HEADER TRANSFERASE 17-SEP-15 5DSX TITLE CRYSTAL STRUCTURE OF DOT1L IN COMPLEX WITH INHIBITOR CPD10 [6'-CHLORO- TITLE 2 1,4-DIMETHYL-5'-(2-METHYL-6-((4-(METHYLAMINO)PYRIMIDIN-2-YL)AMINO)- TITLE 3 1H-INDOL-1-YL)-[3,3'-BIPYRIDIN]-2(1H)-ONE] COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 2-332; COMPND 5 SYNONYM: DOT1-LIKE PROTEIN,HISTONE H3-K79 METHYLTRANSFERASE,H3-K79- COMPND 6 HMTASE,LYSINE N-METHYLTRANSFERASE 4; COMPND 7 EC: 2.1.1.43; COMPND 8 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: DOT1L, KIAA1814, KMT4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, COMPLEX, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.SCHEUFLER,C.GAUL,C.BE,H.MOEBITZ REVDAT 3 10-JAN-24 5DSX 1 REMARK REVDAT 2 07-SEP-16 5DSX 1 JRNL REVDAT 1 15-JUN-16 5DSX 0 JRNL AUTH C.CHEN,H.ZHU,F.STAUFFER,G.CARAVATTI,S.VOLLMER,R.MACHAUER, JRNL AUTH 2 P.HOLZER,H.MOBITZ,C.SCHEUFLER,M.KLUMPP,R.TIEDT,K.S.BEYER, JRNL AUTH 3 K.CALKINS,D.GUTHY,M.KIFFE,J.ZHANG,C.GAUL JRNL TITL DISCOVERY OF NOVEL DOT1L INHIBITORS THROUGH A JRNL TITL 2 STRUCTURE-BASED FRAGMENTATION APPROACH. JRNL REF ACS MED.CHEM.LETT. V. 7 735 2016 JRNL REFN ISSN 1948-5875 JRNL PMID 27563395 JRNL DOI 10.1021/ACSMEDCHEMLETT.6B00167 REMARK 2 REMARK 2 RESOLUTION. 2.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.5 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 40936 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2047 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.41 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.47 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.98 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3004 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2147 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2854 REMARK 3 BIN R VALUE (WORKING SET) : 0.2123 REMARK 3 BIN FREE R VALUE : 0.2623 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.99 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 150 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5050 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 198 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.91790 REMARK 3 B22 (A**2) : 8.91790 REMARK 3 B33 (A**2) : -17.83570 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.339 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.210 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.171 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.215 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.175 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 5258 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 7155 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1742 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 121 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 760 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 5258 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 1 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 675 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 6100 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.05 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.99 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.35 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* L|* } REMARK 3 ORIGIN FOR THE GROUP (A): 43.9418 -7.9812 8.3859 REMARK 3 T TENSOR REMARK 3 T11: -0.2071 T22: -0.1526 REMARK 3 T33: -0.1081 T12: -0.0038 REMARK 3 T13: -0.0525 T23: -0.0059 REMARK 3 L TENSOR REMARK 3 L11: 3.8429 L22: 2.9946 REMARK 3 L33: 0.8148 L12: -1.5365 REMARK 3 L13: 0.3790 L23: -0.1759 REMARK 3 S TENSOR REMARK 3 S11: 0.0024 S12: -0.3483 S13: -0.1574 REMARK 3 S21: 0.2996 S22: 0.0835 S23: -0.5466 REMARK 3 S31: -0.0974 S32: 0.1411 S33: -0.0859 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* M|* } REMARK 3 ORIGIN FOR THE GROUP (A): 35.1942 -37.0688 8.2272 REMARK 3 T TENSOR REMARK 3 T11: -0.1396 T22: -0.1772 REMARK 3 T33: -0.0810 T12: 0.0450 REMARK 3 T13: -0.0232 T23: 0.0663 REMARK 3 L TENSOR REMARK 3 L11: 3.5337 L22: 2.3997 REMARK 3 L33: 0.5453 L12: -0.8829 REMARK 3 L13: -0.6861 L23: 0.2009 REMARK 3 S TENSOR REMARK 3 S11: 0.0203 S12: -0.0801 S13: -0.3980 REMARK 3 S21: 0.0850 S22: -0.1374 S23: -0.3927 REMARK 3 S31: 0.2345 S32: 0.0200 S33: 0.1170 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5DSX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213748. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99988 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40943 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.410 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.41 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 9.30 REMARK 200 R MERGE FOR SHELL (I) : 0.86700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1NW3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4M K/NA TARTRATE TETRAHYDRATE, 0.1M REMARK 280 HEPES PH6.8, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 0.00000 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 0.00000 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 36.99000 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 36.99000 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 36.99000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 0 REMARK 465 PRO A 1 REMARK 465 GLY A 2 REMARK 465 GLU A 3 REMARK 465 LYS A 4 REMARK 465 THR A 93 REMARK 465 GLN A 94 REMARK 465 PRO A 95 REMARK 465 MET A 96 REMARK 465 LYS A 97 REMARK 465 LEU A 98 REMARK 465 ASN A 126 REMARK 465 ASN A 127 REMARK 465 TYR A 128 REMARK 465 GLY A 301 REMARK 465 SER A 302 REMARK 465 VAL A 303 REMARK 465 GLY A 333 REMARK 465 GLY B 0 REMARK 465 PRO B 1 REMARK 465 GLY B 2 REMARK 465 GLU B 3 REMARK 465 THR B 93 REMARK 465 GLN B 94 REMARK 465 ASN B 126 REMARK 465 ASN B 127 REMARK 465 TYR B 128 REMARK 465 GLY B 301 REMARK 465 SER B 302 REMARK 465 PRO B 332 REMARK 465 GLY B 333 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 VAL A 26 CG1 CG2 REMARK 470 LYS A 29 CG CD CE NZ REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 GLU A 56 CG CD OE1 OE2 REMARK 470 LYS A 66 CD CE NZ REMARK 470 GLU A 69 CG CD OE1 OE2 REMARK 470 ARG A 73 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 77 CG CD CE NZ REMARK 470 ARG A 80 CG CD NE CZ NH1 NH2 REMARK 470 THR A 92 OG1 CG2 REMARK 470 ASN A 99 CG OD1 ND2 REMARK 470 THR A 120 OG1 CG2 REMARK 470 ASP A 121 CG OD1 OD2 REMARK 470 GLU A 123 CG CD OE1 OE2 REMARK 470 LYS A 124 CG CD CE NZ REMARK 470 GLU A 129 CG CD OE1 OE2 REMARK 470 GLU A 138 CG CD OE1 OE2 REMARK 470 ASP A 189 CG OD1 OD2 REMARK 470 LYS A 193 CE NZ REMARK 470 ARG A 278 CD NE CZ NH1 NH2 REMARK 470 LYS A 300 CG CD CE NZ REMARK 470 SER A 304 OG REMARK 470 ASN A 331 CG OD1 ND2 REMARK 470 LYS B 4 CD CE NZ REMARK 470 LYS B 29 CG CD CE NZ REMARK 470 MET B 96 CG SD CE REMARK 470 LYS B 97 CG CD CE NZ REMARK 470 GLU B 123 CG CD OE1 OE2 REMARK 470 LYS B 124 CG CD CE NZ REMARK 470 GLU B 129 CG CD OE1 OE2 REMARK 470 GLU B 134 CG CD OE1 OE2 REMARK 470 GLU B 138 CG CD OE1 OE2 REMARK 470 LYS B 180 CD CE NZ REMARK 470 GLU B 248 CG CD OE1 OE2 REMARK 470 LYS B 261 CE NZ REMARK 470 ARG B 278 CG CD NE CZ NH1 NH2 REMARK 470 SER B 281 OG REMARK 470 ARG B 282 CG CD NE CZ NH1 NH2 REMARK 470 VAL B 303 CG1 CG2 REMARK 470 SER B 304 OG REMARK 470 LYS B 330 CG CD CE NZ REMARK 470 ASN B 331 CG OD1 ND2 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 27 -162.72 -103.55 REMARK 500 LYS A 29 -34.94 -39.91 REMARK 500 ILE A 61 -62.87 -107.93 REMARK 500 ASP A 121 77.28 49.56 REMARK 500 THR A 139 -41.74 -135.11 REMARK 500 LYS B 97 2.63 -66.95 REMARK 500 THR B 139 -42.74 -134.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A1001 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 52 O REMARK 620 2 LEU A 53 O 68.4 REMARK 620 3 MET A 55 O 70.8 81.3 REMARK 620 4 ASN A 57 OD1 132.4 158.4 99.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B1001 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS B 52 O REMARK 620 2 LEU B 53 O 81.3 REMARK 620 3 MET B 55 O 84.5 91.1 REMARK 620 4 ASN B 57 OD1 126.9 151.7 90.1 REMARK 620 5 HOH B1175 O 72.9 109.1 146.5 84.4 REMARK 620 6 HOH B1179 O 150.8 77.5 76.2 75.4 133.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5EW A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5EW B 1002 DBREF 5DSX A 2 332 UNP Q8TEK3 DOT1L_HUMAN 2 332 DBREF 5DSX B 2 332 UNP Q8TEK3 DOT1L_HUMAN 2 332 SEQADV 5DSX GLY A 0 UNP Q8TEK3 EXPRESSION TAG SEQADV 5DSX PRO A 1 UNP Q8TEK3 EXPRESSION TAG SEQADV 5DSX GLY A 333 UNP Q8TEK3 CLONING ARTIFACT SEQADV 5DSX GLY B 0 UNP Q8TEK3 EXPRESSION TAG SEQADV 5DSX PRO B 1 UNP Q8TEK3 EXPRESSION TAG SEQADV 5DSX GLY B 333 UNP Q8TEK3 CLONING ARTIFACT SEQRES 1 A 334 GLY PRO GLY GLU LYS LEU GLU LEU ARG LEU LYS SER PRO SEQRES 2 A 334 VAL GLY ALA GLU PRO ALA VAL TYR PRO TRP PRO LEU PRO SEQRES 3 A 334 VAL TYR ASP LYS HIS HIS ASP ALA ALA HIS GLU ILE ILE SEQRES 4 A 334 GLU THR ILE ARG TRP VAL CYS GLU GLU ILE PRO ASP LEU SEQRES 5 A 334 LYS LEU ALA MET GLU ASN TYR VAL LEU ILE ASP TYR ASP SEQRES 6 A 334 THR LYS SER PHE GLU SER MET GLN ARG LEU CYS ASP LYS SEQRES 7 A 334 TYR ASN ARG ALA ILE ASP SER ILE HIS GLN LEU TRP LYS SEQRES 8 A 334 GLY THR THR GLN PRO MET LYS LEU ASN THR ARG PRO SER SEQRES 9 A 334 THR GLY LEU LEU ARG HIS ILE LEU GLN GLN VAL TYR ASN SEQRES 10 A 334 HIS SER VAL THR ASP PRO GLU LYS LEU ASN ASN TYR GLU SEQRES 11 A 334 PRO PHE SER PRO GLU VAL TYR GLY GLU THR SER PHE ASP SEQRES 12 A 334 LEU VAL ALA GLN MET ILE ASP GLU ILE LYS MET THR ASP SEQRES 13 A 334 ASP ASP LEU PHE VAL ASP LEU GLY SER GLY VAL GLY GLN SEQRES 14 A 334 VAL VAL LEU GLN VAL ALA ALA ALA THR ASN CYS LYS HIS SEQRES 15 A 334 HIS TYR GLY VAL GLU LYS ALA ASP ILE PRO ALA LYS TYR SEQRES 16 A 334 ALA GLU THR MET ASP ARG GLU PHE ARG LYS TRP MET LYS SEQRES 17 A 334 TRP TYR GLY LYS LYS HIS ALA GLU TYR THR LEU GLU ARG SEQRES 18 A 334 GLY ASP PHE LEU SER GLU GLU TRP ARG GLU ARG ILE ALA SEQRES 19 A 334 ASN THR SER VAL ILE PHE VAL ASN ASN PHE ALA PHE GLY SEQRES 20 A 334 PRO GLU VAL ASP HIS GLN LEU LYS GLU ARG PHE ALA ASN SEQRES 21 A 334 MET LYS GLU GLY GLY ARG ILE VAL SER SER LYS PRO PHE SEQRES 22 A 334 ALA PRO LEU ASN PHE ARG ILE ASN SER ARG ASN LEU SER SEQRES 23 A 334 ASP ILE GLY THR ILE MET ARG VAL VAL GLU LEU SER PRO SEQRES 24 A 334 LEU LYS GLY SER VAL SER TRP THR GLY LYS PRO VAL SER SEQRES 25 A 334 TYR TYR LEU HIS THR ILE ASP ARG THR ILE LEU GLU ASN SEQRES 26 A 334 TYR PHE SER SER LEU LYS ASN PRO GLY SEQRES 1 B 334 GLY PRO GLY GLU LYS LEU GLU LEU ARG LEU LYS SER PRO SEQRES 2 B 334 VAL GLY ALA GLU PRO ALA VAL TYR PRO TRP PRO LEU PRO SEQRES 3 B 334 VAL TYR ASP LYS HIS HIS ASP ALA ALA HIS GLU ILE ILE SEQRES 4 B 334 GLU THR ILE ARG TRP VAL CYS GLU GLU ILE PRO ASP LEU SEQRES 5 B 334 LYS LEU ALA MET GLU ASN TYR VAL LEU ILE ASP TYR ASP SEQRES 6 B 334 THR LYS SER PHE GLU SER MET GLN ARG LEU CYS ASP LYS SEQRES 7 B 334 TYR ASN ARG ALA ILE ASP SER ILE HIS GLN LEU TRP LYS SEQRES 8 B 334 GLY THR THR GLN PRO MET LYS LEU ASN THR ARG PRO SER SEQRES 9 B 334 THR GLY LEU LEU ARG HIS ILE LEU GLN GLN VAL TYR ASN SEQRES 10 B 334 HIS SER VAL THR ASP PRO GLU LYS LEU ASN ASN TYR GLU SEQRES 11 B 334 PRO PHE SER PRO GLU VAL TYR GLY GLU THR SER PHE ASP SEQRES 12 B 334 LEU VAL ALA GLN MET ILE ASP GLU ILE LYS MET THR ASP SEQRES 13 B 334 ASP ASP LEU PHE VAL ASP LEU GLY SER GLY VAL GLY GLN SEQRES 14 B 334 VAL VAL LEU GLN VAL ALA ALA ALA THR ASN CYS LYS HIS SEQRES 15 B 334 HIS TYR GLY VAL GLU LYS ALA ASP ILE PRO ALA LYS TYR SEQRES 16 B 334 ALA GLU THR MET ASP ARG GLU PHE ARG LYS TRP MET LYS SEQRES 17 B 334 TRP TYR GLY LYS LYS HIS ALA GLU TYR THR LEU GLU ARG SEQRES 18 B 334 GLY ASP PHE LEU SER GLU GLU TRP ARG GLU ARG ILE ALA SEQRES 19 B 334 ASN THR SER VAL ILE PHE VAL ASN ASN PHE ALA PHE GLY SEQRES 20 B 334 PRO GLU VAL ASP HIS GLN LEU LYS GLU ARG PHE ALA ASN SEQRES 21 B 334 MET LYS GLU GLY GLY ARG ILE VAL SER SER LYS PRO PHE SEQRES 22 B 334 ALA PRO LEU ASN PHE ARG ILE ASN SER ARG ASN LEU SER SEQRES 23 B 334 ASP ILE GLY THR ILE MET ARG VAL VAL GLU LEU SER PRO SEQRES 24 B 334 LEU LYS GLY SER VAL SER TRP THR GLY LYS PRO VAL SER SEQRES 25 B 334 TYR TYR LEU HIS THR ILE ASP ARG THR ILE LEU GLU ASN SEQRES 26 B 334 TYR PHE SER SER LEU LYS ASN PRO GLY HET K A1001 1 HET 5EW A1002 35 HET K B1001 1 HET 5EW B1002 35 HETNAM K POTASSIUM ION HETNAM 5EW 6'-CHLORO-1,4-DIMETHYL-5'-(2-METHYL-6-{[4- HETNAM 2 5EW (METHYLAMINO)PYRIMIDIN-2-YL]AMINO}-1H-INDOL-1-YL)-3, HETNAM 3 5EW 3'-BIPYRIDIN-2(1H)-ONE FORMUL 3 K 2(K 1+) FORMUL 4 5EW 2(C26 H24 CL N7 O) FORMUL 7 HOH *198(H2 O) HELIX 1 AA1 ASP A 32 ILE A 48 1 17 HELIX 2 AA2 ILE A 48 MET A 55 1 8 HELIX 3 AA3 GLU A 56 ILE A 61 5 6 HELIX 4 AA4 SER A 67 GLY A 91 1 25 HELIX 5 AA5 SER A 103 VAL A 119 1 17 HELIX 6 AA6 SER A 132 TYR A 136 5 5 HELIX 7 AA7 THR A 139 LYS A 152 1 14 HELIX 8 AA8 GLY A 167 THR A 177 1 11 HELIX 9 AA9 ALA A 188 GLY A 210 1 23 HELIX 10 AB1 SER A 225 ASN A 234 1 10 HELIX 11 AB2 GLY A 246 ALA A 258 1 13 HELIX 12 AB3 ASP A 286 THR A 289 5 4 HELIX 13 AB4 ARG A 319 ASN A 331 1 13 HELIX 14 AB5 ALA B 33 ILE B 48 1 16 HELIX 15 AB6 ILE B 48 MET B 55 1 8 HELIX 16 AB7 GLU B 56 ILE B 61 5 6 HELIX 17 AB8 SER B 67 THR B 92 1 26 HELIX 18 AB9 PRO B 95 ASN B 99 5 5 HELIX 19 AC1 SER B 103 VAL B 119 1 17 HELIX 20 AC2 ASP B 121 LEU B 125 5 5 HELIX 21 AC3 SER B 132 TYR B 136 5 5 HELIX 22 AC4 THR B 139 ILE B 151 1 13 HELIX 23 AC5 GLY B 167 THR B 177 1 11 HELIX 24 AC6 ALA B 188 GLY B 210 1 23 HELIX 25 AC7 SER B 225 ASN B 234 1 10 HELIX 26 AC8 GLY B 246 ALA B 258 1 13 HELIX 27 AC9 ASN B 280 LEU B 284 5 5 HELIX 28 AD1 ASP B 286 THR B 289 5 4 HELIX 29 AD2 ARG B 319 ASN B 331 1 13 SHEET 1 AA1 2 GLU A 6 LEU A 9 0 SHEET 2 AA1 2 ALA A 18 PRO A 21 -1 O TYR A 20 N LEU A 7 SHEET 1 AA2 7 TYR A 216 ARG A 220 0 SHEET 2 AA2 7 HIS A 181 GLU A 186 1 N GLY A 184 O GLU A 219 SHEET 3 AA2 7 LEU A 158 LEU A 162 1 N ASP A 161 O TYR A 183 SHEET 4 AA2 7 VAL A 237 VAL A 240 1 O PHE A 239 N VAL A 160 SHEET 5 AA2 7 ARG A 265 SER A 268 1 O VAL A 267 N ILE A 238 SHEET 6 AA2 7 TYR A 312 ILE A 317 -1 O HIS A 315 N ILE A 266 SHEET 7 AA2 7 MET A 291 LEU A 296 -1 N LEU A 296 O TYR A 312 SHEET 1 AA3 2 GLU B 6 LEU B 9 0 SHEET 2 AA3 2 ALA B 18 PRO B 21 -1 O TYR B 20 N LEU B 7 SHEET 1 AA4 2 VAL B 26 ASP B 28 0 SHEET 2 AA4 2 HIS B 31 ASP B 32 -1 O HIS B 31 N TYR B 27 SHEET 1 AA5 7 TYR B 216 ARG B 220 0 SHEET 2 AA5 7 HIS B 181 GLU B 186 1 N GLY B 184 O GLU B 219 SHEET 3 AA5 7 LEU B 158 LEU B 162 1 N PHE B 159 O TYR B 183 SHEET 4 AA5 7 VAL B 237 VAL B 240 1 O PHE B 239 N VAL B 160 SHEET 5 AA5 7 ARG B 265 SER B 268 1 O VAL B 267 N ILE B 238 SHEET 6 AA5 7 TYR B 312 ILE B 317 -1 O HIS B 315 N ILE B 266 SHEET 7 AA5 7 MET B 291 LEU B 296 -1 N LEU B 296 O TYR B 312 LINK O LYS A 52 K K A1001 1555 1555 3.06 LINK O LEU A 53 K K A1001 1555 1555 3.10 LINK O MET A 55 K K A1001 1555 1555 2.75 LINK OD1 ASN A 57 K K A1001 1555 1555 2.32 LINK O LYS B 52 K K B1001 1555 1555 2.52 LINK O LEU B 53 K K B1001 1555 1555 3.06 LINK O MET B 55 K K B1001 1555 1555 2.51 LINK OD1 ASN B 57 K K B1001 1555 1555 2.89 LINK K K B1001 O HOH B1175 1555 1555 2.91 LINK K K B1001 O HOH B1179 1555 1555 2.87 CISPEP 1 TRP A 22 PRO A 23 0 0.32 CISPEP 2 TRP B 22 PRO B 23 0 -0.07 SITE 1 AC1 4 LYS A 52 LEU A 53 MET A 55 ASN A 57 SITE 1 AC2 15 PHE A 131 SER A 140 VAL A 144 ASP A 161 SITE 2 AC2 15 SER A 164 VAL A 169 VAL A 240 ASN A 241 SITE 3 AC2 15 PHE A 243 VAL A 267 SER A 268 SER A 269 SITE 4 AC2 15 VAL A 310 SER A 311 HOH A1128 SITE 1 AC3 6 LYS B 52 LEU B 53 MET B 55 ASN B 57 SITE 2 AC3 6 HOH B1175 HOH B1179 SITE 1 AC4 16 PHE B 131 SER B 140 VAL B 144 ASP B 161 SITE 2 AC4 16 SER B 164 VAL B 169 PHE B 239 VAL B 240 SITE 3 AC4 16 ASN B 241 PHE B 243 VAL B 267 SER B 268 SITE 4 AC4 16 SER B 269 VAL B 310 SER B 311 HOH B1159 CRYST1 158.140 158.140 73.980 90.00 90.00 120.00 P 63 12 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 0.006324 0.003651 0.000000 0.00000 SCALE2 0.000000 0.007302 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013517 0.00000