HEADER TRANSFERASE/TRANSFERASE INHIBITOR 19-JUN-19 6PDO
TITLE HUMAN PIM1 BOUND TO BENZOTHIOPHENE INHIBITOR 354
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PIM-1;
COMPND 3 CHAIN: A;
COMPND 4 EC: 2.7.11.1;
COMPND 5 ENGINEERED: YES;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: PEPTIDE;
COMPND 8 CHAIN: B;
COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: PIM1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 MOL_ID: 2;
SOURCE 9 SYNTHETIC: YES;
SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 11 ORGANISM_TAXID: 32630
KEYWDS PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1, STRUCTURAL
KEYWDS 2 GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, TRANSFERASE,
KEYWDS 3 TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR P.H.C.GODOI,A.S.SANTIAGO,A.M.FALA,P.Z.RAMOS,D.SRIRANGANADANE,
AUTHOR 2 A.MASCARELLO,N.SEGRETTI,H.AZEVEDO,C.R.W.GUIMARAES,P.ARRUDA,
AUTHOR 3 J.M.ELKINS,R.M.COUNAGO,STRUCTURAL GENOMICS CONSORTIUM (SGC)
REVDAT 3 13-MAR-24 6PDO 1 REMARK
REVDAT 2 01-JAN-20 6PDO 1 REMARK
REVDAT 1 24-JUL-19 6PDO 0
JRNL AUTH P.H.C.GODOI,A.S.SANTIAGO,A.M.FALA,P.Z.RAMOS,
JRNL AUTH 2 D.SRIRANGANADANE,A.MASCARELLO,N.SEGRETTI,H.AZEVEDO,
JRNL AUTH 3 C.R.W.GUIMARAES,P.ARRUDA,J.M.ELKINS,R.M.COUNAGO
JRNL TITL HUMAN PIM1
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 2.40 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0238
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) : 2.40
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.97
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 15682
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) : 0.177
REMARK 3 R VALUE (WORKING SET) : 0.175
REMARK 3 FREE R VALUE : 0.223
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400
REMARK 3 FREE R VALUE TEST SET COUNT : 725
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) : 2.40
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1155
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92
REMARK 3 BIN R VALUE (WORKING SET) : 0.3050
REMARK 3 BIN FREE R VALUE SET COUNT : 43
REMARK 3 BIN FREE R VALUE : 0.2690
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2232
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 24
REMARK 3 SOLVENT ATOMS : 54
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.07
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.27000
REMARK 3 B22 (A**2) : 2.27000
REMARK 3 B33 (A**2) : -7.36000
REMARK 3 B12 (A**2) : 1.13000
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): 0.257
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.209
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.176
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.163
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2325 ; 0.004 ; 0.013
REMARK 3 BOND LENGTHS OTHERS (A): 2128 ; 0.001 ; 0.017
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3156 ; 1.225 ; 1.639
REMARK 3 BOND ANGLES OTHERS (DEGREES): 4903 ; 1.138 ; 1.578
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 274 ; 6.129 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 144 ;27.284 ;20.347
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 381 ;13.834 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;15.977 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 283 ; 0.052 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2620 ; 0.004 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 544 ; 0.001 ; 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): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
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 : 4
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 35 A 89
REMARK 3 ORIGIN FOR THE GROUP (A): -22.4800 28.9960 8.1590
REMARK 3 T TENSOR
REMARK 3 T11: 0.1546 T22: 0.1035
REMARK 3 T33: 0.0659 T12: -0.0775
REMARK 3 T13: -0.0888 T23: 0.0309
REMARK 3 L TENSOR
REMARK 3 L11: 1.1153 L22: 3.4176
REMARK 3 L33: 0.6923 L12: 0.6053
REMARK 3 L13: -0.3956 L23: 0.5517
REMARK 3 S TENSOR
REMARK 3 S11: 0.1995 S12: -0.0319 S13: -0.1478
REMARK 3 S21: 0.0238 S22: -0.2121 S23: 0.1566
REMARK 3 S31: 0.1127 S32: -0.1835 S33: 0.0126
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 90 A 124
REMARK 3 ORIGIN FOR THE GROUP (A): -19.2720 33.7150 11.0480
REMARK 3 T TENSOR
REMARK 3 T11: 0.1985 T22: 0.1442
REMARK 3 T33: 0.0272 T12: -0.0696
REMARK 3 T13: 0.0272 T23: 0.0095
REMARK 3 L TENSOR
REMARK 3 L11: 0.3909 L22: 2.0361
REMARK 3 L33: 1.8715 L12: -0.4173
REMARK 3 L13: 0.5051 L23: -0.4331
REMARK 3 S TENSOR
REMARK 3 S11: 0.1735 S12: -0.0631 S13: 0.0018
REMARK 3 S21: 0.1235 S22: -0.1914 S23: 0.1448
REMARK 3 S31: -0.0335 S32: -0.1480 S33: 0.0179
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 125 A 305
REMARK 3 ORIGIN FOR THE GROUP (A): -2.8140 43.7300 -1.7310
REMARK 3 T TENSOR
REMARK 3 T11: 0.0479 T22: 0.0702
REMARK 3 T33: 0.0078 T12: 0.0140
REMARK 3 T13: -0.0144 T23: -0.0061
REMARK 3 L TENSOR
REMARK 3 L11: 0.6719 L22: 0.7105
REMARK 3 L33: 1.0678 L12: -0.0032
REMARK 3 L13: -0.0485 L23: -0.1866
REMARK 3 S TENSOR
REMARK 3 S11: 0.0332 S12: -0.0016 S13: -0.0194
REMARK 3 S21: -0.0634 S22: 0.0275 S23: 0.0148
REMARK 3 S31: 0.0154 S32: 0.0230 S33: -0.0607
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : B 2 B 9
REMARK 3 ORIGIN FOR THE GROUP (A): -8.2470 35.2840 -13.4730
REMARK 3 T TENSOR
REMARK 3 T11: 0.3914 T22: 0.3470
REMARK 3 T33: 0.0724 T12: -0.1175
REMARK 3 T13: -0.0871 T23: 0.1263
REMARK 3 L TENSOR
REMARK 3 L11: 2.5353 L22: 1.3744
REMARK 3 L33: 3.5770 L12: 1.6367
REMARK 3 L13: -1.0934 L23: -1.0238
REMARK 3 S TENSOR
REMARK 3 S11: 0.0867 S12: 0.6271 S13: 0.1018
REMARK 3 S21: -0.1317 S22: 0.2962 S23: 0.0183
REMARK 3 S31: 1.0228 S32: -0.8126 S33: -0.3829
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 U VALUES : WITH TLS ADDED
REMARK 4
REMARK 4 6PDO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUN-19.
REMARK 100 THE DEPOSITION ID IS D_1000242371.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 28-FEB-19
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I03
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20190315
REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16433
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400
REMARK 200 RESOLUTION RANGE LOW (A) : 19.970
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 20.40
REMARK 200 R MERGE (I) : 0.09800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : 20.70
REMARK 200 R MERGE FOR SHELL (I) : 1.30300
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: PHASER 2.8.2
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 56.98
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.1 M HEPES PH7.5, 0.2 M
REMARK 280 MAGNESIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
REMARK 280 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+1/6
REMARK 290 6555 X-Y,X,Z+5/6
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.23933
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.61967
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.92950
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 13.30983
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 66.54917
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1040 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 12950 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 3.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 SER A 0
REMARK 465 MET A 1
REMARK 465 LEU A 2
REMARK 465 LEU A 3
REMARK 465 SER A 4
REMARK 465 LYS A 5
REMARK 465 ILE A 6
REMARK 465 ASN A 7
REMARK 465 SER A 8
REMARK 465 LEU A 9
REMARK 465 ALA A 10
REMARK 465 HIS A 11
REMARK 465 LEU A 12
REMARK 465 ARG A 13
REMARK 465 ALA A 14
REMARK 465 ALA A 15
REMARK 465 PRO A 16
REMARK 465 CYS A 17
REMARK 465 ASN A 18
REMARK 465 ASP A 19
REMARK 465 LEU A 20
REMARK 465 HIS A 21
REMARK 465 ALA A 22
REMARK 465 THR A 23
REMARK 465 LYS A 24
REMARK 465 LEU A 25
REMARK 465 ALA A 26
REMARK 465 PRO A 27
REMARK 465 GLY A 28
REMARK 465 LYS A 29
REMARK 465 GLU A 30
REMARK 465 LYS A 31
REMARK 465 GLU A 32
REMARK 465 PRO A 33
REMARK 465 LEU A 34
REMARK 465 GLY A 47
REMARK 465 GLY A 48
REMARK 465 PHE A 49
REMARK 465 GLY A 50
REMARK 465 SER A 306
REMARK 465 LEU A 307
REMARK 465 SER A 308
REMARK 465 PRO A 309
REMARK 465 GLY A 310
REMARK 465 PRO A 311
REMARK 465 SER A 312
REMARK 465 ALA B 1
REMARK 465 GLY B 10
REMARK 465 PRO B 11
REMARK 465 PRO B 12
REMARK 465 THR B 13
REMARK 465 ALA B 14
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 GLN A 39 CG CD OE1 NE2
REMARK 470 SER A 46 OG
REMARK 470 SER A 75 OG
REMARK 470 GLU A 135 CG CD OE1 OE2
REMARK 470 GLN A 297 CG CD OE1 NE2
REMARK 470 ARG B 2 CG CD NE CZ NH1 NH2
REMARK 470 LYS B 3 CD CE NZ
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 SER A 97 39.36 -91.35
REMARK 500 SER A 101 30.58 -96.43
REMARK 500 ASP A 167 48.22 -144.36
REMARK 500 ASP A 186 85.20 61.89
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 OD1 A 501
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 6PCW RELATED DB: PDB
REMARK 900 1PCW CONTAINS THE SAME PROTEIN COMPLEX WITH BENZOTHIOPHENE
REMARK 900 INHIBITOR 213
REMARK 900 RELATED ID: 6PDI RELATED DB: PDB
REMARK 900 6PDI CONTAINS THE SAME PROTEIN COMPLEX WITH BENZOTHIOPHENE
REMARK 900 INHIBITOR 224
REMARK 900 RELATED ID: 6PDN RELATED DB: PDB
REMARK 900 6PDN CONTAINS THE SAME PROTEIN COMPLEX WITH BENZOTHIOPHENE
REMARK 900 INHIBITOR 292
DBREF 6PDO A 1 312 UNP P11309 PIM1_HUMAN 1 312
DBREF 6PDO B 1 14 PDB 6PDO 6PDO 1 14
SEQADV 6PDO SER A 0 UNP P11309 EXPRESSION TAG
SEQADV 6PDO GLY A 250 UNP P11309 ARG 250 CONFLICT
SEQRES 1 A 313 SER MET LEU LEU SER LYS ILE ASN SER LEU ALA HIS LEU
SEQRES 2 A 313 ARG ALA ALA PRO CYS ASN ASP LEU HIS ALA THR LYS LEU
SEQRES 3 A 313 ALA PRO GLY LYS GLU LYS GLU PRO LEU GLU SER GLN TYR
SEQRES 4 A 313 GLN VAL GLY PRO LEU LEU GLY SER GLY GLY PHE GLY SER
SEQRES 5 A 313 VAL TYR SER GLY ILE ARG VAL SER ASP ASN LEU PRO VAL
SEQRES 6 A 313 ALA ILE LYS HIS VAL GLU LYS ASP ARG ILE SER ASP TRP
SEQRES 7 A 313 GLY GLU LEU PRO ASN GLY THR ARG VAL PRO MET GLU VAL
SEQRES 8 A 313 VAL LEU LEU LYS LYS VAL SER SER GLY PHE SER GLY VAL
SEQRES 9 A 313 ILE ARG LEU LEU ASP TRP PHE GLU ARG PRO ASP SER PHE
SEQRES 10 A 313 VAL LEU ILE LEU GLU ARG PRO GLU PRO VAL GLN ASP LEU
SEQRES 11 A 313 PHE ASP PHE ILE THR GLU ARG GLY ALA LEU GLN GLU GLU
SEQRES 12 A 313 LEU ALA ARG SER PHE PHE TRP GLN VAL LEU GLU ALA VAL
SEQRES 13 A 313 ARG HIS CYS HIS ASN CYS GLY VAL LEU HIS ARG ASP ILE
SEQRES 14 A 313 LYS ASP GLU ASN ILE LEU ILE ASP LEU ASN ARG GLY GLU
SEQRES 15 A 313 LEU LYS LEU ILE ASP PHE GLY SER GLY ALA LEU LEU LYS
SEQRES 16 A 313 ASP THR VAL TYR THR ASP PHE ASP GLY THR ARG VAL TYR
SEQRES 17 A 313 SER PRO PRO GLU TRP ILE ARG TYR HIS ARG TYR HIS GLY
SEQRES 18 A 313 ARG SER ALA ALA VAL TRP SER LEU GLY ILE LEU LEU TYR
SEQRES 19 A 313 ASP MET VAL CYS GLY ASP ILE PRO PHE GLU HIS ASP GLU
SEQRES 20 A 313 GLU ILE ILE GLY GLY GLN VAL PHE PHE ARG GLN ARG VAL
SEQRES 21 A 313 SER SER GLU CYS GLN HIS LEU ILE ARG TRP CYS LEU ALA
SEQRES 22 A 313 LEU ARG PRO SER ASP ARG PRO THR PHE GLU GLU ILE GLN
SEQRES 23 A 313 ASN HIS PRO TRP MET GLN ASP VAL LEU LEU PRO GLN GLU
SEQRES 24 A 313 THR ALA GLU ILE HIS LEU HIS SER LEU SER PRO GLY PRO
SEQRES 25 A 313 SER
SEQRES 1 B 14 ALA ARG LYS ARG ARG ARG HIS PRO SER GLY PRO PRO THR
SEQRES 2 B 14 ALA
HET OD1 A 501 24
HETNAM OD1 4-{5-[(3-AMINOPROPYL)CARBAMOYL]THIOPHEN-2-YL}-1-
HETNAM 2 OD1 BENZOTHIOPHENE-2-CARBOXAMIDE
FORMUL 3 OD1 C17 H17 N3 O2 S2
FORMUL 4 HOH *54(H2 O)
HELIX 1 AA1 ASP A 72 ILE A 74 5 3
HELIX 2 AA2 MET A 88 SER A 97 1 10
HELIX 3 AA3 LEU A 129 GLY A 137 1 9
HELIX 4 AA4 GLN A 140 CYS A 161 1 22
HELIX 5 AA5 LYS A 169 GLU A 171 5 3
HELIX 6 AA6 THR A 204 SER A 208 5 5
HELIX 7 AA7 PRO A 209 HIS A 216 1 8
HELIX 8 AA8 HIS A 219 GLY A 238 1 20
HELIX 9 AA9 HIS A 244 GLY A 251 1 8
HELIX 10 AB1 SER A 260 LEU A 271 1 12
HELIX 11 AB2 ARG A 274 ARG A 278 5 5
HELIX 12 AB3 THR A 280 ASN A 286 1 7
HELIX 13 AB4 HIS A 287 GLN A 291 5 5
HELIX 14 AB5 LEU A 295 LEU A 304 1 10
SHEET 1 AA1 5 TYR A 38 GLY A 45 0
SHEET 2 AA1 5 VAL A 52 ARG A 57 -1 O SER A 54 N GLY A 41
SHEET 3 AA1 5 LEU A 62 GLU A 70 -1 O LEU A 62 N ARG A 57
SHEET 4 AA1 5 SER A 115 GLU A 121 -1 O LEU A 118 N LYS A 67
SHEET 5 AA1 5 LEU A 106 GLU A 111 -1 N ASP A 108 O ILE A 119
SHEET 1 AA2 2 TRP A 77 GLU A 79 0
SHEET 2 AA2 2 ARG A 85 PRO A 87 -1 O VAL A 86 N GLY A 78
SHEET 1 AA3 3 VAL A 126 ASP A 128 0
SHEET 2 AA3 3 ILE A 173 ASP A 176 -1 O ILE A 175 N GLN A 127
SHEET 3 AA3 3 GLU A 181 LEU A 184 -1 O LYS A 183 N LEU A 174
SHEET 1 AA4 2 VAL A 163 LEU A 164 0
SHEET 2 AA4 2 ALA A 191 LEU A 192 -1 O ALA A 191 N LEU A 164
CISPEP 1 GLU A 124 PRO A 125 0 2.35
SITE 1 AC1 8 ALA A 65 LYS A 67 GLU A 121 ASP A 131
SITE 2 AC1 8 LEU A 174 ILE A 185 ASP A 186 HOH A 629
CRYST1 96.034 96.034 79.859 90.00 90.00 120.00 P 65 6
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 0.010413 0.006012 0.000000 0.00000
SCALE2 0.000000 0.012024 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012522 0.00000