HEADER LIGASE/PEPTIDE 14-DEC-14 4UE1 TITLE STRUCTURE OF THE STAPLED PEPTIDE YS-01 BOUND TO MDM2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE MDM2; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: P53 BINDING DOMAIN, RESIDUES 17-125; COMPND 5 SYNONYM: DOUBLE MINUTE 2 PROTEIN, HDM2, ONCOPROTEIN MDM2, P53-BINDING COMPND 6 PROTEIN MDM2, MDM2; COMPND 7 EC: 6.3.2.-; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: YS-01; COMPND 12 CHAIN: F, G, H, I; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: STAPLED PEPTIDE, COVALENT BOND BETWEEN RESIDUES 20 AND COMPND 15 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: PGEX6P-1; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS LIGASE-PEPTIDE COMPLEX 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 4UE1 1 REMARK REVDAT 4 15-NOV-23 4UE1 1 LINK ATOM REVDAT 3 27-SEP-23 4UE1 1 LINK REVDAT 2 18-JAN-17 4UE1 1 JRNL REVDAT 1 13-JAN-16 4UE1 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. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 76.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 80031 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) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4214 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5170 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE SET COUNT : 279 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3627 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 267 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.47000 REMARK 3 B22 (A**2) : 0.20000 REMARK 3 B33 (A**2) : 0.19000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.14000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.064 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.062 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.040 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.357 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3896 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5295 ; 1.604 ; 2.005 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 467 ; 5.766 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 159 ;43.266 ;24.088 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 702 ;13.500 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;16.363 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 600 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2862 ; 0.009 ; 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): 1870 ; 2.229 ; 1.738 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2338 ; 2.850 ; 2.603 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2026 ; 3.503 ; 2.194 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): NULL ; NULL ; NULL 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): 3896 ; 4.157 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 104 ;21.500 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3968 ;11.440 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY. NCSR LOCAL WAS USED REMARK 3 DURING REFINEMENT. REMARK 4 REMARK 4 4UE1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1290062577. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PIXEL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 84267 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 51.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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 4.2, 0.2 M REMARK 280 SODIUM CHLORIDE AND 20 % 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 34.73100 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: 1280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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: 1280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.6 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.6 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 350 REMARK 350 BIOMOLECULE: 4 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: 1530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.3 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 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 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 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 PHE H 30 REMARK 465 NH2 H 31 REMARK 465 GLU I 28 REMARK 465 ASN I 29 REMARK 465 PHE 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 2043 O HOH B 2047 1.81 REMARK 500 NH1 ARG C 29 O HOH C 2012 2.03 REMARK 500 O HOH D 2022 O HOH D 2048 2.18 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 24 C LEU F 25 N 0.166 REMARK 500 2JN H 24 C LEU H 25 N 0.174 REMARK 500 2JN I 24 C LEU I 25 N 0.202 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 LEU A 57 CB - CG - CD2 ANGL. DEV. = -21.1 DEGREES REMARK 500 MET A 62 CG - SD - CE ANGL. DEV. = -14.6 DEGREES REMARK 500 MET D 62 CG - SD - CE ANGL. DEV. = -16.1 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 18.06 -141.19 REMARK 500 LEU D 66 41.03 -101.78 REMARK 500 CYS D 77 58.23 -94.49 REMARK 500 SER D 78 57.71 -93.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 2-METHYL-D-NORLEUCINE (2JN): RESIDUES 20 AND 24 FORM A REMARK 600 COVALENT BOND, THE HYDROCARBON STAPLE. 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UD7 RELATED DB: PDB REMARK 900 STRUCTURE OF THE STAPLED PEPTIDE YS-02 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 AT THE BEGINNING OF THE REMARK 999 CRYSTALLISATION CONSTRUCT IS AN ARTEFACT OF OUR CLONING REMARK 999 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. NON-NATURAL AMINO REMARK 999 ACIDS ARE USED TO FORM THE HYDROCARBON STAPLE. DBREF 4UE1 A 17 125 UNP Q00987 MDM2_HUMAN 17 125 DBREF 4UE1 B 17 125 UNP Q00987 MDM2_HUMAN 17 125 DBREF 4UE1 C 17 125 UNP Q00987 MDM2_HUMAN 17 125 DBREF 4UE1 D 17 125 UNP Q00987 MDM2_HUMAN 17 125 DBREF 4UE1 F 16 31 PDB 4UE1 4UE1 16 31 DBREF 4UE1 G 16 31 PDB 4UE1 4UE1 16 31 DBREF 4UE1 H 16 31 PDB 4UE1 4UE1 16 31 DBREF 4UE1 I 16 31 PDB 4UE1 4UE1 16 31 SEQADV 4UE1 GLY A 12 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 PRO A 13 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 LEU A 14 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 GLY A 15 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 SER A 16 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 ALA A 69 UNP Q00987 GLU 69 ENGINEERED MUTATION SEQADV 4UE1 ALA A 70 UNP Q00987 LYS 70 ENGINEERED MUTATION SEQADV 4UE1 GLY B 12 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 PRO B 13 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 LEU B 14 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 GLY B 15 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 SER B 16 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 ALA B 69 UNP Q00987 GLU 69 ENGINEERED MUTATION SEQADV 4UE1 ALA B 70 UNP Q00987 LYS 70 ENGINEERED MUTATION SEQADV 4UE1 GLY C 12 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 PRO C 13 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 LEU C 14 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 GLY C 15 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 SER C 16 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 ALA C 69 UNP Q00987 GLU 69 ENGINEERED MUTATION SEQADV 4UE1 ALA C 70 UNP Q00987 LYS 70 ENGINEERED MUTATION SEQADV 4UE1 GLY D 12 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 PRO D 13 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 LEU D 14 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 GLY D 15 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 SER D 16 UNP Q00987 EXPRESSION TAG SEQADV 4UE1 ALA D 69 UNP Q00987 GLU 69 ENGINEERED MUTATION SEQADV 4UE1 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 PHE NH2 SEQRES 1 G 16 ACE THR SER PHE 2JN GLU TYR TRP 2JN LEU LEU PRO GLU SEQRES 2 G 16 ASN PHE NH2 SEQRES 1 H 16 ACE THR SER PHE 2JN GLU TYR TRP 2JN LEU LEU PRO GLU SEQRES 2 H 16 ASN PHE NH2 SEQRES 1 I 16 ACE THR SER PHE 2JN GLU TYR TRP 2JN LEU LEU PRO GLU SEQRES 2 I 16 ASN PHE 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 ACE I 16 3 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 3(C2 H4 O) FORMUL 5 2JN 8(C7 H15 N O2) FORMUL 5 NH2 2(H2 N) FORMUL 9 HOH *267(H2 O) HELIX 1 1 LEU A 14 ILE A 19 5 6 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 LEU B 14 ILE B 19 5 6 HELIX 8 8 PRO B 20 GLN B 24 5 5 HELIX 9 9 LYS B 31 SER B 40 1 10 HELIX 10 10 THR B 49 LYS B 64 1 16 HELIX 11 11 ASP B 80 GLY B 87 1 8 HELIX 12 12 GLU B 95 ARG B 105 1 11 HELIX 13 13 SER C 22 GLU C 25 5 4 HELIX 14 14 LYS C 31 VAL C 41 1 11 HELIX 15 15 MET C 50 LYS C 64 1 15 HELIX 16 16 ASP C 80 GLY C 87 1 8 HELIX 17 17 GLU C 95 ARG C 105 1 11 HELIX 18 18 SER D 22 GLU D 25 5 4 HELIX 19 19 LYS D 31 GLY D 42 1 12 HELIX 20 20 MET D 50 LYS D 64 1 15 HELIX 21 21 ASN D 79 GLY D 87 1 9 HELIX 22 22 GLU D 95 ASN D 106 1 12 HELIX 23 23 LEU F 25 PHE F 30 1 6 HELIX 24 24 LEU G 25 PHE 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 1.34 LINK C PHE F 19 N 2JN F 20 1555 1555 1.41 LINK C 2JN F 20 N GLU F 21 1555 1555 1.42 LINK CAI 2JN F 20 CAI 2JN F 24 1555 1555 1.37 LINK C TRP F 23 N 2JN F 24 1555 1555 1.41 LINK C 2JN F 24 N LEU F 25 1555 1555 1.50 LINK C PHE F 30 N NH2 F 31 1555 1555 1.33 LINK C PHE G 19 N 2JN G 20 1555 1555 1.40 LINK C 2JN G 20 N GLU G 21 1555 1555 1.41 LINK CAI 2JN G 20 CAI 2JN G 24 1555 1555 1.36 LINK C TRP G 23 N 2JN G 24 1555 1555 1.39 LINK C 2JN G 24 N LEU G 25 1555 1555 1.40 LINK C PHE G 30 N NH2 G 31 1555 1555 1.33 LINK C ACE H 16 N THR H 17 1555 1555 1.33 LINK C PHE H 19 N 2JN H 20 1555 1555 1.39 LINK C 2JN H 20 N GLU H 21 1555 1555 1.41 LINK CAI 2JN H 20 CAI 2JN H 24 1555 1555 1.36 LINK C TRP H 23 N 2JN H 24 1555 1555 1.45 LINK C 2JN H 24 N LEU H 25 1555 1555 1.51 LINK C ACE I 16 N THR I 17 1555 1555 1.33 LINK C PHE I 19 N 2JN I 20 1555 1555 1.42 LINK C 2JN I 20 N GLU I 21 1555 1555 1.43 LINK CAI 2JN I 20 CAI 2JN I 24 1555 1555 1.36 LINK C TRP I 23 N 2JN I 24 1555 1555 1.45 LINK C 2JN I 24 N LEU I 25 1555 1555 1.54 CRYST1 46.104 69.462 78.562 90.00 101.96 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 0.021690 0.000000 0.004595 0.00000 SCALE2 0.000000 0.014396 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013011 0.00000