HEADER PROTEIN BINDING/INHIBITOR 20-AUG-15 5DB2 TITLE MENIN IN COMPLEX WITH MI-389 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MENIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-459, 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 5DB2 1 COMPND HETNAM REVDAT 3 04-DEC-19 5DB2 1 REMARK REVDAT 2 27-SEP-17 5DB2 1 JRNL REMARK REVDAT 1 30-MAR-16 5DB2 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. 1.54 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) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 69365 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3687 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) : 1.54 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.58 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5059 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE SET COUNT : 261 REMARK 3 BIN FREE R VALUE : 0.2260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3618 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 94 REMARK 3 SOLVENT ATOMS : 495 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.38000 REMARK 3 B22 (A**2) : 0.34000 REMARK 3 B33 (A**2) : -0.72000 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): 0.071 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.073 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 : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3840 ; 0.017 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3606 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5219 ; 1.780 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8267 ; 3.626 ; 3.006 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 475 ; 5.629 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 167 ;31.170 ;24.012 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 614 ;11.506 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;17.527 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 585 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4318 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 883 ; 0.020 ; 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): 1889 ; 1.394 ; 1.281 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1887 ; 1.392 ; 1.282 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2359 ; 2.193 ; 1.915 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 5DB2 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_1000212845. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-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 : 73171 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.65800 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 (%): 45.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 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 24.54300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.21400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.98800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.21400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.54300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.98800 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 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 LYS A 4 CE NZ REMARK 470 GLU A 30 CG CD OE1 OE2 REMARK 470 ARG A 98 CD NE CZ NH1 NH2 REMARK 470 GLU A 109 CG CD OE1 OE2 REMARK 470 ARG A 131 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 136 CG OD1 OD2 REMARK 470 ARG A 137 CZ NH1 NH2 REMARK 470 LYS A 151 CE NZ REMARK 470 ARG A 171 NE CZ NH1 NH2 REMARK 470 LYS A 201 CG CD CE NZ REMARK 470 GLU A 204 CG CD OE1 OE2 REMARK 470 LEU A 249 CG CD1 CD2 REMARK 470 ARG A 332 CZ NH1 NH2 REMARK 470 ARG A 355 NE CZ NH1 NH2 REMARK 470 GLU A 448 OE1 OE2 REMARK 470 ARG A 456 CG CD NE CZ NH1 NH2 REMARK 470 GLY A 548 N CA REMARK 470 LYS A 562 CD CE NZ REMARK 470 LYS A 569 CG CD CE NZ REMARK 470 LYS A 576 CD CE NZ REMARK 470 GLN A 586 CG CD OE1 NE2 REMARK 470 LYS A 588 CG CD CE NZ REMARK 470 LYS A 589 CA C O CB CG CD CE REMARK 470 LYS A 589 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 NH1 ARG A 335 O HOH A 701 2.07 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 -58.58 -159.32 REMARK 500 SER A 178 -165.84 -100.95 REMARK 500 ASP A 180 13.17 -144.57 REMARK 500 ASN A 189 15.73 58.54 REMARK 500 SER A 226 44.95 -92.39 REMARK 500 GLU A 356 -0.53 85.27 REMARK 500 ASP A 370 -56.40 -135.12 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 58R 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 PG4 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 SO4 A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS 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 PEG A 611 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DB1 RELATED DB: PDB REMARK 900 RELATED ID: 5DB0 RELATED DB: PDB REMARK 900 RELATED ID: 5DB3 RELATED DB: PDB DBREF 5DB2 A 1 459 UNP O00255 MEN1_HUMAN 1 459 DBREF 5DB2 A 537 593 UNP O00255 MEN1_HUMAN 537 593 SEQADV 5DB2 GLY A -4 UNP O00255 EXPRESSION TAG SEQADV 5DB2 GLY A -3 UNP O00255 EXPRESSION TAG SEQADV 5DB2 SER A -2 UNP O00255 EXPRESSION TAG SEQADV 5DB2 SER A -1 UNP O00255 EXPRESSION TAG SEQADV 5DB2 SER A 0 UNP O00255 EXPRESSION TAG SEQADV 5DB2 A UNP O00255 ILE 54 DELETION SEQADV 5DB2 A UNP O00255 PRO 55 DELETION SEQADV 5DB2 A UNP O00255 THR 56 DELETION SEQADV 5DB2 A UNP O00255 ASN 57 DELETION SEQADV 5DB2 A UNP O00255 VAL 58 DELETION SEQADV 5DB2 A UNP O00255 PRO 59 DELETION SEQADV 5DB2 A UNP O00255 GLU 60 DELETION SEQADV 5DB2 A UNP O00255 LEU 61 DELETION SEQADV 5DB2 A UNP O00255 THR 62 DELETION SEQADV 5DB2 A UNP O00255 PHE 63 DELETION SEQADV 5DB2 A UNP O00255 GLN 64 DELETION SEQADV 5DB2 A UNP O00255 PRO 65 DELETION SEQADV 5DB2 A UNP O00255 SER 66 DELETION SEQADV 5DB2 A UNP O00255 PRO 67 DELETION SEQADV 5DB2 A UNP O00255 ALA 68 DELETION SEQADV 5DB2 A UNP O00255 PRO 69 DELETION SEQADV 5DB2 A UNP O00255 ASP 70 DELETION SEQADV 5DB2 A UNP O00255 PRO 71 DELETION SEQADV 5DB2 A UNP O00255 PRO 72 DELETION SEQADV 5DB2 A UNP O00255 GLY 73 DELETION SEQADV 5DB2 A UNP O00255 GLU 387 DELETION SEQADV 5DB2 A UNP O00255 GLU 388 DELETION SEQADV 5DB2 A UNP O00255 ARG 389 DELETION SEQADV 5DB2 A UNP O00255 PRO 390 DELETION SEQADV 5DB2 A UNP O00255 GLY 391 DELETION SEQADV 5DB2 A UNP O00255 GLU 392 DELETION SEQADV 5DB2 A UNP O00255 GLN 393 DELETION SEQADV 5DB2 A UNP O00255 SER 394 DELETION SEQADV 5DB2 A UNP O00255 GLN 395 DELETION SEQADV 5DB2 A UNP O00255 GLY 396 DELETION SEQADV 5DB2 A UNP O00255 THR 397 DELETION SEQADV 5DB2 A UNP O00255 GLN 398 DELETION SEQADV 5DB2 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 58R A 601 37 HET DMS A 602 4 HET PG4 A 603 13 HET SO4 A 604 5 HET SO4 A 605 5 HET SO4 A 606 5 HET SO4 A 607 5 HET SO4 A 608 5 HET DMS A 609 4 HET DMS A 610 4 HET PEG A 611 7 HETNAM 58R 2-{2-CYANO-5-[(4-{[6-(2,2,2-TRIFLUOROETHYL)THIENO[2,3- HETNAM 2 58R D]PYRIMIDIN-4-YL]AMINO}PIPERIDIN-1-YL)METHYL]-1H- HETNAM 3 58R INDOL-1-YL}ACETA MIDE HETNAM DMS DIMETHYL SULFOXIDE HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM SO4 SULFATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN 58R MI-389 FORMUL 2 58R C25 H24 F3 N7 O S FORMUL 3 DMS 3(C2 H6 O S) FORMUL 4 PG4 C8 H18 O5 FORMUL 5 SO4 5(O4 S 2-) FORMUL 12 PEG C4 H10 O3 FORMUL 13 HOH *495(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 GLY A 2 LEU A 3 0 -3.29 CISPEP 2 PHE A 11 PRO A 12 0 2.46 SITE 1 AC1 20 SER A 155 LEU A 177 SER A 178 ASP A 180 SITE 2 AC1 20 HIS A 181 ALA A 182 PHE A 238 TYR A 276 SITE 3 AC1 20 MET A 278 TYR A 319 MET A 322 TYR A 323 SITE 4 AC1 20 GLY A 326 TRP A 341 GLU A 363 GLU A 366 SITE 5 AC1 20 DMS A 602 HOH A 909 HOH A1022 HOH A1051 SITE 1 AC2 4 SER A 155 58R A 601 HOH A 942 HOH A 965 SITE 1 AC3 7 LEU A 75 THR A 76 TYR A 361 PHE A 365 SITE 2 AC3 7 HOH A 706 HOH A 800 HOH A 962 SITE 1 AC4 2 ARG A 14 HOH A 920 SITE 1 AC5 3 TYR A 133 PHE A 134 ARG A 137 SITE 1 AC6 6 ARG A 332 VAL A 334 ARG A 335 GLY A 401 SITE 2 AC6 6 ALA A 403 HOH A 831 SITE 1 AC7 1 ARG A 21 SITE 1 AC8 2 ARG A 446 HOH A 738 SITE 1 AC9 6 PHE A 43 PHE A 47 GLY A 386 GLN A 400 SITE 2 AC9 6 HOH A 973 HOH A1040 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 2 LYS A 135 TRP A 198 CRYST1 49.086 79.976 124.428 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 0.020372 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012504 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008037 0.00000