16 REMARK 465 GLN C 113 REMARK 465 GLU C 114 REMARK 465 SER C 115 REMARK 465 SER C 116 REMARK 465 ASP C 117 REMARK 465 SER C 118 REMARK 465 GLY C 119 REMARK 465 THR C 120 REMARK 465 SER C 121 REMARK 465 VAL C 122 REMARK 465 SER C 123 REMARK 465 GLU C 124 REMARK 465 ASN C 125 REMARK 465 GLY D 12 REMARK 465 PRO D 13 REMARK 465 LEU D 14 REMARK 465 GLY D 15 REMARK 465 SER D 16 REMARK 465 GLN D 113 REMARK 465 GLU D 114 REMARK 465 SER D 115 REMARK 465 SER D 116 REMARK 465 ASP D 117 REMARK 465 SER D 118 REMARK 465 GLY D 119 REMARK 465 THR D 120 REMARK 465 SER D 121 REMARK 465 VAL D 122 REMARK 465 SER D 123 REMARK 465 GLU D 124 REMARK 465 ASN D 125 REMARK 465 ACE G 16 REMARK 465 GLU H 28 REMARK 465 ASN H 29 REMARK 465 TYR H 30 REMARK 465 NH2 H 31 REMARK 465 ACE I 16 REMARK 465 PRO I 27 REMARK 465 GLU I 28 REMARK 465 ASN I 29 REMARK 465 TYR I 30 REMARK 465 NH2 I 31 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH B 2039 O HOH B 2043 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CG2 THR B 63 O HOH D 2032 2546 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 2JN F 20 C GLU F 21 N 0.153 REMARK 500 TRP F 23 C 2JN F 24 N 0.170 REMARK 500 2JN F 24 C LEU F 25 N 0.307 REMARK 500 PHE G 19 C 2JN G 20 N 0.162 REMARK 500 2JN G 20 C GLU G 21 N 0.153 REMARK 500 TRP G 23 C 2JN G 24 N 0.193 REMARK 500 2JN G 24 C LEU G 25 N 0.231 REMARK 500 2JN H 20 C GLU H 21 N 0.170 REMARK 500 TRP H 23 C 2JN H 24 N 0.166 REMARK 500 PHE I 19 C 2JN I 20 N 0.187 REMARK 500 2JN I 20 C GLU I 21 N 0.185 REMARK 500 TRP I 23 C 2JN I 24 N 0.268 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 MET A 62 CG - SD - CE ANGL. DEV. = -11.2 DEGREES REMARK 500 MET D 62 CG - SD - CE ANGL. DEV. = -17.1 DEGREES REMARK 500 2JN F 20 O - C - N ANGL. DEV. = -10.4 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 CYS C 77 19.68 -142.00 REMARK 500 SER D 78 48.39 -96.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 AMINO GROUP (NH2): STAPLED PEPTIDE IS AMIDATED AT THE REMARK 600 C-TERMINUS. REMARK 600 ACETYL GROUP (ACE): STAPLED PEPTIDE IS ACETYLATED AT THE REMARK 600 N-TERMINUS. REMARK 600 2 (R)-2-(4'-PENTENYL)ALANINE (2JN): THIS NON-NATURAL AMINO REMARK 600 ACID FORMS A COVALENT BOND BETWEEN RESIDUES 20 AND 24 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UE1 RELATED DB: PDB REMARK 900 STRUCTURE OF THE STAPLED PEPTIDE YS-01 BOUND TO MDM2 REMARK 999 REMARK 999 SEQUENCE REMARK 999 E69 AND K70 ARE MUTATED TO ALANINES FOR SURFACE ENTROPY REMARK 999 REDUCTION. THE GPLGS OF THE CRYSTALLISATION CONSTRUCT IS REMARK 999 AN ARTEFACT OF OUR CLONING AND PURIFICATION STRATEGIES. REMARK 999 THIS STAPLED PEPTIDE WAS ORIGINALLY BASED ON A P53 PEPTIDE REMARK 999 BUT IS NOW SO HEAVILY MODIFIED SO AS TO BEAR LITTLE REMARK 999 RESEMBLANCE TO THE ORIGINAL SEQUENCE. DBREF 4UD7 A 17 125 UNP Q00987 MDM2_HUMAN 17 125 DBREF 4UD7 B 17 125 UNP Q00987 MDM2_HUMAN 17 125 DBREF 4UD7 C 17 125 UNP Q00987 MDM2_HUMAN 17 125 DBREF 4UD7 D 17 125 UNP Q00987 MDM2_HUMAN 17 125 DBREF 4UD7 F 16 31 PDB 4UD7 4UD7 16 31 DBREF 4UD7 G 16 31 PDB 4UD7 4UD7 16 31 DBREF 4UD7 H 16 31 PDB 4UD7 4UD7 16 31 DBREF 4UD7 I 16 31 PDB 4UD7 4UD7 16 31 SEQADV 4UD7 GLY A 12 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 PRO A 13 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 LEU A 14 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 GLY A 15 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 SER A 16 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 ALA A 69 UNP Q00987 GLU 69 ENGINEERED MUTATION SEQADV 4UD7 ALA A 70 UNP Q00987 LYS 70 ENGINEERED MUTATION SEQADV 4UD7 GLY B 12 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 PRO B 13 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 LEU B 14 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 GLY B 15 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 SER B 16 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 ALA B 69 UNP Q00987 GLU 69 ENGINEERED MUTATION SEQADV 4UD7 ALA B 70 UNP Q00987 LYS 70 ENGINEERED MUTATION SEQADV 4UD7 GLY C 12 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 PRO C 13 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 LEU C 14 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 GLY C 15 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 SER C 16 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 ALA C 69 UNP Q00987 GLU 69 ENGINEERED MUTATION SEQADV 4UD7 ALA C 70 UNP Q00987 LYS 70 ENGINEERED MUTATION SEQADV 4UD7 GLY D 12 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 PRO D 13 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 LEU D 14 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 GLY D 15 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 SER D 16 UNP Q00987 EXPRESSION TAG SEQADV 4UD7 ALA D 69 UNP Q00987 GLU 69 ENGINEERED MUTATION SEQADV 4UD7 ALA D 70 UNP Q00987 LYS 70 ENGINEERED MUTATION SEQRES 1 A 114 GLY PRO LEU GLY SER SER GLN ILE PRO ALA SER GLU GLN SEQRES 2 A 114 GLU THR LEU VAL ARG PRO LYS PRO LEU LEU LEU LYS LEU SEQRES 3 A 114 LEU LYS SER VAL GLY ALA GLN LYS ASP THR TYR THR MET SEQRES 4 A 114 LYS GLU VAL LEU PHE TYR LEU GLY GLN TYR ILE MET THR SEQRES 5 A 114 LYS ARG LEU TYR ASP ALA ALA GLN GLN HIS ILE VAL TYR SEQRES 6 A 114 CYS SER ASN ASP LEU LEU GLY ASP LEU PHE GLY VAL PRO SEQRES 7 A 114 SER PHE SER VAL LYS GLU HIS ARG LYS ILE TYR THR MET SEQRES 8 A 114 ILE TYR ARG ASN LEU VAL VAL VAL ASN GLN GLN GLU SER SEQRES 9 A 114 SER ASP SER GLY THR SER VAL SER GLU ASN SEQRES 1 B 114 GLY PRO LEU GLY SER SER GLN ILE PRO ALA SER GLU GLN SEQRES 2 B 114 GLU THR LEU VAL ARG PRO LYS PRO LEU LEU LEU LYS LEU SEQRES 3 B 114 LEU LYS SER VAL GLY ALA GLN LYS ASP THR TYR THR MET SEQRES 4 B 114 LYS GLU VAL LEU PHE TYR LEU GLY GLN TYR ILE MET THR SEQRES 5 B 114 LYS ARG LEU TYR ASP ALA ALA GLN GLN HIS ILE VAL TYR SEQRES 6 B 114 CYS SER ASN ASP LEU LEU GLY ASP LEU PHE GLY VAL PRO SEQRES 7 B 114 SER PHE SER VAL LYS GLU HIS ARG LYS ILE TYR THR MET SEQRES 8 B 114 ILE TYR ARG ASN LEU VAL VAL VAL ASN GLN GLN GLU SER SEQRES 9 B 114 SER ASP SER GLY THR SER VAL SER GLU ASN SEQRES 1 C 114 GLY PRO LEU GLY SER SER GLN ILE PRO ALA SER GLU GLN SEQRES 2 C 114 GLU THR LEU VAL ARG PRO LYS PRO LEU LEU LEU LYS LEU SEQRES 3 C 114 LEU LYS SER VAL GLY ALA GLN LYS ASP THR TYR THR MET SEQRES 4 C 114 LYS GLU VAL LEU PHE TYR LEU GLY GLN TYR ILE MET THR SEQRES 5 C 114 LYS ARG LEU TYR ASP ALA ALA GLN GLN HIS ILE VAL TYR SEQRES 6 C 114 CYS SER ASN ASP LEU LEU GLY ASP LEU PHE GLY VAL PRO SEQRES 7 C 114 SER PHE SER VAL LYS GLU HIS ARG LYS ILE TYR THR MET SEQRES 8 C 114 ILE TYR ARG ASN LEU VAL VAL VAL ASN GLN GLN GLU SER SEQRES 9 C 114 SER ASP SER GLY THR SER VAL SER GLU ASN SEQRES 1 D 114 GLY PRO LEU GLY SER SER GLN ILE PRO ALA SER GLU GLN SEQRES 2 D 114 GLU THR LEU VAL ARG PRO LYS PRO LEU LEU LEU LYS LEU SEQRES 3 D 114 LEU LYS SER VAL GLY ALA GLN LYS ASP THR TYR THR MET SEQRES 4 D 114 LYS GLU VAL LEU PHE TYR LEU GLY GLN TYR ILE MET THR SEQRES 5 D 114 LYS ARG LEU TYR ASP ALA ALA GLN GLN HIS ILE VAL TYR SEQRES 6 D 114 CYS SER ASN ASP LEU LEU GLY ASP LEU PHE GLY VAL PRO SEQRES 7 D 114 SER PHE SER VAL LYS GLU HIS ARG LYS ILE TYR THR MET SEQRES 8 D 114 ILE TYR ARG ASN LEU VAL VAL VAL ASN GLN GLN GLU SER SEQRES 9 D 114 SER ASP SER GLY THR SER VAL SER GLU ASN SEQRES 1 F 16 ACE THR SER PHE 2JN GLU TYR TRP 2JN LEU LEU PRO GLU SEQRES 2 F 16 ASN TYR NH2 SEQRES 1 G 16 ACE THR SER PHE 2JN GLU TYR TRP 2JN LEU LEU PRO GLU SEQRES 2 G 16 ASN TYR NH2 SEQRES 1 H 16 ACE THR SER PHE 2JN GLU TYR TRP 2JN LEU LEU PRO GLU SEQRES 2 H 16 ASN TYR NH2 SEQRES 1 I 16 ACE THR SER PHE 2JN GLU TYR TRP 2JN LEU LEU PRO GLU SEQRES 2 I 16 ASN TYR NH2 HET ACE F 16 3 HET 2JN F 20 9 HET 2JN F 24 9 HET NH2 F 31 1 HET 2JN G 20 9 HET 2JN G 24 9 HET NH2 G 31 1 HET ACE H 16 3 HET 2JN H 20 9 HET 2JN H 24 9 HET 2JN I 20 9 HET 2JN I 24 9 HETNAM ACE ACETYL GROUP HETNAM 2JN 2-METHYL-D-NORLEUCINE HETNAM NH2 AMINO GROUP FORMUL 5 ACE 2(C2 H4 O) FORMUL 5 2JN 8(C7 H15 N O2) FORMUL 5 NH2 2(H2 N) FORMUL 9 HOH *262(H2 O) HELIX 1 1 GLY A 15 ILE A 19 5 5 HELIX 2 2 PRO A 20 GLN A 24 5 5 HELIX 3 3 LYS A 31 VAL A 41 1 11 HELIX 4 4 THR A 49 LYS A 64 1 16 HELIX 5 5 ASP A 80 GLY A 87 1 8 HELIX 6 6 GLU A 95 ARG A 105 1 11 HELIX 7 7 PRO B 20 GLN B 24 5 5 HELIX 8 8 LYS B 31 SER B 40 1 10 HELIX 9 9 THR B 49 LYS B 64 1 16 HELIX 10 10 ASP B 80 GLY B 87 1 8 HELIX 11 11 GLU B 95 ARG B 105 1 11 HELIX 12 12 SER C 22 GLU C 25 5 4 HELIX 13 13 LYS C 31 VAL C 41 1 11 HELIX 14 14 MET C 50 LYS C 64 1 15 HELIX 15 15 ASP C 80 GLY C 87 1 8 HELIX 16 16 GLU C 95 ARG C 105 1 11 HELIX 17 17 SER D 22 GLU D 25 5 4 HELIX 18 18 LYS D 31 GLY D 42 1 12 HELIX 19 19 MET D 50 LYS D 64 1 15 HELIX 20 20 ASN D 79 GLY D 87 1 9 HELIX 21 21 GLU D 95 ASN D 106 1 12 HELIX 22 22 LEU G 25 TYR G 30 1 6 SHEET 1 AA 2 GLU A 25 LEU A 27 0 SHEET 2 AA 2 GLU B 25 LEU B 27 -1 O GLU B 25 N LEU A 27 SHEET 1 AB 2 ILE A 74 TYR A 76 0 SHEET 2 AB 2 SER A 90 SER A 92 -1 O PHE A 91 N VAL A 75 SHEET 1 BA 2 ILE B 74 TYR B 76 0 SHEET 2 BA 2 SER B 90 SER B 92 -1 O PHE B 91 N VAL B 75 SHEET 1 CA 3 TYR C 48 THR C 49 0 SHEET 2 CA 3 LEU C 27 PRO C 30 -1 O VAL C 28 N TYR C 48 SHEET 3 CA 3 LEU C 107 VAL C 109 -1 O VAL C 108 N ARG C 29 SHEET 1 CB 2 ILE C 74 TYR C 76 0 SHEET 2 CB 2 SER C 90 SER C 92 -1 O PHE C 91 N VAL C 75 SHEET 1 DA 3 TYR D 48 THR D 49 0 SHEET 2 DA 3 LEU D 27 PRO D 30 -1 O VAL D 28 N TYR D 48 SHEET 3 DA 3 LEU D 107 VAL D 109 -1 O VAL D 108 N ARG D 29 SHEET 1 DB 2 ILE D 74 TYR D 76 0 SHEET 2 DB 2 SER D 90 SER D 92 -1 O PHE D 91 N VAL D 75 LINK C ACE F 16 N THR F 17 1555 1555 1.33 LINK C PHE F 19 N 2JN F 20 1555 1555 1.44 LINK C 2JN F 20 N GLU F 21 1555 1555 1.49 LINK CAI 2JN F 20 CAI 2JN F 24 1555 1555 1.35 LINK C TRP F 23 N 2JN F 24 1555 1555 1.51 LINK C 2JN F 24 N LEU F 25 1555 1555 1.64 LINK C TYR F 30 N NH2 F 31 1555 1555 1.33 LINK C PHE G 19 N 2JN G 20 1555 1555 1.50 LINK C 2JN G 20 N GLU G 21 1555 1555 1.49 LINK CAI 2JN G 20 CAI 2JN G 24 1555 1555 1.34 LINK C TRP G 23 N 2JN G 24 1555 1555 1.53 LINK C 2JN G 24 N LEU G 25 1555 1555 1.57 LINK C ACE H 16 N THR H 17 1555 1555 1.33 LINK C PHE H 19 N 2JN H 20 1555 1555 1.47 LINK C 2JN H 20 N GLU H 21 1555 1555 1.51 LINK CAI 2JN H 20 CAI 2JN H 24 1555 1555 1.33 LINK C TRP H 23 N 2JN H 24 1555 1555 1.50 LINK C 2JN H 24 N LEU H 25 1555 1555 1.70 LINK C PHE I 19 N 2JN I 20 1555 1555 1.52 LINK C 2JN I 20 N GLU I 21 1555 1555 1.52 LINK CAI 2JN I 20 CAI 2JN I 24 1555 1555 1.34 LINK C TRP I 23 N 2JN I 24 1555 1555 1.60 LINK C 2JN I 24 N LEU I 25 1555 1555 1.70 CRYST1 46.148 69.538 78.464 90.00 102.36 90.00 P 1 21 1 8 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 0.021669 0.000000 0.004748 0.00000 SCALE2 0.000000 0.014381 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013047 0.00000