HEADER PEPTIDE BINDING PROTEIN 19-APR-20 6YR5 TITLE 14-3-3 SIGMA IN COMPLEX WITH HDMX-367 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 14-3-3 PROTEIN SIGMA; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: EPITHELIAL CELL MARKER PROTEIN 1,STRATIFIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PROTEIN MDM4; COMPND 8 CHAIN: O, P, Q, R; COMPND 9 SYNONYM: DOUBLE MINUTE 4 PROTEIN,MDM2-LIKE P53-BINDING PROTEIN, COMPND 10 PROTEIN MDMX,P53-BINDING PROTEIN MDM4; COMPND 11 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: SFN, HME1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.WOLTER,S.SRDANOVIC,C.OTTMAN,S.WARRINER,A.WILSON REVDAT 3 24-JAN-24 6YR5 1 REMARK REVDAT 2 13-APR-22 6YR5 1 JRNL REVDAT 1 03-NOV-21 6YR5 0 JRNL AUTH S.SRDANOVIC,M.WOLTER,C.H.TRINH,C.OTTMANN,S.L.WARRINER, JRNL AUTH 2 A.J.WILSON JRNL TITL UNDERSTANDING THE INTERACTION OF 14-3-3 PROTEINS WITH HDMX JRNL TITL 2 AND HDM2: A STRUCTURAL AND BIOPHYSICAL STUDY. JRNL REF FEBS J. 2022 JRNL REFN ISSN 1742-464X JRNL PMID 35286747 JRNL DOI 10.1111/FEBS.16433 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 74.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 58664 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2993 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4295 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.32 REMARK 3 BIN R VALUE (WORKING SET) : 0.2950 REMARK 3 BIN FREE R VALUE SET COUNT : 206 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7324 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 371 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.23000 REMARK 3 B22 (A**2) : -1.32000 REMARK 3 B33 (A**2) : 0.06000 REMARK 3 B12 (A**2) : -0.27000 REMARK 3 B13 (A**2) : 0.10000 REMARK 3 B23 (A**2) : -0.10000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.240 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.186 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.128 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.156 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7439 ; 0.011 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 6973 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10034 ; 1.659 ; 1.643 REMARK 3 BOND ANGLES OTHERS (DEGREES): 16140 ; 1.399 ; 1.580 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 933 ; 6.102 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 387 ;33.228 ;22.248 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1343 ;16.740 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 55 ;17.740 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 982 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8286 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1515 ; 0.001 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL 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 REMARK 4 REMARK 4 6YR5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292107822. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033208 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.6.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75667 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 74.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.67300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4DAT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PROPANE PH 7, 0.2 M REMARK 280 SODIUM CITRATE, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, O, B, P 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, Q 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 APPLY THE FOLLOWING TO CHAINS: D, R REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -63.95000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 -4 REMARK 465 GLU A 71 REMARK 465 GLU A 72 REMARK 465 GLY A 73 REMARK 465 SER A 74 REMARK 465 GLU A 75 REMARK 465 GLU A 76 REMARK 465 ASP O 361 REMARK 465 CYS O 362 REMARK 465 ARG O 372 REMARK 465 PRO O 373 REMARK 465 LYS O 374 REMARK 465 GLY B -4 REMARK 465 ASN B 70 REMARK 465 GLU B 71 REMARK 465 GLU B 72 REMARK 465 GLY B 73 REMARK 465 SER B 74 REMARK 465 GLU B 75 REMARK 465 GLU B 76 REMARK 465 ASP P 361 REMARK 465 CYS P 362 REMARK 465 ARG P 363 REMARK 465 LYS P 374 REMARK 465 GLY C -4 REMARK 465 LYS C 68 REMARK 465 SER C 69 REMARK 465 ASN C 70 REMARK 465 GLU C 71 REMARK 465 GLU C 72 REMARK 465 GLY C 73 REMARK 465 SER C 74 REMARK 465 GLU C 75 REMARK 465 GLU C 76 REMARK 465 LYS C 77 REMARK 465 ASP Q 361 REMARK 465 CYS Q 362 REMARK 465 ARG Q 363 REMARK 465 ARG Q 364 REMARK 465 ARG Q 372 REMARK 465 PRO Q 373 REMARK 465 LYS Q 374 REMARK 465 GLU D 71 REMARK 465 GLU D 72 REMARK 465 GLY D 73 REMARK 465 SER D 74 REMARK 465 GLU D 75 REMARK 465 GLU D 76 REMARK 465 THR D 231 REMARK 465 ASP R 361 REMARK 465 CYS R 362 REMARK 465 ARG R 363 REMARK 465 ARG R 364 REMARK 465 VAL R 371 REMARK 465 ARG R 372 REMARK 465 PRO R 373 REMARK 465 LYS R 374 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 20 CG CD OE1 OE2 REMARK 470 GLU A 39 CG CD OE1 OE2 REMARK 470 GLN A 67 CG CD OE1 NE2 REMARK 470 LYS A 68 CG CD CE NZ REMARK 470 ASN A 70 CG OD1 ND2 REMARK 470 GLU A 188 CG CD OE1 OE2 REMARK 470 ASP A 204 CG OD1 OD2 REMARK 470 LYS A 214 CG CD CE NZ REMARK 470 ARG O 364 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 68 CG CD CE NZ REMARK 470 LYS B 77 CG CD CE NZ REMARK 470 LYS B 87 CG CD CE NZ REMARK 470 GLU B 210 CG CD OE1 OE2 REMARK 470 LYS C 160 CE NZ REMARK 470 GLU C 188 CG CD OE1 OE2 REMARK 470 LYS C 195 CG CD CE NZ REMARK 470 GLU D 35 CG CD OE1 OE2 REMARK 470 GLN D 67 CG CD OE1 NE2 REMARK 470 LYS D 68 CG CD CE NZ REMARK 470 LYS D 77 CG CD CE NZ REMARK 470 GLU D 110 CG CD OE1 OE2 REMARK 470 GLU D 115 CG CD OE1 OE2 REMARK 470 LYS D 159 CG CD CE NZ REMARK 470 LYS D 195 CG CD CE NZ REMARK 470 GLU D 210 CG CD OE1 OE2 REMARK 470 ASP D 211 CG OD1 OD2 REMARK 470 LYS D 214 CG CD CE NZ 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 NZ LYS C 49 O2P SEP Q 367 2.18 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 ARG A 117 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 117 NE - CZ - NH2 ANGL. DEV. = -3.2 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 ARG A 18 77.98 -102.64 REMARK 500 LYS A 68 103.60 -56.42 REMARK 500 ARG B 18 77.08 -106.59 REMARK 500 LYS B 68 69.62 -61.87 REMARK 500 GLU B 210 -136.29 60.24 REMARK 500 HIS C 106 -32.54 -132.33 REMARK 500 ASN C 185 53.68 31.75 REMARK 500 GLN D 67 39.73 -88.84 REMARK 500 LYS D 68 -60.18 -109.20 REMARK 500 SER D 69 -108.97 -61.10 REMARK 500 SER D 209 172.39 -55.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 509 DISTANCE = 7.71 ANGSTROMS REMARK 525 HOH B 397 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH P 408 DISTANCE = 6.96 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6YR6 RELATED DB: PDB REMARK 900 HDM2-186 PEPTIDE REMARK 900 RELATED ID: 6YR7 RELATED DB: PDB REMARK 900 HDMX-342+367 PEPTIDE DBREF 6YR5 A 1 231 UNP P31947 1433S_HUMAN 1 231 DBREF 6YR5 O 361 374 UNP O15151 MDM4_HUMAN 361 374 DBREF 6YR5 B 1 231 UNP P31947 1433S_HUMAN 1 231 DBREF 6YR5 P 361 374 UNP O15151 MDM4_HUMAN 361 374 DBREF 6YR5 C 1 231 UNP P31947 1433S_HUMAN 1 231 DBREF 6YR5 Q 361 374 UNP O15151 MDM4_HUMAN 361 374 DBREF 6YR5 D 1 231 UNP P31947 1433S_HUMAN 1 231 DBREF 6YR5 R 361 374 UNP O15151 MDM4_HUMAN 361 374 SEQADV 6YR5 GLY A -4 UNP P31947 EXPRESSION TAG SEQADV 6YR5 ALA A -3 UNP P31947 EXPRESSION TAG SEQADV 6YR5 MET A -2 UNP P31947 EXPRESSION TAG SEQADV 6YR5 GLY A -1 UNP P31947 EXPRESSION TAG SEQADV 6YR5 SER A 0 UNP P31947 EXPRESSION TAG SEQADV 6YR5 GLY B -4 UNP P31947 EXPRESSION TAG SEQADV 6YR5 ALA B -3 UNP P31947 EXPRESSION TAG SEQADV 6YR5 MET B -2 UNP P31947 EXPRESSION TAG SEQADV 6YR5 GLY B -1 UNP P31947 EXPRESSION TAG SEQADV 6YR5 SER B 0 UNP P31947 EXPRESSION TAG SEQADV 6YR5 GLY C -4 UNP P31947 EXPRESSION TAG SEQADV 6YR5 ALA C -3 UNP P31947 EXPRESSION TAG SEQADV 6YR5 MET C -2 UNP P31947 EXPRESSION TAG SEQADV 6YR5 GLY C -1 UNP P31947 EXPRESSION TAG SEQADV 6YR5 SER C 0 UNP P31947 EXPRESSION TAG SEQADV 6YR5 GLY D -4 UNP P31947 EXPRESSION TAG SEQADV 6YR5 ALA D -3 UNP P31947 EXPRESSION TAG SEQADV 6YR5 MET D -2 UNP P31947 EXPRESSION TAG SEQADV 6YR5 GLY D -1 UNP P31947 EXPRESSION TAG SEQADV 6YR5 SER D 0 UNP P31947 EXPRESSION TAG SEQRES 1 A 236 GLY ALA MET GLY SER MET GLU ARG ALA SER LEU ILE GLN SEQRES 2 A 236 LYS ALA LYS LEU ALA GLU GLN ALA GLU ARG TYR GLU ASP SEQRES 3 A 236 MET ALA ALA PHE MET LYS GLY ALA VAL GLU LYS GLY GLU SEQRES 4 A 236 GLU LEU SER CYS GLU GLU ARG ASN LEU LEU SER VAL ALA SEQRES 5 A 236 TYR LYS ASN VAL VAL GLY GLY GLN ARG ALA ALA TRP ARG SEQRES 6 A 236 VAL LEU SER SER ILE GLU GLN LYS SER ASN GLU GLU GLY SEQRES 7 A 236 SER GLU GLU LYS GLY PRO GLU VAL ARG GLU TYR ARG GLU SEQRES 8 A 236 LYS VAL GLU THR GLU LEU GLN GLY VAL CYS ASP THR VAL SEQRES 9 A 236 LEU GLY LEU LEU ASP SER HIS LEU ILE LYS GLU ALA GLY SEQRES 10 A 236 ASP ALA GLU SER ARG VAL PHE TYR LEU LYS MET LYS GLY SEQRES 11 A 236 ASP TYR TYR ARG TYR LEU ALA GLU VAL ALA THR GLY ASP SEQRES 12 A 236 ASP LYS LYS ARG ILE ILE ASP SER ALA ARG SER ALA TYR SEQRES 13 A 236 GLN GLU ALA MET ASP ILE SER LYS LYS GLU MET PRO PRO SEQRES 14 A 236 THR ASN PRO ILE ARG LEU GLY LEU ALA LEU ASN PHE SER SEQRES 15 A 236 VAL PHE HIS TYR GLU ILE ALA ASN SER PRO GLU GLU ALA SEQRES 16 A 236 ILE SER LEU ALA LYS THR THR PHE ASP GLU ALA MET ALA SEQRES 17 A 236 ASP LEU HIS THR LEU SER GLU ASP SER TYR LYS ASP SER SEQRES 18 A 236 THR LEU ILE MET GLN LEU LEU ARG ASP ASN LEU THR LEU SEQRES 19 A 236 TRP THR SEQRES 1 O 14 ASP CYS ARG ARG THR ILE SEP ALA PRO VAL VAL ARG PRO SEQRES 2 O 14 LYS SEQRES 1 B 236 GLY ALA MET GLY SER MET GLU ARG ALA SER LEU ILE GLN SEQRES 2 B 236 LYS ALA LYS LEU ALA GLU GLN ALA GLU ARG TYR GLU ASP SEQRES 3 B 236 MET ALA ALA PHE MET LYS GLY ALA VAL GLU LYS GLY GLU SEQRES 4 B 236 GLU LEU SER CYS GLU GLU ARG ASN LEU LEU SER VAL ALA SEQRES 5 B 236 TYR LYS ASN VAL VAL GLY GLY GLN ARG ALA ALA TRP ARG SEQRES 6 B 236 VAL LEU SER SER ILE GLU GLN LYS SER ASN GLU GLU GLY SEQRES 7 B 236 SER GLU GLU LYS GLY PRO GLU VAL ARG GLU TYR ARG GLU SEQRES 8 B 236 LYS VAL GLU THR GLU LEU GLN GLY VAL CYS ASP THR VAL SEQRES 9 B 236 LEU GLY LEU LEU ASP SER HIS LEU ILE LYS GLU ALA GLY SEQRES 10 B 236 ASP ALA GLU SER ARG VAL PHE TYR LEU LYS MET LYS GLY SEQRES 11 B 236 ASP TYR TYR ARG TYR LEU ALA GLU VAL ALA THR GLY ASP SEQRES 12 B 236 ASP LYS LYS ARG ILE ILE ASP SER ALA ARG SER ALA TYR SEQRES 13 B 236 GLN GLU ALA MET ASP ILE SER LYS LYS GLU MET PRO PRO SEQRES 14 B 236 THR ASN PRO ILE ARG LEU GLY LEU ALA LEU ASN PHE SER SEQRES 15 B 236 VAL PHE HIS TYR GLU ILE ALA ASN SER PRO GLU GLU ALA SEQRES 16 B 236 ILE SER LEU ALA LYS THR THR PHE ASP GLU ALA MET ALA SEQRES 17 B 236 ASP LEU HIS THR LEU SER GLU ASP SER TYR LYS ASP SER SEQRES 18 B 236 THR LEU ILE MET GLN LEU LEU ARG ASP ASN LEU THR LEU SEQRES 19 B 236 TRP THR SEQRES 1 P 14 ASP CYS ARG ARG THR ILE SEP ALA PRO VAL VAL ARG PRO SEQRES 2 P 14 LYS SEQRES 1 C 236 GLY ALA MET GLY SER MET GLU ARG ALA SER LEU ILE GLN SEQRES 2 C 236 LYS ALA LYS LEU ALA GLU GLN ALA GLU ARG TYR GLU ASP SEQRES 3 C 236 MET ALA ALA PHE MET LYS GLY ALA VAL GLU LYS GLY GLU SEQRES 4 C 236 GLU LEU SER CYS GLU GLU ARG ASN LEU LEU SER VAL ALA SEQRES 5 C 236 TYR LYS ASN VAL VAL GLY GLY GLN ARG ALA ALA TRP ARG SEQRES 6 C 236 VAL LEU SER SER ILE GLU GLN LYS SER ASN GLU GLU GLY SEQRES 7 C 236 SER GLU GLU LYS GLY PRO GLU VAL ARG GLU TYR ARG GLU SEQRES 8 C 236 LYS VAL GLU THR GLU LEU GLN GLY VAL CYS ASP THR VAL SEQRES 9 C 236 LEU GLY LEU LEU ASP SER HIS LEU ILE LYS GLU ALA GLY SEQRES 10 C 236 ASP ALA GLU SER ARG VAL PHE TYR LEU LYS MET LYS GLY SEQRES 11 C 236 ASP TYR TYR ARG TYR LEU ALA GLU VAL ALA THR GLY ASP SEQRES 12 C 236 ASP LYS LYS ARG ILE ILE ASP SER ALA ARG SER ALA TYR SEQRES 13 C 236 GLN GLU ALA MET ASP ILE SER LYS LYS GLU MET PRO PRO SEQRES 14 C 236 THR ASN PRO ILE ARG LEU GLY LEU ALA LEU ASN PHE SER SEQRES 15 C 236 VAL PHE HIS TYR GLU ILE ALA ASN SER PRO GLU GLU ALA SEQRES 16 C 236 ILE SER LEU ALA LYS THR THR PHE ASP GLU ALA MET ALA SEQRES 17 C 236 ASP LEU HIS THR LEU SER GLU ASP SER TYR LYS ASP SER SEQRES 18 C 236 THR LEU ILE MET GLN LEU LEU ARG ASP ASN LEU THR LEU SEQRES 19 C 236 TRP THR SEQRES 1 Q 14 ASP CYS ARG ARG THR ILE SEP ALA PRO VAL VAL ARG PRO SEQRES 2 Q 14 LYS SEQRES 1 D 236 GLY ALA MET GLY SER MET GLU ARG ALA SER LEU ILE GLN SEQRES 2 D 236 LYS ALA LYS LEU ALA GLU GLN ALA GLU ARG TYR GLU ASP SEQRES 3 D 236 MET ALA ALA PHE MET LYS GLY ALA VAL GLU LYS GLY GLU SEQRES 4 D 236 GLU LEU SER CYS GLU GLU ARG ASN LEU LEU SER VAL ALA SEQRES 5 D 236 TYR LYS ASN VAL VAL GLY GLY GLN ARG ALA ALA TRP ARG SEQRES 6 D 236 VAL LEU SER SER ILE GLU GLN LYS SER ASN GLU GLU GLY SEQRES 7 D 236 SER GLU GLU LYS GLY PRO GLU VAL ARG GLU TYR ARG GLU SEQRES 8 D 236 LYS VAL GLU THR GLU LEU GLN GLY VAL CYS ASP THR VAL SEQRES 9 D 236 LEU GLY LEU LEU ASP SER HIS LEU ILE LYS GLU ALA GLY SEQRES 10 D 236 ASP ALA GLU SER ARG VAL PHE TYR LEU LYS MET LYS GLY SEQRES 11 D 236 ASP TYR TYR ARG TYR LEU ALA GLU VAL ALA THR GLY ASP SEQRES 12 D 236 ASP LYS LYS ARG ILE ILE ASP SER ALA ARG SER ALA TYR SEQRES 13 D 236 GLN GLU ALA MET ASP ILE SER LYS LYS GLU MET PRO PRO SEQRES 14 D 236 THR ASN PRO ILE ARG LEU GLY LEU ALA LEU ASN PHE SER SEQRES 15 D 236 VAL PHE HIS TYR GLU ILE ALA ASN SER PRO GLU GLU ALA SEQRES 16 D 236 ILE SER LEU ALA LYS THR THR PHE ASP GLU ALA MET ALA SEQRES 17 D 236 ASP LEU HIS THR LEU SER GLU ASP SER TYR LYS ASP SER SEQRES 18 D 236 THR LEU ILE MET GLN LEU LEU ARG ASP ASN LEU THR LEU SEQRES 19 D 236 TRP THR SEQRES 1 R 14 ASP CYS ARG ARG THR ILE SEP ALA PRO VAL VAL ARG PRO SEQRES 2 R 14 LYS MODRES 6YR5 SEP O 367 SER MODIFIED RESIDUE MODRES 6YR5 SEP P 367 SER MODIFIED RESIDUE MODRES 6YR5 SEP Q 367 SER MODIFIED RESIDUE MODRES 6YR5 SEP R 367 SER MODIFIED RESIDUE HET SEP O 367 10 HET SEP P 367 10 HET SEP Q 367 10 HET SEP R 367 10 HET SO4 A 301 5 HETNAM SEP PHOSPHOSERINE HETNAM SO4 SULFATE ION HETSYN SEP PHOSPHONOSERINE FORMUL 2 SEP 4(C3 H8 N O6 P) FORMUL 9 SO4 O4 S 2- FORMUL 10 HOH *371(H2 O) HELIX 1 AA1 GLU A 2 ALA A 16 1 15 HELIX 2 AA2 ARG A 18 GLU A 31 1 14 HELIX 3 AA3 SER A 37 LYS A 68 1 32 HELIX 4 AA4 PRO A 79 LEU A 107 1 29 HELIX 5 AA5 ASP A 113 GLU A 133 1 21 HELIX 6 AA6 THR A 136 MET A 162 1 27 HELIX 7 AA7 ASN A 166 ILE A 183 1 18 HELIX 8 AA8 SER A 186 ALA A 203 1 18 HELIX 9 AA9 ASP A 204 LEU A 208 5 5 HELIX 10 AB1 SER A 209 THR A 231 1 23 HELIX 11 AB2 GLU B 2 ALA B 16 1 15 HELIX 12 AB3 ARG B 18 GLU B 31 1 14 HELIX 13 AB4 SER B 37 LYS B 68 1 32 HELIX 14 AB5 PRO B 79 LEU B 107 1 29 HELIX 15 AB6 ASP B 113 GLU B 133 1 21 HELIX 16 AB7 THR B 136 MET B 162 1 27 HELIX 17 AB8 ASN B 166 ILE B 183 1 18 HELIX 18 AB9 SER B 186 LEU B 205 1 20 HELIX 19 AC1 HIS B 206 LEU B 208 5 3 HELIX 20 AC2 SER B 209 THR B 231 1 23 HELIX 21 AC3 GLU C 2 ALA C 16 1 15 HELIX 22 AC4 ARG C 18 GLU C 31 1 14 HELIX 23 AC5 SER C 37 GLU C 66 1 30 HELIX 24 AC6 PRO C 79 LEU C 107 1 29 HELIX 25 AC7 ASP C 113 ALA C 135 1 23 HELIX 26 AC8 THR C 136 MET C 162 1 27 HELIX 27 AC9 ASN C 166 ILE C 183 1 18 HELIX 28 AD1 SER C 186 ALA C 203 1 18 HELIX 29 AD2 ASP C 204 LEU C 208 5 5 HELIX 30 AD3 SER C 209 ASP C 215 1 7 HELIX 31 AD4 SER C 216 THR C 231 1 16 HELIX 32 AD5 GLU D 2 ALA D 16 1 15 HELIX 33 AD6 ARG D 18 GLU D 31 1 14 HELIX 34 AD7 SER D 37 GLN D 67 1 31 HELIX 35 AD8 PRO D 79 LEU D 107 1 29 HELIX 36 AD9 ASP D 113 GLU D 133 1 21 HELIX 37 AE1 THR D 136 MET D 162 1 27 HELIX 38 AE2 ASN D 166 ILE D 183 1 18 HELIX 39 AE3 SER D 186 ALA D 203 1 18 HELIX 40 AE4 ASP D 204 LEU D 208 5 5 HELIX 41 AE5 SER D 209 TRP D 230 1 22 LINK C ILE O 366 N SEP O 367 1555 1555 1.34 LINK C SEP O 367 N ALA O 368 1555 1555 1.35 LINK C ILE P 366 N SEP P 367 1555 1555 1.35 LINK C SEP P 367 N ALA P 368 1555 1555 1.34 LINK C ILE Q 366 N SEP Q 367 1555 1555 1.35 LINK C SEP Q 367 N ALA Q 368 1555 1555 1.35 LINK C ILE R 366 N SEP R 367 1555 1555 1.34 LINK C SEP R 367 N ALA R 368 1555 1555 1.34 SITE 1 AC1 3 ASP A 97 ASP A 139 ILE A 143 CRYST1 63.950 75.300 78.390 95.15 113.14 93.84 P 1 4 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 0.015637 0.001050 0.006871 0.00000 SCALE2 0.000000 0.013310 0.001698 0.00000 SCALE3 0.000000 0.000000 0.013985 0.00000