HEADER TRANSCRIPTION 29-JUN-19 6PKC TITLE INHIBITION OF HUMAN MENIN BY VTP-50469 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MENIN,MENIN; COMPND 3 CHAIN: A, B; 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 VARIANT: 2; SOURCE 6 GENE: MEN1, SCG2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS HUMAN MENIN, TRANSCRIPTION, INHIBITOR COMPLEX, VTP-50469 EXPDTA X-RAY DIFFRACTION AUTHOR B.M.MCKEEVER,G.CHEN,R.VAN ORTON REVDAT 2 11-OCT-23 6PKC 1 REMARK REVDAT 1 18-DEC-19 6PKC 0 JRNL AUTH A.V.KRIVTSOV,K.EVANS,J.Y.GADREY,B.K.ESCHLE,C.HATTON, JRNL AUTH 2 H.J.UCKELMANN,K.N.ROSS,F.PERNER,S.N.OLSEN,T.PRITCHARD, JRNL AUTH 3 L.MCDERMOTT,C.D.JONES,D.JING,A.BRAYTEE,D.CHACON,E.EARLEY, JRNL AUTH 4 B.M.MCKEEVER,D.CLAREMON,A.J.GIFFORD,H.J.LEE,B.A.TEICHER, JRNL AUTH 5 J.E.PIMANDA,D.BECK,J.A.PERRY,M.A.SMITH,G.M.MCGEEHAN, JRNL AUTH 6 R.B.LOCK,S.A.ARMSTRONG JRNL TITL A MENIN-MLL INHIBITOR INDUCES SPECIFIC CHROMATIN CHANGES AND JRNL TITL 2 ERADICATES DISEASE IN MODELS OF MLL-REARRANGED LEUKEMIA. JRNL REF CANCER CELL V. 36 660 2019 JRNL REFN ISSN 1535-6108 JRNL PMID 31821784 JRNL DOI 10.1016/J.CCELL.2019.11.001 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 77796 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4146 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5650 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.1870 REMARK 3 BIN FREE R VALUE SET COUNT : 311 REMARK 3 BIN FREE R VALUE : 0.2260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7304 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 572 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.05000 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): 0.138 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.129 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.820 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7730 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 7370 ; 0.009 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10518 ; 2.006 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): 16935 ; 1.547 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 954 ; 6.682 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 351 ;33.293 ;23.561 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1278 ;15.765 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 55 ;20.107 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1162 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8763 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1804 ; 0.008 ; 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): 3789 ; 3.088 ; 2.698 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3788 ; 3.087 ; 2.696 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4756 ; 4.450 ; 4.015 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4753 ; 4.450 ; 4.018 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3941 ; 3.882 ; 3.015 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3942 ; 3.881 ; 3.015 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5759 ; 6.014 ; 4.369 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 9276 ; 8.173 ;21.488 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 9082 ; 8.138 ;21.253 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 2 583 B 2 583 56876 0.10 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 REMARK 4 REMARK 4 6PKC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000241311. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 - 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1. REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81943 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 58.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 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: PDB ENTRY 4GPQ REMARK 200 REMARK 200 REMARK: ORTHORHOMBIC PRISMS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 14%(W/V) PEG3350 0.2M POTASSIUM REMARK 280 THIOCYANATE 0.1M MES PH=6.0 15%(V/V) ETHYLENE GLYCOL, PH 6.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 29.48500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 101.02000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.04000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 101.02000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.48500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.04000 REMARK 290 SMTRY3 4 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: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 0 REMARK 465 SER A 1 REMARK 465 VAL A 53 REMARK 465 ILE A 54 REMARK 465 PRO A 55 REMARK 465 THR A 56 REMARK 465 ASN A 57 REMARK 465 VAL A 58 REMARK 465 PRO A 59 REMARK 465 GLU A 60 REMARK 465 LEU A 61 REMARK 465 THR A 62 REMARK 465 PHE A 63 REMARK 465 GLN A 64 REMARK 465 PRO A 65 REMARK 465 GLU A 388 REMARK 465 ARG A 389 REMARK 465 PRO A 390 REMARK 465 GLY A 391 REMARK 465 GLU A 392 REMARK 465 GLN A 393 REMARK 465 SER A 394 REMARK 465 GLN A 395 REMARK 465 GLY A 396 REMARK 465 THR A 397 REMARK 465 GLN A 398 REMARK 465 SER A 399 REMARK 465 GLN A 400 REMARK 465 GLY B 0 REMARK 465 SER B 1 REMARK 465 VAL B 53 REMARK 465 ILE B 54 REMARK 465 PRO B 55 REMARK 465 THR B 56 REMARK 465 ASN B 57 REMARK 465 VAL B 58 REMARK 465 PRO B 59 REMARK 465 GLU B 60 REMARK 465 LEU B 61 REMARK 465 THR B 62 REMARK 465 PHE B 63 REMARK 465 GLN B 64 REMARK 465 PRO B 65 REMARK 465 GLU B 388 REMARK 465 ARG B 389 REMARK 465 PRO B 390 REMARK 465 GLY B 391 REMARK 465 GLU B 392 REMARK 465 GLN B 393 REMARK 465 SER B 394 REMARK 465 GLN B 395 REMARK 465 GLY B 396 REMARK 465 THR B 397 REMARK 465 GLN B 398 REMARK 465 SER B 399 REMARK 465 GLN B 400 REMARK 465 SER B 583 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLU A 109 N GLY B 111 1445 1.83 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 GLY A 386 C GLU A 387 N 0.179 REMARK 500 ARG B 207 CD ARG B 207 NE -0.104 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 29 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 137 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 137 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 207 NE - CZ - NH1 ANGL. DEV. = 8.4 DEGREES REMARK 500 ARG A 207 NE - CZ - NH2 ANGL. DEV. = -9.7 DEGREES REMARK 500 ARG A 218 NE - CZ - NH1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG A 218 NE - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 GLU A 358 CA - CB - CG ANGL. DEV. = 14.8 DEGREES REMARK 500 ARG A 415 CG - CD - NE ANGL. DEV. = 14.8 DEGREES REMARK 500 ARG A 415 CD - NE - CZ ANGL. DEV. = 15.0 DEGREES REMARK 500 ARG A 415 NE - CZ - NH1 ANGL. DEV. = -8.0 DEGREES REMARK 500 ASP A 418 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG B 29 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 137 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG B 137 NE - CZ - NH2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG B 207 NE - CZ - NH1 ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG B 207 NE - CZ - NH2 ANGL. DEV. = -9.8 DEGREES REMARK 500 ARG B 218 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG B 218 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ASP B 231 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP B 315 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 GLY B 386 CA - C - N ANGL. DEV. = -19.7 DEGREES REMARK 500 GLY B 386 O - C - N ANGL. DEV. = 18.0 DEGREES REMARK 500 GLU B 387 C - N - CA ANGL. DEV. = -26.3 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 ALA A 49 54.56 -98.89 REMARK 500 SER A 178 -156.87 -95.68 REMARK 500 SER A 226 47.42 -94.79 REMARK 500 ARG A 314 18.40 59.66 REMARK 500 ASP A 370 -59.09 -148.10 REMARK 500 ASN B 51 45.33 -91.92 REMARK 500 PRO B 107 98.59 -52.53 REMARK 500 SER B 178 -158.65 -95.31 REMARK 500 ASP B 180 9.58 -151.85 REMARK 500 SER B 226 43.99 -94.30 REMARK 500 ASP B 370 -61.67 -144.77 REMARK 500 VAL B 431 -50.67 -121.01 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 415 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLY A 386 -10.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OP4 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OP4 B 601 DBREF 6PKC A 2 457 UNP O00255 MEN1_HUMAN 2 457 DBREF 6PKC A 552 583 UNP O00255 MEN1_HUMAN 552 583 DBREF 6PKC B 2 457 UNP O00255 MEN1_HUMAN 2 457 DBREF 6PKC B 552 583 UNP O00255 MEN1_HUMAN 552 583 SEQADV 6PKC GLY A 0 UNP O00255 EXPRESSION TAG SEQADV 6PKC SER A 1 UNP O00255 EXPRESSION TAG SEQADV 6PKC THR A 5 UNP O00255 ALA 5 ENGINEERED MUTATION SEQADV 6PKC GLY B 0 UNP O00255 EXPRESSION TAG SEQADV 6PKC SER B 1 UNP O00255 EXPRESSION TAG SEQADV 6PKC THR B 5 UNP O00255 ALA 5 ENGINEERED MUTATION SEQRES 1 A 490 GLY SER GLY LEU LYS THR ALA GLN LYS THR LEU PHE PRO SEQRES 2 A 490 LEU ARG SER ILE ASP ASP VAL VAL ARG LEU PHE ALA ALA SEQRES 3 A 490 GLU LEU GLY ARG GLU GLU PRO ASP LEU VAL LEU LEU SER SEQRES 4 A 490 LEU VAL LEU GLY PHE VAL GLU HIS PHE LEU ALA VAL ASN SEQRES 5 A 490 ARG VAL ILE PRO THR ASN VAL PRO GLU LEU THR PHE GLN SEQRES 6 A 490 PRO SER PRO ALA PRO ASP PRO PRO GLY GLY LEU THR TYR SEQRES 7 A 490 PHE PRO VAL ALA ASP LEU SER ILE ILE ALA ALA LEU TYR SEQRES 8 A 490 ALA ARG PHE THR ALA GLN ILE ARG GLY ALA VAL ASP LEU SEQRES 9 A 490 SER LEU TYR PRO ARG GLU GLY GLY VAL SER SER ARG GLU SEQRES 10 A 490 LEU VAL LYS LYS VAL SER ASP VAL ILE TRP ASN SER LEU SEQRES 11 A 490 SER ARG SER TYR PHE LYS ASP ARG ALA HIS ILE GLN SER SEQRES 12 A 490 LEU PHE SER PHE ILE THR GLY THR LYS LEU ASP SER SER SEQRES 13 A 490 GLY VAL ALA PHE ALA VAL VAL GLY ALA CYS GLN ALA LEU SEQRES 14 A 490 GLY LEU ARG ASP VAL HIS LEU ALA LEU SER GLU ASP HIS SEQRES 15 A 490 ALA TRP VAL VAL PHE GLY PRO ASN GLY GLU GLN THR ALA SEQRES 16 A 490 GLU VAL THR TRP HIS GLY LYS GLY ASN GLU ASP ARG ARG SEQRES 17 A 490 GLY GLN THR VAL ASN ALA GLY VAL ALA GLU ARG SER TRP SEQRES 18 A 490 LEU TYR LEU LYS GLY SER TYR MET ARG CYS ASP ARG LYS SEQRES 19 A 490 MET GLU VAL ALA PHE MET VAL CYS ALA ILE ASN PRO SER SEQRES 20 A 490 ILE ASP LEU HIS THR ASP SER LEU GLU LEU LEU GLN LEU SEQRES 21 A 490 GLN GLN LYS LEU LEU TRP LEU LEU TYR ASP LEU GLY HIS SEQRES 22 A 490 LEU GLU ARG TYR PRO MET ALA LEU GLY ASN LEU ALA ASP SEQRES 23 A 490 LEU GLU GLU LEU GLU PRO THR PRO GLY ARG PRO ASP PRO SEQRES 24 A 490 LEU THR LEU TYR HIS LYS GLY ILE ALA SER ALA LYS THR SEQRES 25 A 490 TYR TYR ARG ASP GLU HIS ILE TYR PRO TYR MET TYR LEU SEQRES 26 A 490 ALA GLY TYR HIS CYS ARG ASN ARG ASN VAL ARG GLU ALA SEQRES 27 A 490 LEU GLN ALA TRP ALA ASP THR ALA THR VAL ILE GLN ASP SEQRES 28 A 490 TYR ASN TYR CYS ARG GLU ASP GLU GLU ILE TYR LYS GLU SEQRES 29 A 490 PHE PHE GLU VAL ALA ASN ASP VAL ILE PRO ASN LEU LEU SEQRES 30 A 490 LYS GLU ALA ALA SER LEU LEU GLU ALA GLY GLU GLU ARG SEQRES 31 A 490 PRO GLY GLU GLN SER GLN GLY THR GLN SER GLN GLY SER SEQRES 32 A 490 ALA LEU GLN ASP PRO GLU CYS PHE ALA HIS LEU LEU ARG SEQRES 33 A 490 PHE TYR ASP GLY ILE CYS LYS TRP GLU GLU GLY SER PRO SEQRES 34 A 490 THR PRO VAL LEU HIS VAL GLY TRP ALA THR PHE LEU VAL SEQRES 35 A 490 GLN SER LEU GLY ARG PHE GLU GLY GLN VAL ARG GLN LYS SEQRES 36 A 490 VAL ARG ILE THR PHE GLN SER GLU LYS MET LYS GLY MET SEQRES 37 A 490 LYS GLU LEU LEU VAL ALA THR LYS ILE ASN SER SER ALA SEQRES 38 A 490 ILE LYS LEU GLN LEU THR ALA GLN SER SEQRES 1 B 490 GLY SER GLY LEU LYS THR ALA GLN LYS THR LEU PHE PRO SEQRES 2 B 490 LEU ARG SER ILE ASP ASP VAL VAL ARG LEU PHE ALA ALA SEQRES 3 B 490 GLU LEU GLY ARG GLU GLU PRO ASP LEU VAL LEU LEU SER SEQRES 4 B 490 LEU VAL LEU GLY PHE VAL GLU HIS PHE LEU ALA VAL ASN SEQRES 5 B 490 ARG VAL ILE PRO THR ASN VAL PRO GLU LEU THR PHE GLN SEQRES 6 B 490 PRO SER PRO ALA PRO ASP PRO PRO GLY GLY LEU THR TYR SEQRES 7 B 490 PHE PRO VAL ALA ASP LEU SER ILE ILE ALA ALA LEU TYR SEQRES 8 B 490 ALA ARG PHE THR ALA GLN ILE ARG GLY ALA VAL ASP LEU SEQRES 9 B 490 SER LEU TYR PRO ARG GLU GLY GLY VAL SER SER ARG GLU SEQRES 10 B 490 LEU VAL LYS LYS VAL SER ASP VAL ILE TRP ASN SER LEU SEQRES 11 B 490 SER ARG SER TYR PHE LYS ASP ARG ALA HIS ILE GLN SER SEQRES 12 B 490 LEU PHE SER PHE ILE THR GLY THR LYS LEU ASP SER SER SEQRES 13 B 490 GLY VAL ALA PHE ALA VAL VAL GLY ALA CYS GLN ALA LEU SEQRES 14 B 490 GLY LEU ARG ASP VAL HIS LEU ALA LEU SER GLU ASP HIS SEQRES 15 B 490 ALA TRP VAL VAL PHE GLY PRO ASN GLY GLU GLN THR ALA SEQRES 16 B 490 GLU VAL THR TRP HIS GLY LYS GLY ASN GLU ASP ARG ARG SEQRES 17 B 490 GLY GLN THR VAL ASN ALA GLY VAL ALA GLU ARG SER TRP SEQRES 18 B 490 LEU TYR LEU LYS GLY SER TYR MET ARG CYS ASP ARG LYS SEQRES 19 B 490 MET GLU VAL ALA PHE MET VAL CYS ALA ILE ASN PRO SER SEQRES 20 B 490 ILE ASP LEU HIS THR ASP SER LEU GLU LEU LEU GLN LEU SEQRES 21 B 490 GLN GLN LYS LEU LEU TRP LEU LEU TYR ASP LEU GLY HIS SEQRES 22 B 490 LEU GLU ARG TYR PRO MET ALA LEU GLY ASN LEU ALA ASP SEQRES 23 B 490 LEU GLU GLU LEU GLU PRO THR PRO GLY ARG PRO ASP PRO SEQRES 24 B 490 LEU THR LEU TYR HIS LYS GLY ILE ALA SER ALA LYS THR SEQRES 25 B 490 TYR TYR ARG ASP GLU HIS ILE TYR PRO TYR MET TYR LEU SEQRES 26 B 490 ALA GLY TYR HIS CYS ARG ASN ARG ASN VAL ARG GLU ALA SEQRES 27 B 490 LEU GLN ALA TRP ALA ASP THR ALA THR VAL ILE GLN ASP SEQRES 28 B 490 TYR ASN TYR CYS ARG GLU ASP GLU GLU ILE TYR LYS GLU SEQRES 29 B 490 PHE PHE GLU VAL ALA ASN ASP VAL ILE PRO ASN LEU LEU SEQRES 30 B 490 LYS GLU ALA ALA SER LEU LEU GLU ALA GLY GLU GLU ARG SEQRES 31 B 490 PRO GLY GLU GLN SER GLN GLY THR GLN SER GLN GLY SER SEQRES 32 B 490 ALA LEU GLN ASP PRO GLU CYS PHE ALA HIS LEU LEU ARG SEQRES 33 B 490 PHE TYR ASP GLY ILE CYS LYS TRP GLU GLU GLY SER PRO SEQRES 34 B 490 THR PRO VAL LEU HIS VAL GLY TRP ALA THR PHE LEU VAL SEQRES 35 B 490 GLN SER LEU GLY ARG PHE GLU GLY GLN VAL ARG GLN LYS SEQRES 36 B 490 VAL ARG ILE THR PHE GLN SER GLU LYS MET LYS GLY MET SEQRES 37 B 490 LYS GLU LEU LEU VAL ALA THR LYS ILE ASN SER SER ALA SEQRES 38 B 490 ILE LYS LEU GLN LEU THR ALA GLN SER HET OP4 A 601 44 HET OP4 B 601 44 HETNAM OP4 5-FLUORO-2-({4-[7-({TRANS-4-[(METHYLSULFONYL) HETNAM 2 OP4 AMINO]CYCLOHEXYL}METHYL)-2,7-DIAZASPIRO[3.5]NONAN-2- HETNAM 3 OP4 YL]PYRIMIDIN-5-YL}OXY)-N,N-DI(PROPAN-2-YL)BENZAMIDE FORMUL 3 OP4 2(C32 H47 F N6 O4 S) FORMUL 5 HOH *572(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 ALA A 49 1 17 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 SER A 114 SER A 128 1 15 HELIX 7 AA7 SER A 142 THR A 150 1 9 HELIX 8 AA8 ASP A 153 LEU A 168 1 16 HELIX 9 AA9 VAL A 211 GLU A 217 1 7 HELIX 10 AB1 SER A 219 SER A 226 5 8 HELIX 11 AB2 ASP A 231 ALA A 242 1 12 HELIX 12 AB3 SER A 253 LEU A 270 1 18 HELIX 13 AB4 TYR A 276 GLU A 290 1 15 HELIX 14 AB5 ASP A 297 TYR A 313 1 17 HELIX 15 AB6 ILE A 318 ASN A 331 1 14 HELIX 16 AB7 ASN A 333 GLN A 349 1 17 HELIX 17 AB8 ASP A 357 ASP A 370 1 14 HELIX 18 AB9 ASP A 370 GLY A 386 1 17 HELIX 19 AC1 SER A 402 GLN A 405 5 4 HELIX 20 AC2 ASP A 406 GLU A 425 1 20 HELIX 21 AC3 HIS A 433 GLY A 445 1 13 HELIX 22 AC4 GLU A 448 GLN A 453 1 6 HELIX 23 AC5 SER A 555 GLY A 560 1 6 HELIX 24 AC6 MET A 561 ALA A 567 1 7 HELIX 25 AC7 ASN A 571 ALA A 581 1 11 HELIX 26 AC8 LYS B 4 THR B 9 1 6 HELIX 27 AC9 SER B 15 GLY B 28 1 14 HELIX 28 AD1 ASP B 33 ALA B 49 1 17 HELIX 29 AD2 ASP B 82 VAL B 101 1 20 HELIX 30 AD3 ASP B 102 TYR B 106 5 5 HELIX 31 AD4 SER B 114 LEU B 129 1 16 HELIX 32 AD5 SER B 142 THR B 150 1 9 HELIX 33 AD6 ASP B 153 LEU B 168 1 16 HELIX 34 AD7 VAL B 211 GLU B 217 1 7 HELIX 35 AD8 SER B 219 SER B 226 5 8 HELIX 36 AD9 ASP B 231 ALA B 242 1 12 HELIX 37 AE1 SER B 253 LEU B 270 1 18 HELIX 38 AE2 TYR B 276 GLU B 290 1 15 HELIX 39 AE3 ASP B 297 TYR B 313 1 17 HELIX 40 AE4 ILE B 318 ASN B 331 1 14 HELIX 41 AE5 ASN B 333 GLN B 349 1 17 HELIX 42 AE6 CYS B 354 GLU B 356 5 3 HELIX 43 AE7 ASP B 357 ASP B 370 1 14 HELIX 44 AE8 ASP B 370 GLY B 386 1 17 HELIX 45 AE9 SER B 402 GLN B 405 5 4 HELIX 46 AF1 ASP B 406 GLU B 425 1 20 HELIX 47 AF2 HIS B 433 ARG B 446 1 14 HELIX 48 AF3 GLU B 448 GLN B 453 1 6 HELIX 49 AF4 SER B 555 ALA B 567 1 13 HELIX 50 AF5 ASN B 571 THR B 580 1 10 SHEET 1 AA1 4 GLN A 192 ALA A 194 0 SHEET 2 AA1 4 ALA A 182 PHE A 186 -1 N PHE A 186 O GLN A 192 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 4 GLN B 192 ALA B 194 0 SHEET 2 AA3 4 ALA B 182 PHE B 186 -1 N PHE B 186 O GLN B 192 SHEET 3 AA3 4 HIS B 174 LEU B 177 -1 N ALA B 176 O TRP B 183 SHEET 4 AA3 4 MET B 228 ARG B 229 -1 O MET B 228 N LEU B 177 SHEET 1 AA4 2 SER B 246 ASP B 248 0 SHEET 2 AA4 2 THR B 251 ASP B 252 -1 O THR B 251 N ILE B 247 CISPEP 1 PHE A 11 PRO A 12 0 -0.25 CISPEP 2 PHE B 11 PRO B 12 0 1.16 SITE 1 AC1 16 SER A 155 SER A 178 GLU A 179 HIS A 181 SITE 2 AC1 16 ALA A 182 PHE A 238 CYS A 241 TYR A 276 SITE 3 AC1 16 MET A 278 TYR A 319 MET A 322 TYR A 323 SITE 4 AC1 16 TRP A 341 GLU A 363 VAL A 367 HOH A 777 SITE 1 AC2 19 SER B 155 SER B 178 GLU B 179 HIS B 181 SITE 2 AC2 19 ALA B 182 PHE B 238 CYS B 241 TYR B 276 SITE 3 AC2 19 MET B 278 TYR B 319 MET B 322 TYR B 323 SITE 4 AC2 19 TRP B 341 VAL B 367 HOH B 705 HOH B 719 SITE 5 AC2 19 HOH B 810 HOH B 813 HOH B 841 CRYST1 58.970 86.080 202.040 90.00 90.00 90.00 P 21 21 21 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 0.016958 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011617 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004950 0.00000