HEADER PROTEIN BINDING 07-AUG-25 9PY9 TITLE MENIN MUTANT - M327I IN COMPLEX WITH ZIFTOMENIB COMPND MOL_ID: 1; COMPND 2 MOLECULE: MENIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MEN1, SCG2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR B.D.CLEGG,J.M.RAY,T.CIERPICKI,J.GREMBECKA REVDAT 1 28-OCT-26 9PY9 0 JRNL AUTH B.D.CLEGG,J.M.RAY,T.CIERPICKI,J.GREMBECKA JRNL TITL MENIN MUTANT - M327I IN COMPLEX WITH ZIFTOMENIB JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0430 (REFMACAT 0.4.105) REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 62194 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.087 REMARK 3 FREE R VALUE TEST SET COUNT : 3164 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) : 4286 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.18 REMARK 3 BIN R VALUE (WORKING SET) : 0.2230 REMARK 3 BIN FREE R VALUE SET COUNT : 231 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3711 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 89 REMARK 3 SOLVENT ATOMS : 434 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.20500 REMARK 3 B22 (A**2) : -0.43200 REMARK 3 B33 (A**2) : -0.77400 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): 0.080 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.086 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.695 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4055 ; 0.016 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3818 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5525 ; 2.304 ; 1.845 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8776 ; 0.800 ; 1.762 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 504 ; 6.723 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 32 ;11.168 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 667 ;11.680 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 607 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4864 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 953 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 842 ; 0.228 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 113 ; 0.220 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1991 ; 0.192 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 302 ; 0.144 ; 0.200 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): 1974 ; 2.520 ; 1.593 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1974 ; 2.510 ; 1.593 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2492 ; 3.579 ; 2.843 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2493 ; 3.583 ; 2.847 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2081 ; 4.255 ; 1.980 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2082 ; 4.254 ; 1.981 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3033 ; 5.895 ; 3.422 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3034 ; 5.894 ; 3.423 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 : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9PY9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1000297778. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-FEB-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62287 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4300 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 (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.37600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE, 0.1 M HEPES, PH REMARK 280 7.5, 25% (W/V) PEG-3,350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 285K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 24.50950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.19500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.14900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.19500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.50950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.14900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 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 GLY A -3 REMARK 465 SER A -2 REMARK 465 SER A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 PRO A 538 REMARK 465 ALA A 539 REMARK 465 PRO A 540 REMARK 465 ALA A 541 REMARK 465 ALA A 542 REMARK 465 SER A 543 REMARK 465 LYS A 589 REMARK 465 GLN A 590 REMARK 465 LYS A 591 REMARK 465 VAL A 592 REMARK 465 SER A 593 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 109 CG CD OE1 OE2 REMARK 470 ASP A 136 CG OD1 OD2 REMARK 470 LEU A 249 CG CD1 CD2 REMARK 470 LYS A 569 CG CD CE NZ REMARK 470 GLN A 586 CG CD OE1 NE2 REMARK 470 LYS A 588 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 HD1 HIS A 433 H GLY A 435 1.30 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 GLU A 217 CD GLU A 217 OE1 -0.070 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 21 NE - CZ - NH1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 21 NE - CZ - NH2 ANGL. DEV. = -6.4 DEGREES REMARK 500 TYR A 90 CB - CG - CD1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 92 CD - NE - CZ ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 92 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 206 CA - CB - CG ANGL. DEV. = 14.9 DEGREES REMARK 500 ARG A 206 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 206 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG A 207 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 207 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG A 314 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 335 CD - NE - CZ ANGL. DEV. = 14.9 DEGREES REMARK 500 ARG A 335 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES REMARK 500 LEU A 565 CB - CG - CD2 ANGL. DEV. = 12.9 DEGREES REMARK 500 ALA A 581 CB - CA - C ANGL. DEV. = 10.1 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 TYR A 77 -59.88 -159.38 REMARK 500 SER A 178 -166.53 -100.08 REMARK 500 ASP A 180 12.73 -149.36 REMARK 500 PHE A 186 -178.92 -170.42 REMARK 500 ASN A 189 11.48 59.61 REMARK 500 SER A 226 45.36 -91.26 REMARK 500 GLU A 290 84.89 -151.62 REMARK 500 GLU A 356 2.33 95.00 REMARK 500 ASP A 370 -53.00 -136.29 REMARK 500 GLU A 547 156.30 -43.63 REMARK 500 MET A 587 -71.84 -74.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 21 0.19 SIDE CHAIN REMARK 500 ARG A 206 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 9PY9 A 1 593 UNP O00255 MEN1_HUMAN 1 593 SEQADV 9PY9 GLY A -4 UNP O00255 EXPRESSION TAG SEQADV 9PY9 GLY A -3 UNP O00255 EXPRESSION TAG SEQADV 9PY9 SER A -2 UNP O00255 EXPRESSION TAG SEQADV 9PY9 SER A -1 UNP O00255 EXPRESSION TAG SEQADV 9PY9 SER A 0 UNP O00255 EXPRESSION TAG SEQADV 9PY9 A UNP O00255 ILE 54 DELETION SEQADV 9PY9 A UNP O00255 PRO 55 DELETION SEQADV 9PY9 A UNP O00255 THR 56 DELETION SEQADV 9PY9 A UNP O00255 ASN 57 DELETION SEQADV 9PY9 A UNP O00255 VAL 58 DELETION SEQADV 9PY9 A UNP O00255 PRO 59 DELETION SEQADV 9PY9 A UNP O00255 GLU 60 DELETION SEQADV 9PY9 A UNP O00255 LEU 61 DELETION SEQADV 9PY9 A UNP O00255 THR 62 DELETION SEQADV 9PY9 A UNP O00255 PHE 63 DELETION SEQADV 9PY9 A UNP O00255 GLN 64 DELETION SEQADV 9PY9 A UNP O00255 PRO 65 DELETION SEQADV 9PY9 A UNP O00255 SER 66 DELETION SEQADV 9PY9 A UNP O00255 PRO 67 DELETION SEQADV 9PY9 A UNP O00255 ALA 68 DELETION SEQADV 9PY9 A UNP O00255 PRO 69 DELETION SEQADV 9PY9 A UNP O00255 ASP 70 DELETION SEQADV 9PY9 A UNP O00255 PRO 71 DELETION SEQADV 9PY9 A UNP O00255 PRO 72 DELETION SEQADV 9PY9 A UNP O00255 GLY 73 DELETION SEQADV 9PY9 ILE A 322 UNP O00255 MET 322 ENGINEERED MUTATION SEQADV 9PY9 A UNP O00255 GLU 387 DELETION SEQADV 9PY9 A UNP O00255 GLU 388 DELETION SEQADV 9PY9 A UNP O00255 ARG 389 DELETION SEQADV 9PY9 A UNP O00255 PRO 390 DELETION SEQADV 9PY9 A UNP O00255 GLY 391 DELETION SEQADV 9PY9 A UNP O00255 GLU 392 DELETION SEQADV 9PY9 A UNP O00255 GLN 393 DELETION SEQADV 9PY9 A UNP O00255 SER 394 DELETION SEQADV 9PY9 A UNP O00255 GLN 395 DELETION SEQADV 9PY9 A UNP O00255 GLY 396 DELETION SEQADV 9PY9 A UNP O00255 THR 397 DELETION SEQADV 9PY9 A UNP O00255 GLN 398 DELETION SEQADV 9PY9 A UNP O00255 ARG 460 DELETION SEQADV 9PY9 A UNP O00255 GLU 461 DELETION SEQADV 9PY9 A UNP O00255 ALA 462 DELETION SEQADV 9PY9 A UNP O00255 GLU 463 DELETION SEQADV 9PY9 A UNP O00255 ALA 464 DELETION SEQADV 9PY9 A UNP O00255 ALA 465 DELETION SEQADV 9PY9 A UNP O00255 GLU 466 DELETION SEQADV 9PY9 A UNP O00255 ALA 467 DELETION SEQADV 9PY9 A UNP O00255 GLU 468 DELETION SEQADV 9PY9 A UNP O00255 GLU 469 DELETION SEQADV 9PY9 A UNP O00255 PRO 470 DELETION SEQADV 9PY9 A UNP O00255 TRP 471 DELETION SEQADV 9PY9 A UNP O00255 GLY 472 DELETION SEQADV 9PY9 A UNP O00255 GLU 473 DELETION SEQADV 9PY9 A UNP O00255 GLU 474 DELETION SEQADV 9PY9 A UNP O00255 ALA 475 DELETION SEQADV 9PY9 A UNP O00255 ARG 476 DELETION SEQADV 9PY9 A UNP O00255 GLU 477 DELETION SEQADV 9PY9 A UNP O00255 GLY 478 DELETION SEQADV 9PY9 A UNP O00255 ARG 479 DELETION SEQADV 9PY9 A UNP O00255 ARG 480 DELETION SEQADV 9PY9 A UNP O00255 ARG 481 DELETION SEQADV 9PY9 A UNP O00255 GLY 482 DELETION SEQADV 9PY9 A UNP O00255 PRO 483 DELETION SEQADV 9PY9 A UNP O00255 ARG 484 DELETION SEQADV 9PY9 A UNP O00255 ARG 485 DELETION SEQADV 9PY9 A UNP O00255 GLU 486 DELETION SEQADV 9PY9 A UNP O00255 SER 487 DELETION SEQADV 9PY9 A UNP O00255 LYS 488 DELETION SEQADV 9PY9 A UNP O00255 PRO 489 DELETION SEQADV 9PY9 A UNP O00255 GLU 490 DELETION SEQADV 9PY9 A UNP O00255 GLU 491 DELETION SEQADV 9PY9 A UNP O00255 PRO 492 DELETION SEQADV 9PY9 A UNP O00255 PRO 493 DELETION SEQADV 9PY9 A UNP O00255 PRO 494 DELETION SEQADV 9PY9 A UNP O00255 PRO 495 DELETION SEQADV 9PY9 A UNP O00255 LYS 496 DELETION SEQADV 9PY9 A UNP O00255 LYS 497 DELETION SEQADV 9PY9 A UNP O00255 PRO 498 DELETION SEQADV 9PY9 A UNP O00255 ALA 499 DELETION SEQADV 9PY9 A UNP O00255 LEU 500 DELETION SEQADV 9PY9 A UNP O00255 ASP 501 DELETION SEQADV 9PY9 A UNP O00255 LYS 502 DELETION SEQADV 9PY9 A UNP O00255 GLY 503 DELETION SEQADV 9PY9 A UNP O00255 LEU 504 DELETION SEQADV 9PY9 A UNP O00255 GLY 505 DELETION SEQADV 9PY9 A UNP O00255 THR 506 DELETION SEQADV 9PY9 A UNP O00255 GLY 507 DELETION SEQADV 9PY9 A UNP O00255 GLN 508 DELETION SEQADV 9PY9 A UNP O00255 GLY 509 DELETION SEQADV 9PY9 A UNP O00255 ALA 510 DELETION SEQADV 9PY9 A UNP O00255 VAL 511 DELETION SEQADV 9PY9 A UNP O00255 SER 512 DELETION SEQADV 9PY9 A UNP O00255 GLY 513 DELETION SEQADV 9PY9 A UNP O00255 PRO 514 DELETION SEQADV 9PY9 A UNP O00255 PRO 515 DELETION SEQADV 9PY9 A UNP O00255 ARG 516 DELETION SEQADV 9PY9 A UNP O00255 LYS 517 DELETION SEQADV 9PY9 A UNP O00255 PRO 518 DELETION SEQADV 9PY9 A UNP O00255 PRO 519 DELETION SEQADV 9PY9 A UNP O00255 GLY 520 DELETION SEQADV 9PY9 A UNP O00255 THR 521 DELETION SEQADV 9PY9 A UNP O00255 VAL 522 DELETION SEQADV 9PY9 A UNP O00255 ALA 523 DELETION SEQADV 9PY9 A UNP O00255 GLY 524 DELETION SEQADV 9PY9 A UNP O00255 THR 525 DELETION SEQADV 9PY9 A UNP O00255 ALA 526 DELETION SEQADV 9PY9 A UNP O00255 ARG 527 DELETION SEQADV 9PY9 A UNP O00255 GLY 528 DELETION SEQADV 9PY9 A UNP O00255 PRO 529 DELETION SEQADV 9PY9 A UNP O00255 GLU 530 DELETION SEQADV 9PY9 A UNP O00255 GLY 531 DELETION SEQADV 9PY9 A UNP O00255 GLY 532 DELETION SEQADV 9PY9 A UNP O00255 SER 533 DELETION SEQADV 9PY9 A UNP O00255 THR 534 DELETION SEQADV 9PY9 A UNP O00255 ALA 535 DELETION SEQADV 9PY9 A UNP O00255 GLN 536 DELETION SEQADV 9PY9 ALA A 541 UNP O00255 THR 541 CONFLICT SEQRES 1 A 489 GLY GLY SER SER SER MET GLY LEU LYS ALA ALA GLN LYS SEQRES 2 A 489 THR LEU PHE PRO LEU ARG SER ILE ASP ASP VAL VAL ARG SEQRES 3 A 489 LEU PHE ALA ALA GLU LEU GLY ARG GLU GLU PRO ASP LEU SEQRES 4 A 489 VAL LEU LEU SER LEU VAL LEU GLY PHE VAL GLU HIS PHE SEQRES 5 A 489 LEU ALA VAL ASN ARG VAL GLY LEU THR TYR PHE PRO VAL SEQRES 6 A 489 ALA ASP LEU SER ILE ILE ALA ALA LEU TYR ALA ARG PHE SEQRES 7 A 489 THR ALA GLN ILE ARG GLY ALA VAL ASP LEU SER LEU TYR SEQRES 8 A 489 PRO ARG GLU GLY GLY VAL SER SER ARG GLU LEU VAL LYS SEQRES 9 A 489 LYS VAL SER ASP VAL ILE TRP ASN SER LEU SER ARG SER SEQRES 10 A 489 TYR PHE LYS ASP ARG ALA HIS ILE GLN SER LEU PHE SER SEQRES 11 A 489 PHE ILE THR GLY THR LYS LEU ASP SER SER GLY VAL ALA SEQRES 12 A 489 PHE ALA VAL VAL GLY ALA CYS GLN ALA LEU GLY LEU ARG SEQRES 13 A 489 ASP VAL HIS LEU ALA LEU SER GLU ASP HIS ALA TRP VAL SEQRES 14 A 489 VAL PHE GLY PRO ASN GLY GLU GLN THR ALA GLU VAL THR SEQRES 15 A 489 TRP HIS GLY LYS GLY ASN GLU ASP ARG ARG GLY GLN THR SEQRES 16 A 489 VAL ASN ALA GLY VAL ALA GLU ARG SER TRP LEU TYR LEU SEQRES 17 A 489 LYS GLY SER TYR MET ARG CYS ASP ARG LYS MET GLU VAL SEQRES 18 A 489 ALA PHE MET VAL CYS ALA ILE ASN PRO SER ILE ASP LEU SEQRES 19 A 489 HIS THR ASP SER LEU GLU LEU LEU GLN LEU GLN GLN LYS SEQRES 20 A 489 LEU LEU TRP LEU LEU TYR ASP LEU GLY HIS LEU GLU ARG SEQRES 21 A 489 TYR PRO MET ALA LEU GLY ASN LEU ALA ASP LEU GLU GLU SEQRES 22 A 489 LEU GLU PRO THR PRO GLY ARG PRO ASP PRO LEU THR LEU SEQRES 23 A 489 TYR HIS LYS GLY ILE ALA SER ALA LYS THR TYR TYR ARG SEQRES 24 A 489 ASP GLU HIS ILE TYR PRO TYR ILE TYR LEU ALA GLY TYR SEQRES 25 A 489 HIS CYS ARG ASN ARG ASN VAL ARG GLU ALA LEU GLN ALA SEQRES 26 A 489 TRP ALA ASP THR ALA THR VAL ILE GLN ASP TYR ASN TYR SEQRES 27 A 489 CYS ARG GLU ASP GLU GLU ILE TYR LYS GLU PHE PHE GLU SEQRES 28 A 489 VAL ALA ASN ASP VAL ILE PRO ASN LEU LEU LYS GLU ALA SEQRES 29 A 489 ALA SER LEU LEU GLU ALA GLY SER GLN GLY SER ALA LEU SEQRES 30 A 489 GLN ASP PRO GLU CYS PHE ALA HIS LEU LEU ARG PHE TYR SEQRES 31 A 489 ASP GLY ILE CYS LYS TRP GLU GLU GLY SER PRO THR PRO SEQRES 32 A 489 VAL LEU HIS VAL GLY TRP ALA THR PHE LEU VAL GLN SER SEQRES 33 A 489 LEU GLY ARG PHE GLU GLY GLN VAL ARG GLN LYS VAL ARG SEQRES 34 A 489 ILE VAL SER VAL PRO ALA PRO ALA ALA SER PRO PRO PRO SEQRES 35 A 489 GLU GLY PRO VAL LEU THR PHE GLN SER GLU LYS MET LYS SEQRES 36 A 489 GLY MET LYS GLU LEU LEU VAL ALA THR LYS ILE ASN SER SEQRES 37 A 489 SER ALA ILE LYS LEU GLN LEU THR ALA GLN SER GLN VAL SEQRES 38 A 489 GLN MET LYS LYS GLN LYS VAL SER HET K5O A 601 91 HET SO4 A 602 5 HET SO4 A 603 5 HET PG4 A 604 31 HET EDO A 605 10 HET EDO A 606 10 HET SO4 A 607 5 HET DMS A 608 10 HETNAM K5O ZIFTOMENIB HETNAM SO4 SULFATE ION HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM EDO 1,2-ETHANEDIOL HETNAM DMS DIMETHYL SULFOXIDE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 K5O C33 H42 F3 N9 O2 S2 FORMUL 3 SO4 3(O4 S 2-) FORMUL 5 PG4 C8 H18 O5 FORMUL 6 EDO 2(C2 H6 O2) FORMUL 9 DMS C2 H6 O S FORMUL 10 HOH *434(H2 O) HELIX 1 AA1 LYS A 4 THR A 9 1 6 HELIX 2 AA2 SER A 15 GLY A 28 1 14 HELIX 3 AA3 ASP A 33 VAL A 50 1 18 HELIX 4 AA4 ASP A 82 VAL A 101 1 20 HELIX 5 AA5 ASP A 102 TYR A 106 5 5 HELIX 6 AA6 ARG A 108 VAL A 112 5 5 HELIX 7 AA7 SER A 114 SER A 128 1 15 HELIX 8 AA8 SER A 142 THR A 150 1 9 HELIX 9 AA9 ASP A 153 LEU A 168 1 16 HELIX 10 AB1 GLY A 187 GLU A 191 5 5 HELIX 11 AB2 VAL A 211 GLU A 217 1 7 HELIX 12 AB3 SER A 219 SER A 226 5 8 HELIX 13 AB4 ASP A 231 ALA A 242 1 12 HELIX 14 AB5 SER A 253 LEU A 270 1 18 HELIX 15 AB6 TYR A 276 GLU A 290 1 15 HELIX 16 AB7 ASP A 297 TYR A 313 1 17 HELIX 17 AB8 ILE A 318 ASN A 331 1 14 HELIX 18 AB9 ASN A 333 GLN A 349 1 17 HELIX 19 AC1 ASP A 357 ASP A 370 1 14 HELIX 20 AC2 ASP A 370 ALA A 385 1 16 HELIX 21 AC3 SER A 402 GLN A 405 5 4 HELIX 22 AC4 ASP A 406 GLU A 425 1 20 HELIX 23 AC5 HIS A 433 ARG A 446 1 14 HELIX 24 AC6 GLU A 448 GLN A 453 1 6 HELIX 25 AC7 SER A 555 LYS A 562 1 8 HELIX 26 AC8 GLU A 563 ALA A 567 5 5 HELIX 27 AC9 ASN A 571 ALA A 581 1 11 SHEET 1 AA1 4 GLN A 192 ALA A 194 0 SHEET 2 AA1 4 ALA A 182 PHE A 186 -1 N VAL A 184 O ALA A 194 SHEET 3 AA1 4 HIS A 174 LEU A 177 -1 N ALA A 176 O TRP A 183 SHEET 4 AA1 4 MET A 228 ARG A 229 -1 O MET A 228 N LEU A 177 SHEET 1 AA2 2 SER A 246 ASP A 248 0 SHEET 2 AA2 2 THR A 251 ASP A 252 -1 O THR A 251 N ILE A 247 SHEET 1 AA3 2 ARG A 456 ILE A 457 0 SHEET 2 AA3 2 VAL A 550 LEU A 551 1 O LEU A 551 N ARG A 456 CISPEP 1 PHE A 11 PRO A 12 0 5.34 CRYST1 49.019 80.298 124.390 90.00 90.00 90.00 P 21 21 21 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 0.020400 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012454 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008039 0.00000 CONECT 7732 7733 7781 7782 7783 CONECT 7733 7732 7734 7784 CONECT 7734 7733 7735 7780 CONECT 7735 7734 7736 CONECT 7736 7735 7737 7770 CONECT 7737 7736 7738 7785 CONECT 7738 7737 7739 7769 7786 CONECT 7739 7738 7740 7787 7788 CONECT 7740 7739 7741 7789 7790 CONECT 7741 7740 7742 7768 CONECT 7742 7741 7743 7791 7792 CONECT 7743 7742 7744 7764 CONECT 7744 7743 7745 7793 CONECT 7745 7744 7746 7794 CONECT 7746 7745 7747 7763 CONECT 7747 7746 7748 7761 CONECT 7748 7747 7749 7795 7796 CONECT 7749 7748 7750 7751 7797 CONECT 7750 7749 7798 7799 7800 CONECT 7751 7749 7752 7756 CONECT 7752 7751 7753 7801 7802 CONECT 7753 7752 7754 7803 7804 CONECT 7754 7753 7755 7757 CONECT 7755 7754 7756 7805 7806 CONECT 7756 7751 7755 7807 7808 CONECT 7757 7754 7758 7759 7760 CONECT 7758 7757 7809 7810 7811 CONECT 7759 7757 CONECT 7760 7757 CONECT 7761 7747 7762 7766 CONECT 7762 7761 7763 7812 CONECT 7763 7746 7762 7764 CONECT 7764 7743 7763 7765 CONECT 7765 7764 7813 7814 7815 CONECT 7766 7761 7767 CONECT 7767 7766 CONECT 7768 7741 7769 7816 7817 CONECT 7769 7738 7768 7818 7819 CONECT 7770 7736 7771 7779 CONECT 7771 7770 7772 7820 CONECT 7772 7771 7773 7778 CONECT 7773 7772 7774 7821 7822 CONECT 7774 7773 7775 7776 7777 CONECT 7775 7774 CONECT 7776 7774 CONECT 7777 7774 CONECT 7778 7772 7779 CONECT 7779 7770 7778 7780 CONECT 7780 7734 7779 CONECT 7781 7732 CONECT 7782 7732 CONECT 7783 7732 CONECT 7784 7733 CONECT 7785 7737 CONECT 7786 7738 CONECT 7787 7739 CONECT 7788 7739 CONECT 7789 7740 CONECT 7790 7740 CONECT 7791 7742 CONECT 7792 7742 CONECT 7793 7744 CONECT 7794 7745 CONECT 7795 7748 CONECT 7796 7748 CONECT 7797 7749 CONECT 7798 7750 CONECT 7799 7750 CONECT 7800 7750 CONECT 7801 7752 CONECT 7802 7752 CONECT 7803 7753 CONECT 7804 7753 CONECT 7805 7755 CONECT 7806 7755 CONECT 7807 7756 CONECT 7808 7756 CONECT 7809 7758 CONECT 7810 7758 CONECT 7811 7758 CONECT 7812 7762 CONECT 7813 7765 CONECT 7814 7765 CONECT 7815 7765 CONECT 7816 7768 CONECT 7817 7768 CONECT 7818 7769 CONECT 7819 7769 CONECT 7820 7771 CONECT 7821 7773 CONECT 7822 7773 CONECT 7823 7824 7825 7826 7827 CONECT 7824 7823 CONECT 7825 7823 CONECT 7826 7823 CONECT 7827 7823 CONECT 7828 7829 7830 7831 7832 CONECT 7829 7828 CONECT 7830 7828 CONECT 7831 7828 CONECT 7832 7828 CONECT 7833 7834 7846 CONECT 7834 7833 7835 7847 7848 CONECT 7835 7834 7836 7849 7850 CONECT 7836 7835 7837 CONECT 7837 7836 7838 7851 7852 CONECT 7838 7837 7839 7853 7854 CONECT 7839 7838 7840 CONECT 7840 7839 7841 7855 7856 CONECT 7841 7840 7842 7857 7858 CONECT 7842 7841 7843 CONECT 7843 7842 7844 7859 7860 CONECT 7844 7843 7845 7861 7862 CONECT 7845 7844 7863 CONECT 7846 7833 CONECT 7847 7834 CONECT 7848 7834 CONECT 7849 7835 CONECT 7850 7835 CONECT 7851 7837 CONECT 7852 7837 CONECT 7853 7838 CONECT 7854 7838 CONECT 7855 7840 CONECT 7856 7840 CONECT 7857 7841 CONECT 7858 7841 CONECT 7859 7843 CONECT 7860 7843 CONECT 7861 7844 CONECT 7862 7844 CONECT 7863 7845 CONECT 7864 7865 7866 7868 7869 CONECT 7865 7864 7870 CONECT 7866 7864 7867 7871 7872 CONECT 7867 7866 7873 CONECT 7868 7864 CONECT 7869 7864 CONECT 7870 7865 CONECT 7871 7866 CONECT 7872 7866 CONECT 7873 7867 CONECT 7874 7875 7876 7878 7879 CONECT 7875 7874 7880 CONECT 7876 7874 7877 7881 7882 CONECT 7877 7876 7883 CONECT 7878 7874 CONECT 7879 7874 CONECT 7880 7875 CONECT 7881 7876 CONECT 7882 7876 CONECT 7883 7877 CONECT 7884 7885 7886 7887 7888 CONECT 7885 7884 CONECT 7886 7884 CONECT 7887 7884 CONECT 7888 7884 CONECT 7889 7890 7891 7892 CONECT 7890 7889 CONECT 7891 7889 7893 7894 7895 CONECT 7892 7889 7896 7897 7898 CONECT 7893 7891 CONECT 7894 7891 CONECT 7895 7891 CONECT 7896 7892 CONECT 7897 7892 CONECT 7898 7892 MASTER 378 0 8 27 8 0 0 6 4234 1 167 38 END