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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
