HEADER PROTEIN BINDING 07-AUG-25 9PY8 TITLE MENIN MUTANT - G331R 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,T.CIERPICKI,J.GREMBECKA REVDAT 1 28-OCT-26 9PY8 0 JRNL AUTH B.D.CLEGG,T.CIERPICKI,J.GREMBECKA JRNL TITL MENIN MUTANT - G331R IN COMPLEX WITH ZIFTOMENIB JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.25 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 136628 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) : 0.146 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.113 REMARK 3 FREE R VALUE TEST SET COUNT : 6986 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) : 1.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 9456 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 517 REMARK 3 BIN FREE R VALUE : 0.2500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3695 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 563 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.84400 REMARK 3 B22 (A**2) : -0.75800 REMARK 3 B33 (A**2) : 1.60200 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): 0.042 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.041 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.033 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.614 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4221 ; 0.012 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3984 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5775 ; 1.928 ; 1.833 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9157 ; 0.698 ; 1.754 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 541 ; 5.952 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 33 ;10.255 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 712 ;11.287 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 629 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5169 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1002 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 868 ; 0.227 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 83 ; 0.202 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2026 ; 0.186 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 332 ; 0.140 ; 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): 2068 ; 5.052 ; 1.327 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2068 ; 5.053 ; 9.182 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2641 ; 7.286 ; 2.386 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2642 ; 7.290 ; 2.555 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2153 ; 7.248 ; 1.582 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2154 ; 7.273 ;99.453 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3134 ; 9.927 ; 2.783 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3135 ; 9.926 ; 2.784 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): 4221 ; 7.112 ; 3.000 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 9PY8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1000298206. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-23 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 : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9801 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 138049 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.246 REMARK 200 RESOLUTION RANGE LOW (A) : 67.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.10 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.10 REMARK 200 R MERGE FOR SHELL (I) : 1.07900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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 (%): 45.21 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 24.54150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.41000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.06300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.41000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.54150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.06300 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 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 PRO A 544 REMARK 465 PRO A 545 REMARK 465 PRO A 546 REMARK 465 GLU A 547 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 ARG A 355 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 569 CG CD CE NZ REMARK 470 SER A 583 OG REMARK 470 GLN A 586 CG CD OE1 NE2 REMARK 470 MET A 587 CG SD CE 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 1.29 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. = 3.2 DEGREES REMARK 500 ARG A 207 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 207 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 229 CG - CD - NE ANGL. DEV. = 15.7 DEGREES REMARK 500 ARG A 229 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 232 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 232 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 446 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 452 NE - CZ - NH2 ANGL. DEV. = -3.6 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 -63.29 -160.75 REMARK 500 ASP A 180 19.44 -147.24 REMARK 500 ASN A 189 14.98 59.35 REMARK 500 SER A 226 45.97 -90.93 REMARK 500 GLU A 356 4.60 95.82 REMARK 500 ASP A 370 -59.30 -137.69 REMARK 500 VAL A 431 -63.49 -107.71 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 108 0.08 SIDE CHAIN REMARK 500 ARG A 229 0.20 SIDE CHAIN REMARK 500 ARG A 330 0.09 SIDE CHAIN 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 A1262 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A1263 DISTANCE = 6.94 ANGSTROMS DBREF 9PY8 A 1 593 UNP O00255 MEN1_HUMAN 1 593 SEQADV 9PY8 GLY A -4 UNP O00255 EXPRESSION TAG SEQADV 9PY8 GLY A -3 UNP O00255 EXPRESSION TAG SEQADV 9PY8 SER A -2 UNP O00255 EXPRESSION TAG SEQADV 9PY8 SER A -1 UNP O00255 EXPRESSION TAG SEQADV 9PY8 SER A 0 UNP O00255 EXPRESSION TAG SEQADV 9PY8 A UNP O00255 ILE 54 DELETION SEQADV 9PY8 A UNP O00255 PRO 55 DELETION SEQADV 9PY8 A UNP O00255 THR 56 DELETION SEQADV 9PY8 A UNP O00255 ASN 57 DELETION SEQADV 9PY8 A UNP O00255 VAL 58 DELETION SEQADV 9PY8 A UNP O00255 PRO 59 DELETION SEQADV 9PY8 A UNP O00255 GLU 60 DELETION SEQADV 9PY8 A UNP O00255 LEU 61 DELETION SEQADV 9PY8 A UNP O00255 THR 62 DELETION SEQADV 9PY8 A UNP O00255 PHE 63 DELETION SEQADV 9PY8 A UNP O00255 GLN 64 DELETION SEQADV 9PY8 A UNP O00255 PRO 65 DELETION SEQADV 9PY8 A UNP O00255 SER 66 DELETION SEQADV 9PY8 A UNP O00255 PRO 67 DELETION SEQADV 9PY8 A UNP O00255 ALA 68 DELETION SEQADV 9PY8 A UNP O00255 PRO 69 DELETION SEQADV 9PY8 A UNP O00255 ASP 70 DELETION SEQADV 9PY8 A UNP O00255 PRO 71 DELETION SEQADV 9PY8 A UNP O00255 PRO 72 DELETION SEQADV 9PY8 A UNP O00255 GLY 73 DELETION SEQADV 9PY8 ARG A 326 UNP O00255 GLY 326 ENGINEERED MUTATION SEQADV 9PY8 A UNP O00255 GLU 387 DELETION SEQADV 9PY8 A UNP O00255 GLU 388 DELETION SEQADV 9PY8 A UNP O00255 ARG 389 DELETION SEQADV 9PY8 A UNP O00255 PRO 390 DELETION SEQADV 9PY8 A UNP O00255 GLY 391 DELETION SEQADV 9PY8 A UNP O00255 GLU 392 DELETION SEQADV 9PY8 A UNP O00255 GLN 393 DELETION SEQADV 9PY8 A UNP O00255 SER 394 DELETION SEQADV 9PY8 A UNP O00255 GLN 395 DELETION SEQADV 9PY8 A UNP O00255 GLY 396 DELETION SEQADV 9PY8 A UNP O00255 THR 397 DELETION SEQADV 9PY8 A UNP O00255 GLN 398 DELETION SEQADV 9PY8 A UNP O00255 ARG 460 DELETION SEQADV 9PY8 A UNP O00255 GLU 461 DELETION SEQADV 9PY8 A UNP O00255 ALA 462 DELETION SEQADV 9PY8 A UNP O00255 GLU 463 DELETION SEQADV 9PY8 A UNP O00255 ALA 464 DELETION SEQADV 9PY8 A UNP O00255 ALA 465 DELETION SEQADV 9PY8 A UNP O00255 GLU 466 DELETION SEQADV 9PY8 A UNP O00255 ALA 467 DELETION SEQADV 9PY8 A UNP O00255 GLU 468 DELETION SEQADV 9PY8 A UNP O00255 GLU 469 DELETION SEQADV 9PY8 A UNP O00255 PRO 470 DELETION SEQADV 9PY8 A UNP O00255 TRP 471 DELETION SEQADV 9PY8 A UNP O00255 GLY 472 DELETION SEQADV 9PY8 A UNP O00255 GLU 473 DELETION SEQADV 9PY8 A UNP O00255 GLU 474 DELETION SEQADV 9PY8 A UNP O00255 ALA 475 DELETION SEQADV 9PY8 A UNP O00255 ARG 476 DELETION SEQADV 9PY8 A UNP O00255 GLU 477 DELETION SEQADV 9PY8 A UNP O00255 GLY 478 DELETION SEQADV 9PY8 A UNP O00255 ARG 479 DELETION SEQADV 9PY8 A UNP O00255 ARG 480 DELETION SEQADV 9PY8 A UNP O00255 ARG 481 DELETION SEQADV 9PY8 A UNP O00255 GLY 482 DELETION SEQADV 9PY8 A UNP O00255 PRO 483 DELETION SEQADV 9PY8 A UNP O00255 ARG 484 DELETION SEQADV 9PY8 A UNP O00255 ARG 485 DELETION SEQADV 9PY8 A UNP O00255 GLU 486 DELETION SEQADV 9PY8 A UNP O00255 SER 487 DELETION SEQADV 9PY8 A UNP O00255 LYS 488 DELETION SEQADV 9PY8 A UNP O00255 PRO 489 DELETION SEQADV 9PY8 A UNP O00255 GLU 490 DELETION SEQADV 9PY8 A UNP O00255 GLU 491 DELETION SEQADV 9PY8 A UNP O00255 PRO 492 DELETION SEQADV 9PY8 A UNP O00255 PRO 493 DELETION SEQADV 9PY8 A UNP O00255 PRO 494 DELETION SEQADV 9PY8 A UNP O00255 PRO 495 DELETION SEQADV 9PY8 A UNP O00255 LYS 496 DELETION SEQADV 9PY8 A UNP O00255 LYS 497 DELETION SEQADV 9PY8 A UNP O00255 PRO 498 DELETION SEQADV 9PY8 A UNP O00255 ALA 499 DELETION SEQADV 9PY8 A UNP O00255 LEU 500 DELETION SEQADV 9PY8 A UNP O00255 ASP 501 DELETION SEQADV 9PY8 A UNP O00255 LYS 502 DELETION SEQADV 9PY8 A UNP O00255 GLY 503 DELETION SEQADV 9PY8 A UNP O00255 LEU 504 DELETION SEQADV 9PY8 A UNP O00255 GLY 505 DELETION SEQADV 9PY8 A UNP O00255 THR 506 DELETION SEQADV 9PY8 A UNP O00255 GLY 507 DELETION SEQADV 9PY8 A UNP O00255 GLN 508 DELETION SEQADV 9PY8 A UNP O00255 GLY 509 DELETION SEQADV 9PY8 A UNP O00255 ALA 510 DELETION SEQADV 9PY8 A UNP O00255 VAL 511 DELETION SEQADV 9PY8 A UNP O00255 SER 512 DELETION SEQADV 9PY8 A UNP O00255 GLY 513 DELETION SEQADV 9PY8 A UNP O00255 PRO 514 DELETION SEQADV 9PY8 A UNP O00255 PRO 515 DELETION SEQADV 9PY8 A UNP O00255 ARG 516 DELETION SEQADV 9PY8 A UNP O00255 LYS 517 DELETION SEQADV 9PY8 A UNP O00255 PRO 518 DELETION SEQADV 9PY8 A UNP O00255 PRO 519 DELETION SEQADV 9PY8 A UNP O00255 GLY 520 DELETION SEQADV 9PY8 A UNP O00255 THR 521 DELETION SEQADV 9PY8 A UNP O00255 VAL 522 DELETION SEQADV 9PY8 A UNP O00255 ALA 523 DELETION SEQADV 9PY8 A UNP O00255 GLY 524 DELETION SEQADV 9PY8 A UNP O00255 THR 525 DELETION SEQADV 9PY8 A UNP O00255 ALA 526 DELETION SEQADV 9PY8 A UNP O00255 ARG 527 DELETION SEQADV 9PY8 A UNP O00255 GLY 528 DELETION SEQADV 9PY8 A UNP O00255 PRO 529 DELETION SEQADV 9PY8 A UNP O00255 GLU 530 DELETION SEQADV 9PY8 A UNP O00255 GLY 531 DELETION SEQADV 9PY8 A UNP O00255 GLY 532 DELETION SEQADV 9PY8 A UNP O00255 SER 533 DELETION SEQADV 9PY8 A UNP O00255 THR 534 DELETION SEQADV 9PY8 A UNP O00255 ALA 535 DELETION SEQADV 9PY8 A UNP O00255 GLN 536 DELETION SEQADV 9PY8 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 MET TYR LEU ALA ARG 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 DMS A 603 10 HET PEG A 604 17 HET PEG A 605 17 HETNAM K5O ZIFTOMENIB HETNAM SO4 SULFATE ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 K5O C33 H42 F3 N9 O2 S2 FORMUL 3 SO4 O4 S 2- FORMUL 4 DMS C2 H6 O S FORMUL 5 PEG 2(C4 H10 O3) FORMUL 7 HOH *563(H2 O) HELIX 1 AA1 LYS A 4 LYS A 8 5 5 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 LEU A 129 1 16 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 LEU A 565 5 3 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 -1.94 CISPEP 2 VAL A 460 PRO A 461 0 -5.89 CRYST1 49.083 80.126 124.820 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 0.020374 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012480 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008012 0.00000 CONECT 8076 8077 8125 8126 8127 CONECT 8077 8076 8078 8128 CONECT 8078 8077 8079 8124 CONECT 8079 8078 8080 CONECT 8080 8079 8081 8114 CONECT 8081 8080 8082 8129 CONECT 8082 8081 8083 8113 8130 CONECT 8083 8082 8084 8131 8132 CONECT 8084 8083 8085 8133 8134 CONECT 8085 8084 8086 8112 CONECT 8086 8085 8087 8135 8136 CONECT 8087 8086 8088 8108 CONECT 8088 8087 8089 8137 CONECT 8089 8088 8090 8138 CONECT 8090 8089 8091 8107 CONECT 8091 8090 8092 8105 CONECT 8092 8091 8093 8139 8140 CONECT 8093 8092 8094 8095 8141 CONECT 8094 8093 8142 8143 8144 CONECT 8095 8093 8096 8100 CONECT 8096 8095 8097 8145 8146 CONECT 8097 8096 8098 8147 8148 CONECT 8098 8097 8099 8101 CONECT 8099 8098 8100 8149 8150 CONECT 8100 8095 8099 8151 8152 CONECT 8101 8098 8102 8103 8104 CONECT 8102 8101 8153 8154 8155 CONECT 8103 8101 CONECT 8104 8101 CONECT 8105 8091 8106 8110 CONECT 8106 8105 8107 8156 CONECT 8107 8090 8106 8108 CONECT 8108 8087 8107 8109 CONECT 8109 8108 8157 8158 8159 CONECT 8110 8105 8111 CONECT 8111 8110 CONECT 8112 8085 8113 8160 8161 CONECT 8113 8082 8112 8162 8163 CONECT 8114 8080 8115 8123 CONECT 8115 8114 8116 8164 CONECT 8116 8115 8117 8122 CONECT 8117 8116 8118 8165 8166 CONECT 8118 8117 8119 8120 8121 CONECT 8119 8118 CONECT 8120 8118 CONECT 8121 8118 CONECT 8122 8116 8123 CONECT 8123 8114 8122 8124 CONECT 8124 8078 8123 CONECT 8125 8076 CONECT 8126 8076 CONECT 8127 8076 CONECT 8128 8077 CONECT 8129 8081 CONECT 8130 8082 CONECT 8131 8083 CONECT 8132 8083 CONECT 8133 8084 CONECT 8134 8084 CONECT 8135 8086 CONECT 8136 8086 CONECT 8137 8088 CONECT 8138 8089 CONECT 8139 8092 CONECT 8140 8092 CONECT 8141 8093 CONECT 8142 8094 CONECT 8143 8094 CONECT 8144 8094 CONECT 8145 8096 CONECT 8146 8096 CONECT 8147 8097 CONECT 8148 8097 CONECT 8149 8099 CONECT 8150 8099 CONECT 8151 8100 CONECT 8152 8100 CONECT 8153 8102 CONECT 8154 8102 CONECT 8155 8102 CONECT 8156 8106 CONECT 8157 8109 CONECT 8158 8109 CONECT 8159 8109 CONECT 8160 8112 CONECT 8161 8112 CONECT 8162 8113 CONECT 8163 8113 CONECT 8164 8115 CONECT 8165 8117 CONECT 8166 8117 CONECT 8167 8168 8169 8170 8171 CONECT 8168 8167 CONECT 8169 8167 CONECT 8170 8167 CONECT 8171 8167 CONECT 8172 8173 8174 8175 CONECT 8173 8172 CONECT 8174 8172 8176 8177 8178 CONECT 8175 8172 8179 8180 8181 CONECT 8176 8174 CONECT 8177 8174 CONECT 8178 8174 CONECT 8179 8175 CONECT 8180 8175 CONECT 8181 8175 CONECT 8182 8183 8184 8189 8190 CONECT 8183 8182 8191 CONECT 8184 8182 8185 8192 8193 CONECT 8185 8184 8186 CONECT 8186 8185 8187 8194 8195 CONECT 8187 8186 8188 8196 8197 CONECT 8188 8187 8198 CONECT 8189 8182 CONECT 8190 8182 CONECT 8191 8183 CONECT 8192 8184 CONECT 8193 8184 CONECT 8194 8186 CONECT 8195 8186 CONECT 8196 8187 CONECT 8197 8187 CONECT 8198 8188 CONECT 8199 8200 8201 8206 8207 CONECT 8200 8199 8208 CONECT 8201 8199 8202 8209 8210 CONECT 8202 8201 8203 CONECT 8203 8202 8204 8211 8212 CONECT 8204 8203 8205 8213 8214 CONECT 8205 8204 8215 CONECT 8206 8199 CONECT 8207 8199 CONECT 8208 8200 CONECT 8209 8201 CONECT 8210 8201 CONECT 8211 8203 CONECT 8212 8203 CONECT 8213 8204 CONECT 8214 8204 CONECT 8215 8205 MASTER 366 0 5 27 8 0 0 6 4330 1 140 38 END