HEADER PROTEIN BINDING/INHIBITOR 20-AUG-15 5DB1 TITLE MENIN IN COMPLEX WITH MI-336 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MENIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-489, 537-593; COMPND 5 ENGINEERED: YES; COMPND 6 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 PROTEIN BINDING, PROTEIN BINDING-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.POLLOCK,B.DMITRY,T.CIERPICKI,J.GREMBECKA REVDAT 4 27-SEP-23 5DB1 1 REMARK REVDAT 3 04-DEC-19 5DB1 1 REMARK REVDAT 2 27-SEP-17 5DB1 1 JRNL REMARK REVDAT 1 30-MAR-16 5DB1 0 JRNL AUTH D.BORKIN,J.POLLOCK,K.KEMPINSKA,T.PUROHIT,X.LI,B.WEN,T.ZHAO, JRNL AUTH 2 H.MIAO,S.SHUKLA,M.HE,D.SUN,T.CIERPICKI,J.GREMBECKA JRNL TITL PROPERTY FOCUSED STRUCTURE-BASED OPTIMIZATION OF SMALL JRNL TITL 2 MOLECULE INHIBITORS OF THE PROTEIN-PROTEIN INTERACTION JRNL TITL 3 BETWEEN MENIN AND MIXED LINEAGE LEUKEMIA (MLL). JRNL REF J.MED.CHEM. V. 59 892 2016 JRNL REFN ISSN 0022-2623 JRNL PMID 26744767 JRNL DOI 10.1021/ACS.JMEDCHEM.5B01305 REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 38899 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2060 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) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2697 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 146 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3630 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 102 REMARK 3 SOLVENT ATOMS : 319 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.67000 REMARK 3 B22 (A**2) : 0.60000 REMARK 3 B33 (A**2) : -1.27000 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): 0.132 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.121 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3852 ; 0.015 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3628 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5228 ; 1.633 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8313 ; 3.625 ; 3.007 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 472 ; 5.795 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;31.244 ;23.728 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 615 ;12.538 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;14.834 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 584 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4317 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 889 ; 0.016 ; 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): 1884 ; 1.923 ; 2.077 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1883 ; 1.921 ; 2.075 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2357 ; 2.985 ; 3.101 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5DB1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212843. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41023 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.65200 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: NULL REMARK 200 STARTING MODEL: 4GPQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M HEPES PH REMARK 280 7.5 AND 25% W/V PEG 3,350. THIS SOLUTION WAS MIXED 1:1 WITH REMARK 280 2.5MG/ML PROTEIN IN 50MM TRIS-HCL (PH 8.0), 50MM NACL, AND 1MM REMARK 280 TCEP. PRIOR TO DATA COLLECTION, CRYSTALS WERE TRANSFERRED INTO A REMARK 280 CRYO-SOLUTION CONTAINING 20% PEG550 MME AND FLASH-FROZEN IN REMARK 280 LIQUID NITROGEN, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 283K 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 24.15900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.39000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.90800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.39000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.15900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.90800 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 VAL A 537 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 PRO A 544 REMARK 465 PRO A 545 REMARK 465 PRO A 546 REMARK 465 GLU A 547 REMARK 465 GLY A 548 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 GLY A 2 N REMARK 470 LYS A 4 CE NZ REMARK 470 GLU A 109 CG CD OE1 OE2 REMARK 470 ARG A 131 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 171 CD NE CZ NH1 NH2 REMARK 470 LYS A 201 CG CD CE NZ REMARK 470 ASN A 203 CG OD1 ND2 REMARK 470 GLU A 204 CG CD OE1 OE2 REMARK 470 ASP A 205 CG OD1 OD2 REMARK 470 LEU A 249 CG CD1 CD2 REMARK 470 ARG A 335 NE CZ NH1 NH2 REMARK 470 ARG A 355 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 562 CE NZ REMARK 470 LYS A 569 CG CD CE NZ 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 OE1 GLU A 363 O HOH A 701 2.14 REMARK 500 N GLU A 356 OE2 GLU A 358 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 CB ASP A 205 O HOH A 929 1655 2.19 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. = 4.1 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 -57.90 -160.05 REMARK 500 ASP A 180 26.30 -148.50 REMARK 500 SER A 226 44.05 -93.05 REMARK 500 GLU A 356 -11.60 96.90 REMARK 500 ASP A 370 -55.16 -137.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PG4 A 609 REMARK 610 PG4 A 612 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 58O A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 609 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 610 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 611 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 612 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DB0 RELATED DB: PDB REMARK 900 RELATED ID: 5DB2 RELATED DB: PDB REMARK 900 RELATED ID: 5DB3 RELATED DB: PDB DBREF 5DB1 A 1 459 UNP O00255 MEN1_HUMAN 1 459 DBREF 5DB1 A 537 593 UNP O00255 MEN1_HUMAN 537 593 SEQADV 5DB1 GLY A -4 UNP O00255 EXPRESSION TAG SEQADV 5DB1 GLY A -3 UNP O00255 EXPRESSION TAG SEQADV 5DB1 SER A -2 UNP O00255 EXPRESSION TAG SEQADV 5DB1 SER A -1 UNP O00255 EXPRESSION TAG SEQADV 5DB1 SER A 0 UNP O00255 EXPRESSION TAG SEQADV 5DB1 A UNP O00255 ILE 54 DELETION SEQADV 5DB1 A UNP O00255 PRO 55 DELETION SEQADV 5DB1 A UNP O00255 THR 56 DELETION SEQADV 5DB1 A UNP O00255 ASN 57 DELETION SEQADV 5DB1 A UNP O00255 VAL 58 DELETION SEQADV 5DB1 A UNP O00255 PRO 59 DELETION SEQADV 5DB1 A UNP O00255 GLU 60 DELETION SEQADV 5DB1 A UNP O00255 LEU 61 DELETION SEQADV 5DB1 A UNP O00255 THR 62 DELETION SEQADV 5DB1 A UNP O00255 PHE 63 DELETION SEQADV 5DB1 A UNP O00255 GLN 64 DELETION SEQADV 5DB1 A UNP O00255 PRO 65 DELETION SEQADV 5DB1 A UNP O00255 SER 66 DELETION SEQADV 5DB1 A UNP O00255 PRO 67 DELETION SEQADV 5DB1 A UNP O00255 ALA 68 DELETION SEQADV 5DB1 A UNP O00255 PRO 69 DELETION SEQADV 5DB1 A UNP O00255 ASP 70 DELETION SEQADV 5DB1 A UNP O00255 PRO 71 DELETION SEQADV 5DB1 A UNP O00255 PRO 72 DELETION SEQADV 5DB1 A UNP O00255 GLY 73 DELETION SEQADV 5DB1 A UNP O00255 GLU 387 DELETION SEQADV 5DB1 A UNP O00255 GLU 388 DELETION SEQADV 5DB1 A UNP O00255 ARG 389 DELETION SEQADV 5DB1 A UNP O00255 PRO 390 DELETION SEQADV 5DB1 A UNP O00255 GLY 391 DELETION SEQADV 5DB1 A UNP O00255 GLU 392 DELETION SEQADV 5DB1 A UNP O00255 GLN 393 DELETION SEQADV 5DB1 A UNP O00255 SER 394 DELETION SEQADV 5DB1 A UNP O00255 GLN 395 DELETION SEQADV 5DB1 A UNP O00255 GLY 396 DELETION SEQADV 5DB1 A UNP O00255 THR 397 DELETION SEQADV 5DB1 A UNP O00255 GLN 398 DELETION SEQADV 5DB1 ALA A 541 UNP O00255 THR 541 ENGINEERED MUTATION 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 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 58O A 601 35 HET DMS A 602 4 HET SO4 A 603 5 HET SO4 A 604 5 HET SO4 A 605 5 HET SO4 A 606 5 HET SO4 A 607 5 HET PG4 A 608 13 HET PG4 A 609 7 HET DMS A 610 4 HET DMS A 611 4 HET PG4 A 612 10 HETNAM 58O 6-METHOXY-5-[(4-{[6-(2,2,2-TRIFLUOROETHYL)THIENO[2,3- HETNAM 2 58O D]PYRIMIDIN-4-YL]AMINO}PIPERIDIN-1-YL)METHYL]-1H- HETNAM 3 58O INDOLE-2-CARBONITRILE HETNAM DMS DIMETHYL SULFOXIDE HETNAM SO4 SULFATE ION HETNAM PG4 TETRAETHYLENE GLYCOL HETSYN 58O MI-336 FORMUL 2 58O C24 H23 F3 N6 O S FORMUL 3 DMS 3(C2 H6 O S) FORMUL 4 SO4 5(O4 S 2-) FORMUL 9 PG4 3(C8 H18 O5) FORMUL 14 HOH *319(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 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 GLY A 187 GLU A 191 5 5 HELIX 10 AB1 VAL A 211 GLU A 217 1 7 HELIX 11 AB2 SER A 219 SER A 226 5 8 HELIX 12 AB3 ASP A 231 ALA A 242 1 12 HELIX 13 AB4 SER A 253 LEU A 270 1 18 HELIX 14 AB5 TYR A 276 GLU A 290 1 15 HELIX 15 AB6 ASP A 297 TYR A 313 1 17 HELIX 16 AB7 ILE A 318 ASN A 331 1 14 HELIX 17 AB8 ASN A 333 GLN A 349 1 17 HELIX 18 AB9 ASP A 357 ASP A 370 1 14 HELIX 19 AC1 ASP A 370 ALA A 385 1 16 HELIX 20 AC2 SER A 402 GLN A 405 5 4 HELIX 21 AC3 ASP A 406 GLU A 425 1 20 HELIX 22 AC4 HIS A 433 ARG A 446 1 14 HELIX 23 AC5 GLU A 448 GLN A 453 1 6 HELIX 24 AC6 SER A 555 VAL A 566 1 12 HELIX 25 AC7 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 1.15 SITE 1 AC1 17 SER A 155 LEU A 177 SER A 178 HIS A 181 SITE 2 AC1 17 ALA A 182 PHE A 238 TYR A 276 MET A 278 SITE 3 AC1 17 MET A 322 TYR A 323 TRP A 341 GLU A 363 SITE 4 AC1 17 DMS A 602 HOH A 701 HOH A 765 HOH A 877 SITE 5 AC1 17 HOH A 881 SITE 1 AC2 3 SER A 155 58O A 601 HOH A 925 SITE 1 AC3 4 TYR A 133 PHE A 134 ARG A 137 ARG A 332 SITE 1 AC4 2 PRO A 12 ARG A 14 SITE 1 AC5 3 LYS A 377 ARG A 446 HOH A 919 SITE 1 AC6 4 ARG A 332 VAL A 334 ARG A 335 ALA A 403 SITE 1 AC7 4 ARG A 108 GLY A 111 GLY A 169 ARG A 171 SITE 1 AC8 6 LEU A 75 THR A 76 TYR A 361 PHE A 365 SITE 2 AC8 6 HOH A 768 HOH A 954 SITE 1 AC9 4 SER A 130 LYS A 135 TRP A 198 HOH A 916 SITE 1 AD1 6 VAL A 185 GLY A 190 GLU A 191 TYR A 227 SITE 2 AD1 6 ARG A 229 SER A 583 SITE 1 AD2 6 PHE A 43 PHE A 47 GLY A 386 GLN A 400 SITE 2 AD2 6 HOH A 841 HOH A 842 SITE 1 AD3 6 TYR A 268 ASP A 269 GLU A 274 LYS A 304 SITE 2 AD3 6 ARG A 456 HOH A 805 CRYST1 48.318 79.816 124.780 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 0.020696 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012529 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008014 0.00000