HEADER TRANSFERASE 16-SEP-15 5DRY
TITLE CRYSTAL STRUCTURE OF DOT1L IN COMPLEX WITH INHIBITOR CPD3 [N-(1-(2-
TITLE 2 CHLOROPHENYL)-1H-INDOL-6-YL)-2-(2-(5-(2-CHLOROPHENYL)-1H-TETRAZOL-1-
TITLE 3 YL)ACETYL)HYDRAZINECARBOXAMIDE]
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 2-333;
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, METHYLTRANSFERASE, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR C.SCHEUFLER,C.GAUL,C.BE,H.MOEBITZ
REVDAT 3 10-JAN-24 5DRY 1 LINK
REVDAT 2 07-SEP-16 5DRY 1 JRNL
REVDAT 1 15-JUN-16 5DRY 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) : 45.83
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 41500
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) : 0.178
REMARK 3 R VALUE (WORKING SET) : 0.177
REMARK 3 FREE R VALUE : 0.199
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2075
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) (%) : 99.99
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3054
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2256
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2902
REMARK 3 BIN R VALUE (WORKING SET) : 0.2243
REMARK 3 BIN FREE R VALUE : 0.2528
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.98
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 152
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 : 5110
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 74
REMARK 3 SOLVENT ATOMS : 302
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 53.33
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.24
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 5.77270
REMARK 3 B22 (A**2) : 5.77270
REMARK 3 B33 (A**2) : -11.54550
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) : 0.313
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.225
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.172
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.225
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.174
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 : 0.946
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 5321 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 7236 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 1789 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : 131 ; 2.000 ; HARMONIC
REMARK 3 GENERAL PLANES : 767 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 5321 ; 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 : 678 ; 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 : 6013 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 1.06
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.08
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.27
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): 44.2137 -8.2318 8.4957
REMARK 3 T TENSOR
REMARK 3 T11: -0.1757 T22: -0.1319
REMARK 3 T33: -0.0944 T12: -0.0062
REMARK 3 T13: -0.0397 T23: -0.0002
REMARK 3 L TENSOR
REMARK 3 L11: 3.2012 L22: 2.7435
REMARK 3 L33: 0.7450 L12: -1.6104
REMARK 3 L13: 0.3445 L23: -0.1720
REMARK 3 S TENSOR
REMARK 3 S11: -0.0107 S12: -0.2042 S13: -0.1479
REMARK 3 S21: 0.2221 S22: 0.0884 S23: -0.4272
REMARK 3 S31: -0.0795 S32: 0.1522 S33: -0.0777
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: { B|* M|* }
REMARK 3 ORIGIN FOR THE GROUP (A): 35.6781 -37.2093 8.3820
REMARK 3 T TENSOR
REMARK 3 T11: -0.1375 T22: -0.1506
REMARK 3 T33: -0.0682 T12: 0.0316
REMARK 3 T13: -0.0178 T23: 0.0411
REMARK 3 L TENSOR
REMARK 3 L11: 3.1178 L22: 2.5145
REMARK 3 L33: 0.5389 L12: -1.3245
REMARK 3 L13: -0.6853 L23: 0.1402
REMARK 3 S TENSOR
REMARK 3 S11: 0.0445 S12: -0.1145 S13: -0.2485
REMARK 3 S21: 0.0375 S22: -0.1042 S23: -0.3817
REMARK 3 S31: 0.1949 S32: 0.0491 S33: 0.0598
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5DRY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-SEP-15.
REMARK 100 THE DEPOSITION ID IS D_1000213713.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 23-MAY-13
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) : 0.99997
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 : 41501
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) : 0.09700
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.8500
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 (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 9.70
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.780
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 (%): 65.08
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.52
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2M K/NA TARTRATE 0.1M HEPES PH7.2,
REMARK 280 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 37.23000
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 37.23000
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 37.23000
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 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 PRO B 95
REMARK 465 MET B 96
REMARK 465 LYS B 97
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 GLU A 56 CG CD OE1 OE2
REMARK 470 ARG A 73 NE CZ NH1 NH2
REMARK 470 LYS A 77 CD CE NZ
REMARK 470 THR A 92 OG1 CG2
REMARK 470 ASN A 99 CG OD1 ND2
REMARK 470 GLU A 123 CG CD OE1 OE2
REMARK 470 LYS A 124 CD CE NZ
REMARK 470 ASN A 126 CG OD1 ND2
REMARK 470 ASN A 127 CG OD1 ND2
REMARK 470 TYR A 128 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 GLU A 129 CG CD OE1 OE2
REMARK 470 ILE A 190 CD1
REMARK 470 LYS A 193 CD CE NZ
REMARK 470 LYS A 212 CD CE NZ
REMARK 470 LYS A 300 CG CD CE NZ
REMARK 470 SER A 304 OG
REMARK 470 LYS B 4 CG CD CE NZ
REMARK 470 LYS B 29 CD CE NZ
REMARK 470 LYS B 66 CE NZ
REMARK 470 LEU B 98 CG CD1 CD2
REMARK 470 LYS B 124 CG CD CE NZ
REMARK 470 ASN B 126 CG OD1 ND2
REMARK 470 ASN B 127 CG OD1 ND2
REMARK 470 TYR B 128 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 GLU B 129 CG CD OE1 OE2
REMARK 470 LYS B 180 CD CE NZ
REMARK 470 LYS B 193 CD CE NZ
REMARK 470 LYS B 207 CD CE NZ
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 LYS B 300 CG CD CE NZ
REMARK 470 VAL B 303 CG1 CG2
REMARK 470 SER B 304 OG
REMARK 470 LYS B 330 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 ASN A 126 80.54 -67.84
REMARK 500 LYS A 152 70.51 52.87
REMARK 500 ASN B 126 80.31 -67.98
REMARK 500 THR B 306 19.99 -141.65
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 A 401 K
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 MET A 55 O
REMARK 620 2 HOH A 591 O 68.9
REMARK 620 3 HOH A 614 O 165.6 97.6
REMARK 620 N 1 2
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 83.5
REMARK 620 3 MET B 55 O 84.2 90.4
REMARK 620 4 HOH B1222 O 132.1 140.6 79.2
REMARK 620 5 HOH B1230 O 70.3 106.0 147.4 102.8
REMARK 620 N 1 2 3 4
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 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 5EK A 402
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 5EK B 1002
DBREF 5DRY A 2 333 UNP Q8TEK3 DOT1L_HUMAN 2 333
DBREF 5DRY B 2 333 UNP Q8TEK3 DOT1L_HUMAN 2 333
SEQADV 5DRY GLY A 0 UNP Q8TEK3 EXPRESSION TAG
SEQADV 5DRY PRO A 1 UNP Q8TEK3 EXPRESSION TAG
SEQADV 5DRY GLY A 333 UNP Q8TEK3 LYS 333 CLONING ARTIFACT
SEQADV 5DRY GLY B 0 UNP Q8TEK3 EXPRESSION TAG
SEQADV 5DRY PRO B 1 UNP Q8TEK3 EXPRESSION TAG
SEQADV 5DRY GLY B 333 UNP Q8TEK3 LYS 333 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 A 401 1
HET 5EK A 402 36
HET K B1001 1
HET 5EK B1002 36
HETNAM K POTASSIUM ION
HETNAM 5EK N-[1-(2-CHLOROPHENYL)-1H-INDOL-6-YL]-2-{[5-(2-
HETNAM 2 5EK CHLOROPHENYL)-1H-TETRAZOL-1-
HETNAM 3 5EK YL]ACETYL}HYDRAZINECARBOXAMIDE
FORMUL 3 K 2(K 1+)
FORMUL 4 5EK 2(C24 H18 CL2 N8 O2)
FORMUL 7 HOH *302(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 ASN A 57 ILE A 61 5 5
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 GLU A 134 5 3
HELIX 7 AA7 VAL A 135 SER A 140 1 6
HELIX 8 AA8 SER A 140 LYS A 152 1 13
HELIX 9 AA9 GLY A 167 THR A 177 1 11
HELIX 10 AB1 ALA A 188 GLY A 210 1 23
HELIX 11 AB2 SER A 225 ASN A 234 1 10
HELIX 12 AB3 GLY A 246 ALA A 258 1 13
HELIX 13 AB4 ASP A 286 THR A 289 5 4
HELIX 14 AB5 ARG A 319 ASN A 331 1 13
HELIX 15 AB6 ASP B 32 ILE B 48 1 17
HELIX 16 AB7 ILE B 48 MET B 55 1 8
HELIX 17 AB8 GLU B 56 ILE B 61 5 6
HELIX 18 AB9 SER B 67 GLY B 91 1 25
HELIX 19 AC1 SER B 103 VAL B 119 1 17
HELIX 20 AC2 SER B 132 GLU B 134 5 3
HELIX 21 AC3 VAL B 135 SER B 140 1 6
HELIX 22 AC4 SER B 140 ILE B 151 1 12
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 ASP B 286 THR B 289 5 4
HELIX 28 AD1 ARG B 319 LYS B 330 1 12
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 PHE A 159 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 7 TYR B 216 ARG B 220 0
SHEET 2 AA4 7 HIS B 181 GLU B 186 1 N GLY B 184 O GLU B 219
SHEET 3 AA4 7 LEU B 158 LEU B 162 1 N ASP B 161 O TYR B 183
SHEET 4 AA4 7 VAL B 237 VAL B 240 1 O PHE B 239 N VAL B 160
SHEET 5 AA4 7 ARG B 265 SER B 268 1 O VAL B 267 N ILE B 238
SHEET 6 AA4 7 TYR B 312 ILE B 317 -1 O HIS B 315 N ILE B 266
SHEET 7 AA4 7 MET B 291 LEU B 296 -1 N LEU B 296 O TYR B 312
LINK O MET A 55 K K A 401 1555 1555 2.74
LINK K K A 401 O HOH A 591 1555 1555 2.82
LINK K K A 401 O HOH A 614 1555 1555 2.46
LINK O LYS B 52 K K B1001 1555 1555 2.55
LINK O LEU B 53 K K B1001 1555 1555 2.92
LINK O MET B 55 K K B1001 1555 1555 2.81
LINK K K B1001 O HOH B1222 1555 1555 3.35
LINK K K B1001 O HOH B1230 1555 1555 3.31
CISPEP 1 TRP A 22 PRO A 23 0 1.27
CISPEP 2 TRP B 22 PRO B 23 0 -0.02
SITE 1 AC1 5 LEU A 53 MET A 55 ASN A 57 HOH A 591
SITE 2 AC1 5 HOH A 614
SITE 1 AC2 18 PHE A 131 PRO A 133 TYR A 136 SER A 140
SITE 2 AC2 18 LEU A 143 VAL A 144 MET A 147 ASP A 161
SITE 3 AC2 18 GLY A 163 SER A 164 GLY A 165 VAL A 166
SITE 4 AC2 18 GLN A 168 VAL A 240 ASN A 241 VAL A 267
SITE 5 AC2 18 SER A 268 HOH A 516
SITE 1 AC3 4 LYS B 52 LEU B 53 MET B 55 ASN B 57
SITE 1 AC4 20 PHE B 131 PRO B 133 TYR B 136 SER B 140
SITE 2 AC4 20 LEU B 143 VAL B 144 MET B 147 ASP B 161
SITE 3 AC4 20 GLY B 163 SER B 164 GLY B 165 VAL B 166
SITE 4 AC4 20 GLN B 168 PHE B 239 VAL B 240 ASN B 241
SITE 5 AC4 20 VAL B 267 SER B 268 SER B 269 HOH B1143
CRYST1 158.760 158.760 74.460 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 0.006299 0.003637 0.000000 0.00000
SCALE2 0.000000 0.007273 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013430 0.00000