HEADER OXIDOREDUCTASE/INHIBITOR 09-JAN-23 8FRV TITLE LSD1-COREST IN COMPLEX WITH T17, SHORT SOAKING COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BRAF35-HDAC COMPLEX PROTEIN BHC110,FLAVIN-CONTAINING AMINE COMPND 5 OXIDASE DOMAIN-CONTAINING PROTEIN 2,[HISTONE H3]-DIMETHYL-L-LYSINE(4) COMPND 6 FAD-DEPENDENT DEMETHYLASE 1A; COMPND 7 EC: 1.14.99.66; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: REST COREPRESSOR 1; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: PROTEIN COREST; COMPND 13 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: KDM1A, AOF2, KDM1, KIAA0601, LSD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: RCOR1, KIAA0071, RCOR; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS EPIGENETICS, HISTONE DEMETHYLASE, DRUG RESISTANCE, COVALENT KEYWDS 2 INHIBITOR, OXIDOREDUCTASE, OXIDOREDUCTASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.CAROLI,A.MATTEVI REVDAT 1 07-AUG-24 8FRV 0 JRNL AUTH J.CAROLI,A.MATTEVI JRNL TITL DISTAL DRUG RESISTANCE MUTATIONS PROMOTE COVALENT JRNL TITL 2 INHIBITOR-ADDUCT GROB FRAGMENTATION IN LSD1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 3 NUMBER OF REFLECTIONS : 61919 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1839 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 59.3400 - 6.3900 0.99 5243 160 0.1707 0.2203 REMARK 3 2 6.3900 - 5.0800 1.00 5109 157 0.2000 0.1917 REMARK 3 3 5.0800 - 4.4300 1.00 5051 155 0.1703 0.2003 REMARK 3 4 4.4300 - 4.0300 1.00 5050 154 0.1862 0.2251 REMARK 3 5 4.0300 - 3.7400 1.00 5010 152 0.2220 0.2711 REMARK 3 6 3.7400 - 3.5200 1.00 4988 153 0.2382 0.2595 REMARK 3 7 3.5200 - 3.3400 1.00 5017 153 0.2558 0.2634 REMARK 3 8 3.3400 - 3.2000 1.00 4977 151 0.2851 0.3044 REMARK 3 9 3.2000 - 3.0800 1.00 4985 153 0.3626 0.3798 REMARK 3 10 3.0700 - 2.9700 1.00 4988 152 0.3826 0.4227 REMARK 3 11 2.9700 - 2.8800 0.97 4856 147 0.4220 0.4451 REMARK 3 12 2.8800 - 2.7900 0.73 3590 117 0.4638 0.4576 REMARK 3 13 2.7900 - 2.7200 0.24 1216 35 0.4711 0.5441 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.520 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 6497 REMARK 3 ANGLE : 1.438 8820 REMARK 3 CHIRALITY : 0.073 989 REMARK 3 PLANARITY : 0.009 1141 REMARK 3 DIHEDRAL : 13.372 917 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8FRV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1000271261. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96770 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67413 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.720 REMARK 200 RESOLUTION RANGE LOW (A) : 59.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.77 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 14.50 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 78.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 SODIUM/POTASSIUM TARTRATE, 100 MM REMARK 280 ADA PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 59.34050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 89.32750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 117.85100 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 59.34050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 89.32750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 117.85100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 59.34050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 89.32750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 117.85100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 59.34050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 89.32750 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 117.85100 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: 5340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 LEU A 2 REMARK 465 SER A 3 REMARK 465 GLY A 4 REMARK 465 LYS A 5 REMARK 465 LYS A 6 REMARK 465 ALA A 7 REMARK 465 ALA A 8 REMARK 465 ALA A 9 REMARK 465 ALA A 10 REMARK 465 ALA A 11 REMARK 465 ALA A 12 REMARK 465 ALA A 13 REMARK 465 ALA A 14 REMARK 465 ALA A 15 REMARK 465 ALA A 16 REMARK 465 ALA A 17 REMARK 465 ALA A 18 REMARK 465 THR A 19 REMARK 465 GLY A 20 REMARK 465 THR A 21 REMARK 465 GLU A 22 REMARK 465 ALA A 23 REMARK 465 GLY A 24 REMARK 465 PRO A 25 REMARK 465 GLY A 26 REMARK 465 THR A 27 REMARK 465 ALA A 28 REMARK 465 GLY A 29 REMARK 465 GLY A 30 REMARK 465 SER A 31 REMARK 465 GLU A 32 REMARK 465 ASN A 33 REMARK 465 GLY A 34 REMARK 465 SER A 35 REMARK 465 GLU A 36 REMARK 465 VAL A 37 REMARK 465 ALA A 38 REMARK 465 ALA A 39 REMARK 465 GLN A 40 REMARK 465 PRO A 41 REMARK 465 ALA A 42 REMARK 465 GLY A 43 REMARK 465 LEU A 44 REMARK 465 SER A 45 REMARK 465 GLY A 46 REMARK 465 PRO A 47 REMARK 465 ALA A 48 REMARK 465 GLU A 49 REMARK 465 VAL A 50 REMARK 465 GLY A 51 REMARK 465 PRO A 52 REMARK 465 GLY A 53 REMARK 465 ALA A 54 REMARK 465 VAL A 55 REMARK 465 GLY A 56 REMARK 465 GLU A 57 REMARK 465 ARG A 58 REMARK 465 THR A 59 REMARK 465 PRO A 60 REMARK 465 ARG A 61 REMARK 465 LYS A 62 REMARK 465 LYS A 63 REMARK 465 GLU A 64 REMARK 465 PRO A 65 REMARK 465 PRO A 66 REMARK 465 ARG A 67 REMARK 465 ALA A 68 REMARK 465 SER A 69 REMARK 465 PRO A 70 REMARK 465 PRO A 71 REMARK 465 GLY A 72 REMARK 465 GLY A 73 REMARK 465 LEU A 74 REMARK 465 ALA A 75 REMARK 465 GLU A 76 REMARK 465 PRO A 77 REMARK 465 PRO A 78 REMARK 465 GLY A 79 REMARK 465 SER A 80 REMARK 465 ALA A 81 REMARK 465 GLY A 82 REMARK 465 PRO A 83 REMARK 465 GLN A 84 REMARK 465 ALA A 85 REMARK 465 GLY A 86 REMARK 465 PRO A 87 REMARK 465 THR A 88 REMARK 465 VAL A 89 REMARK 465 VAL A 90 REMARK 465 PRO A 91 REMARK 465 GLY A 92 REMARK 465 SER A 93 REMARK 465 ALA A 94 REMARK 465 THR A 95 REMARK 465 PRO A 96 REMARK 465 MET A 97 REMARK 465 GLU A 98 REMARK 465 THR A 99 REMARK 465 GLY A 100 REMARK 465 ILE A 101 REMARK 465 ALA A 102 REMARK 465 GLU A 103 REMARK 465 THR A 104 REMARK 465 PRO A 105 REMARK 465 GLU A 106 REMARK 465 GLY A 107 REMARK 465 ARG A 108 REMARK 465 ARG A 109 REMARK 465 THR A 110 REMARK 465 SER A 111 REMARK 465 ARG A 112 REMARK 465 ARG A 113 REMARK 465 LYS A 114 REMARK 465 ARG A 115 REMARK 465 ALA A 116 REMARK 465 LYS A 117 REMARK 465 VAL A 118 REMARK 465 GLU A 119 REMARK 465 TYR A 120 REMARK 465 ARG A 121 REMARK 465 GLU A 122 REMARK 465 MET A 123 REMARK 465 ASP A 124 REMARK 465 GLU A 125 REMARK 465 SER A 126 REMARK 465 LEU A 127 REMARK 465 ALA A 128 REMARK 465 ASN A 129 REMARK 465 LEU A 130 REMARK 465 SER A 131 REMARK 465 GLU A 132 REMARK 465 ASP A 133 REMARK 465 GLU A 134 REMARK 465 TYR A 135 REMARK 465 TYR A 136 REMARK 465 SER A 137 REMARK 465 GLU A 138 REMARK 465 GLU A 139 REMARK 465 GLU A 140 REMARK 465 ARG A 141 REMARK 465 ASN A 142 REMARK 465 ALA A 143 REMARK 465 LYS A 144 REMARK 465 ALA A 145 REMARK 465 GLU A 146 REMARK 465 LYS A 147 REMARK 465 GLU A 148 REMARK 465 LYS A 149 REMARK 465 LYS A 150 REMARK 465 LEU A 151 REMARK 465 PRO A 152 REMARK 465 PRO A 153 REMARK 465 PRO A 154 REMARK 465 PRO A 155 REMARK 465 PRO A 156 REMARK 465 GLN A 157 REMARK 465 ALA A 158 REMARK 465 PRO A 159 REMARK 465 PRO A 160 REMARK 465 GLU A 161 REMARK 465 GLU A 162 REMARK 465 GLU A 163 REMARK 465 ASN A 164 REMARK 465 GLU A 165 REMARK 465 SER A 166 REMARK 465 GLU A 167 REMARK 465 PRO A 168 REMARK 465 GLU A 169 REMARK 465 GLU A 170 REMARK 465 PRO A 837 REMARK 465 ARG A 838 REMARK 465 GLN A 839 REMARK 465 ALA A 840 REMARK 465 THR A 841 REMARK 465 PRO A 842 REMARK 465 GLY A 843 REMARK 465 VAL A 844 REMARK 465 PRO A 845 REMARK 465 ALA A 846 REMARK 465 GLN A 847 REMARK 465 GLN A 848 REMARK 465 SER A 849 REMARK 465 PRO A 850 REMARK 465 SER A 851 REMARK 465 MET A 852 REMARK 465 GLY B 297 REMARK 465 PRO B 298 REMARK 465 LEU B 299 REMARK 465 GLY B 300 REMARK 465 SER B 301 REMARK 465 PRO B 302 REMARK 465 GLU B 303 REMARK 465 PHE B 304 REMARK 465 ARG B 305 REMARK 465 ALA B 306 REMARK 465 LYS B 307 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 O ALA A 539 C19 YAF A 901 1.66 REMARK 500 NH2 ARG A 384 O LYS B 312 1.85 REMARK 500 NH1 ARG A 384 O LYS B 312 1.94 REMARK 500 CZ PHE A 670 CG2 VAL A 740 2.02 REMARK 500 NZ LYS A 374 OD2 ASP A 525 2.03 REMARK 500 OE1 GLU B 387 ND2 ASN B 411 2.06 REMARK 500 OE1 GLU A 352 NZ LYS A 699 2.09 REMARK 500 O ALA A 343 OG SER A 346 2.12 REMARK 500 NH1 ARG A 568 N LYS A 699 2.14 REMARK 500 O VAL B 415 ND2 ASN B 419 2.16 REMARK 500 NH1 ARG B 400 OE2 GLU B 438 2.17 REMARK 500 CZ ARG A 384 O LYS B 312 2.17 REMARK 500 OD1 ASP A 486 OH TYR B 398 2.18 REMARK 500 NH1 ARG A 568 C TYR A 698 2.18 REMARK 500 SD MET A 332 NZ LYS A 661 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU A 601 OE2 GLU A 601 2565 2.10 REMARK 500 NH1 ARG A 668 OG SER B 344 8455 2.17 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 THR A 335 57.01 -104.93 REMARK 500 ASN A 514 59.02 -116.35 REMARK 500 THR A 610 0.07 -68.06 REMARK 500 ALA A 757 -57.21 -135.91 REMARK 500 SER A 785 -70.83 -68.71 REMARK 500 TYR A 807 47.64 -144.01 REMARK 500 ASN B 327 -158.76 -132.74 REMARK 500 ALA B 381 -31.72 -132.51 REMARK 500 REMARK 500 REMARK: NULL DBREF 8FRV A 1 852 UNP O60341 KDM1A_HUMAN 1 852 DBREF 8FRV B 305 440 UNP Q9UKL0 RCOR1_HUMAN 308 443 SEQADV 8FRV GLY A -18 UNP O60341 EXPRESSION TAG SEQADV 8FRV SER A -17 UNP O60341 EXPRESSION TAG SEQADV 8FRV SER A -16 UNP O60341 EXPRESSION TAG SEQADV 8FRV HIS A -15 UNP O60341 EXPRESSION TAG SEQADV 8FRV HIS A -14 UNP O60341 EXPRESSION TAG SEQADV 8FRV HIS A -13 UNP O60341 EXPRESSION TAG SEQADV 8FRV HIS A -12 UNP O60341 EXPRESSION TAG SEQADV 8FRV HIS A -11 UNP O60341 EXPRESSION TAG SEQADV 8FRV HIS A -10 UNP O60341 EXPRESSION TAG SEQADV 8FRV SER A -9 UNP O60341 EXPRESSION TAG SEQADV 8FRV SER A -8 UNP O60341 EXPRESSION TAG SEQADV 8FRV GLY A -7 UNP O60341 EXPRESSION TAG SEQADV 8FRV LEU A -6 UNP O60341 EXPRESSION TAG SEQADV 8FRV VAL A -5 UNP O60341 EXPRESSION TAG SEQADV 8FRV PRO A -4 UNP O60341 EXPRESSION TAG SEQADV 8FRV ARG A -3 UNP O60341 EXPRESSION TAG SEQADV 8FRV GLY A -2 UNP O60341 EXPRESSION TAG SEQADV 8FRV SER A -1 UNP O60341 EXPRESSION TAG SEQADV 8FRV HIS A 0 UNP O60341 EXPRESSION TAG SEQADV 8FRV GLY B 297 UNP Q9UKL0 EXPRESSION TAG SEQADV 8FRV PRO B 298 UNP Q9UKL0 EXPRESSION TAG SEQADV 8FRV LEU B 299 UNP Q9UKL0 EXPRESSION TAG SEQADV 8FRV GLY B 300 UNP Q9UKL0 EXPRESSION TAG SEQADV 8FRV SER B 301 UNP Q9UKL0 EXPRESSION TAG SEQADV 8FRV PRO B 302 UNP Q9UKL0 EXPRESSION TAG SEQADV 8FRV GLU B 303 UNP Q9UKL0 EXPRESSION TAG SEQADV 8FRV PHE B 304 UNP Q9UKL0 EXPRESSION TAG SEQRES 1 A 871 GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY LEU SEQRES 2 A 871 VAL PRO ARG GLY SER HIS MET LEU SER GLY LYS LYS ALA SEQRES 3 A 871 ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA THR GLY SEQRES 4 A 871 THR GLU ALA GLY PRO GLY THR ALA GLY GLY SER GLU ASN SEQRES 5 A 871 GLY SER GLU VAL ALA ALA GLN PRO ALA GLY LEU SER GLY SEQRES 6 A 871 PRO ALA GLU VAL GLY PRO GLY ALA VAL GLY GLU ARG THR SEQRES 7 A 871 PRO ARG LYS LYS GLU PRO PRO ARG ALA SER PRO PRO GLY SEQRES 8 A 871 GLY LEU ALA GLU PRO PRO GLY SER ALA GLY PRO GLN ALA SEQRES 9 A 871 GLY PRO THR VAL VAL PRO GLY SER ALA THR PRO MET GLU SEQRES 10 A 871 THR GLY ILE ALA GLU THR PRO GLU GLY ARG ARG THR SER SEQRES 11 A 871 ARG ARG LYS ARG ALA LYS VAL GLU TYR ARG GLU MET ASP SEQRES 12 A 871 GLU SER LEU ALA ASN LEU SER GLU ASP GLU TYR TYR SER SEQRES 13 A 871 GLU GLU GLU ARG ASN ALA LYS ALA GLU LYS GLU LYS LYS SEQRES 14 A 871 LEU PRO PRO PRO PRO PRO GLN ALA PRO PRO GLU GLU GLU SEQRES 15 A 871 ASN GLU SER GLU PRO GLU GLU PRO SER GLY VAL GLU GLY SEQRES 16 A 871 ALA ALA PHE GLN SER ARG LEU PRO HIS ASP ARG MET THR SEQRES 17 A 871 SER GLN GLU ALA ALA CYS PHE PRO ASP ILE ILE SER GLY SEQRES 18 A 871 PRO GLN GLN THR GLN LYS VAL PHE LEU PHE ILE ARG ASN SEQRES 19 A 871 ARG THR LEU GLN LEU TRP LEU ASP ASN PRO LYS ILE GLN SEQRES 20 A 871 LEU THR PHE GLU ALA THR LEU GLN GLN LEU GLU ALA PRO SEQRES 21 A 871 TYR ASN SER ASP THR VAL LEU VAL HIS ARG VAL HIS SER SEQRES 22 A 871 TYR LEU GLU ARG HIS GLY LEU ILE ASN PHE GLY ILE TYR SEQRES 23 A 871 LYS ARG ILE LYS PRO LEU PRO THR LYS LYS THR GLY LYS SEQRES 24 A 871 VAL ILE ILE ILE GLY SER GLY VAL SER GLY LEU ALA ALA SEQRES 25 A 871 ALA ARG GLN LEU GLN SER PHE GLY MET ASP VAL THR LEU SEQRES 26 A 871 LEU GLU ALA ARG ASP ARG VAL GLY GLY ARG VAL ALA THR SEQRES 27 A 871 PHE ARG LYS GLY ASN TYR VAL ALA ASP LEU GLY ALA MET SEQRES 28 A 871 VAL VAL THR GLY LEU GLY GLY ASN PRO MET ALA VAL VAL SEQRES 29 A 871 SER LYS GLN VAL ASN MET GLU LEU ALA LYS ILE LYS GLN SEQRES 30 A 871 LYS CYS PRO LEU TYR GLU ALA ASN GLY GLN ALA VAL PRO SEQRES 31 A 871 LYS GLU LYS ASP GLU MET VAL GLU GLN GLU PHE ASN ARG SEQRES 32 A 871 LEU LEU GLU ALA THR SER TYR LEU SER HIS GLN LEU ASP SEQRES 33 A 871 PHE ASN VAL LEU ASN ASN LYS PRO VAL SER LEU GLY GLN SEQRES 34 A 871 ALA LEU GLU VAL VAL ILE GLN LEU GLN GLU LYS HIS VAL SEQRES 35 A 871 LYS ASP GLU GLN ILE GLU HIS TRP LYS LYS ILE VAL LYS SEQRES 36 A 871 THR GLN GLU GLU LEU LYS GLU LEU LEU ASN LYS MET VAL SEQRES 37 A 871 ASN LEU LYS GLU LYS ILE LYS GLU LEU HIS GLN GLN TYR SEQRES 38 A 871 LYS GLU ALA SER GLU VAL LYS PRO PRO ARG ASP ILE THR SEQRES 39 A 871 ALA GLU PHE LEU VAL LYS SER LYS HIS ARG ASP LEU THR SEQRES 40 A 871 ALA LEU CYS LYS GLU TYR ASP GLU LEU ALA GLU THR GLN SEQRES 41 A 871 GLY LYS LEU GLU GLU LYS LEU GLN GLU LEU GLU ALA ASN SEQRES 42 A 871 PRO PRO SER ASP VAL TYR LEU SER SER ARG ASP ARG GLN SEQRES 43 A 871 ILE LEU ASP TRP HIS PHE ALA ASN LEU GLU PHE ALA ASN SEQRES 44 A 871 ALA THR PRO LEU SER THR LEU SER LEU LYS HIS TRP ASP SEQRES 45 A 871 GLN ASP ASP ASP PHE GLU PHE THR GLY SER HIS LEU THR SEQRES 46 A 871 VAL ARG ASN GLY TYR SER CYS VAL PRO VAL ALA LEU ALA SEQRES 47 A 871 GLU GLY LEU ASP ILE LYS LEU ASN THR ALA VAL ARG GLN SEQRES 48 A 871 VAL ARG TYR THR ALA SER GLY CYS GLU VAL ILE ALA VAL SEQRES 49 A 871 ASN THR ARG SER THR SER GLN THR PHE ILE TYR LYS CYS SEQRES 50 A 871 ASP ALA VAL LEU CYS THR LEU PRO LEU GLY VAL LEU LYS SEQRES 51 A 871 GLN GLN PRO PRO ALA VAL GLN PHE VAL PRO PRO LEU PRO SEQRES 52 A 871 GLU TRP LYS THR SER ALA VAL GLN ARG MET GLY PHE GLY SEQRES 53 A 871 ASN LEU ASN LYS VAL VAL LEU CYS PHE ASP ARG VAL PHE SEQRES 54 A 871 TRP ASP PRO SER VAL ASN LEU PHE GLY HIS VAL GLY SER SEQRES 55 A 871 THR THR ALA SER ARG GLY GLU LEU PHE LEU PHE TRP ASN SEQRES 56 A 871 LEU TYR LYS ALA PRO ILE LEU LEU ALA LEU VAL ALA GLY SEQRES 57 A 871 GLU ALA ALA GLY ILE MET GLU ASN ILE SER ASP ASP VAL SEQRES 58 A 871 ILE VAL GLY ARG CYS LEU ALA ILE LEU LYS GLY ILE PHE SEQRES 59 A 871 GLY SER SER ALA VAL PRO GLN PRO LYS GLU THR VAL VAL SEQRES 60 A 871 SER ARG TRP ARG ALA ASP PRO TRP ALA ARG GLY SER TYR SEQRES 61 A 871 SER TYR VAL ALA ALA GLY SER SER GLY ASN ASP TYR ASP SEQRES 62 A 871 LEU MET ALA GLN PRO ILE THR PRO GLY PRO SER ILE PRO SEQRES 63 A 871 GLY ALA PRO GLN PRO ILE PRO ARG LEU PHE PHE ALA GLY SEQRES 64 A 871 GLU HIS THR ILE ARG ASN TYR PRO ALA THR VAL HIS GLY SEQRES 65 A 871 ALA LEU LEU SER GLY LEU ARG GLU ALA GLY ARG ILE ALA SEQRES 66 A 871 ASP GLN PHE LEU GLY ALA MET TYR THR LEU PRO ARG GLN SEQRES 67 A 871 ALA THR PRO GLY VAL PRO ALA GLN GLN SER PRO SER MET SEQRES 1 B 144 GLY PRO LEU GLY SER PRO GLU PHE ARG ALA LYS ARG LYS SEQRES 2 B 144 PRO PRO LYS GLY MET PHE LEU SER GLN GLU ASP VAL GLU SEQRES 3 B 144 ALA VAL SER ALA ASN ALA THR ALA ALA THR THR VAL LEU SEQRES 4 B 144 ARG GLN LEU ASP MET GLU LEU VAL SER VAL LYS ARG GLN SEQRES 5 B 144 ILE GLN ASN ILE LYS GLN THR ASN SER ALA LEU LYS GLU SEQRES 6 B 144 LYS LEU ASP GLY GLY ILE GLU PRO TYR ARG LEU PRO GLU SEQRES 7 B 144 VAL ILE GLN LYS CYS ASN ALA ARG TRP THR THR GLU GLU SEQRES 8 B 144 GLN LEU LEU ALA VAL GLN ALA ILE ARG LYS TYR GLY ARG SEQRES 9 B 144 ASP PHE GLN ALA ILE SER ASP VAL ILE GLY ASN LYS SER SEQRES 10 B 144 VAL VAL GLN VAL LYS ASN PHE PHE VAL ASN TYR ARG ARG SEQRES 11 B 144 ARG PHE ASN ILE ASP GLU VAL LEU GLN GLU TRP GLU ALA SEQRES 12 B 144 GLU HET YAF A 901 68 HETNAM YAF [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4- HETNAM 2 YAF DIHYDROXYOXOLAN-2-YL]METHYL (2R,3S,4S)-5-[(1R,3S,3AS, HETNAM 3 YAF 13R)-3-[3-(DIMETHYLCARBAMOYL)PHENYL]-1-HYDROXY-10,11- HETNAM 4 YAF DIMETHYL-4,6-DIOXO-2,3,5,6-TETRAHYDRO-1H- HETNAM 5 YAF BENZO[G]PYRROLO[2,1-E]PTERIDIN-8(4H)-YL]-2,3,4- HETNAM 6 YAF TRIHYDROXYPENTYL DIHYDROGEN DIPHOSPHATE (NON-PREFERRED HETNAM 7 YAF NAME) FORMUL 3 YAF C39 H48 N10 O17 P2 HELIX 1 AA1 GLY A 173 SER A 181 1 9 HELIX 2 AA2 THR A 189 PHE A 196 1 8 HELIX 3 AA3 PHE A 196 GLY A 202 1 7 HELIX 4 AA4 PRO A 203 ASN A 224 1 22 HELIX 5 AA5 THR A 230 LEU A 238 1 9 HELIX 6 AA6 PRO A 241 SER A 244 5 4 HELIX 7 AA7 ASP A 245 HIS A 259 1 15 HELIX 8 AA8 GLY A 287 PHE A 300 1 14 HELIX 9 AA9 ASN A 340 VAL A 349 1 10 HELIX 10 AB1 PRO A 371 ASP A 397 1 27 HELIX 11 AB2 SER A 407 VAL A 468 1 62 HELIX 12 AB3 ASP A 473 ASN A 514 1 42 HELIX 13 AB4 SER A 522 ASN A 540 1 19 HELIX 14 AB5 ASP A 553 GLU A 559 5 7 HELIX 15 AB6 SER A 572 GLU A 580 1 9 HELIX 16 AB7 PRO A 626 GLN A 632 1 7 HELIX 17 AB8 PRO A 644 MET A 654 1 11 HELIX 18 AB9 ALA A 708 GLU A 716 1 9 HELIX 19 AC1 SER A 719 GLY A 736 1 18 HELIX 20 AC2 GLY A 770 GLN A 778 1 9 HELIX 21 AC3 GLY A 800 ILE A 804 5 5 HELIX 22 AC4 THR A 810 LEU A 830 1 21 HELIX 23 AC5 ALA A 832 LEU A 836 5 5 HELIX 24 AC6 SER B 317 ALA B 326 1 10 HELIX 25 AC7 THR B 329 LEU B 363 1 35 HELIX 26 AC8 ILE B 367 ARG B 371 5 5 HELIX 27 AC9 THR B 384 GLY B 399 1 16 HELIX 28 AD1 ASP B 401 GLY B 410 1 10 HELIX 29 AD2 SER B 413 TYR B 424 1 12 HELIX 30 AD3 ASN B 429 GLU B 440 1 12 SHEET 1 AA1 5 ASP A 583 LYS A 585 0 SHEET 2 AA1 5 ASP A 303 LEU A 307 1 N LEU A 306 O LYS A 585 SHEET 3 AA1 5 LYS A 280 ILE A 284 1 N ILE A 283 O THR A 305 SHEET 4 AA1 5 ALA A 620 CYS A 623 1 O LEU A 622 N ILE A 284 SHEET 5 AA1 5 LEU A 796 PHE A 798 1 O PHE A 797 N CYS A 623 SHEET 1 AA2 2 THR A 319 LYS A 322 0 SHEET 2 AA2 2 TYR A 325 ASP A 328 -1 O ALA A 327 N PHE A 320 SHEET 1 AA3 3 VAL A 333 VAL A 334 0 SHEET 2 AA3 3 LEU A 565 VAL A 567 -1 O LEU A 565 N VAL A 334 SHEET 3 AA3 3 LEU A 353 LYS A 355 -1 N ALA A 354 O THR A 566 SHEET 1 AA4 2 VAL A 400 LEU A 401 0 SHEET 2 AA4 2 LYS A 404 PRO A 405 -1 O LYS A 404 N LEU A 401 SHEET 1 AA5 4 THR A 613 CYS A 618 0 SHEET 2 AA5 4 GLY A 599 ASN A 606 -1 N ALA A 604 O PHE A 614 SHEET 3 AA5 4 THR A 588 THR A 596 -1 N THR A 596 O GLY A 599 SHEET 4 AA5 4 GLN A 638 VAL A 640 1 O VAL A 640 N VAL A 593 SHEET 1 AA6 2 GLY A 655 PHE A 656 0 SHEET 2 AA6 2 SER A 762 TYR A 763 -1 O TYR A 763 N GLY A 655 SHEET 1 AA7 5 LEU A 677 GLY A 679 0 SHEET 2 AA7 5 LEU A 693 ASN A 696 -1 O PHE A 694 N PHE A 678 SHEET 3 AA7 5 ILE A 702 VAL A 707 -1 O LEU A 704 N TRP A 695 SHEET 4 AA7 5 ASN A 660 CYS A 665 -1 N LEU A 664 O LEU A 703 SHEET 5 AA7 5 GLU A 745 VAL A 748 -1 O VAL A 747 N VAL A 663 CISPEP 1 ALA A 240 PRO A 241 0 10.42 CISPEP 2 PRO A 470 PRO A 471 0 22.49 CISPEP 3 GLN A 633 PRO A 634 0 5.24 CISPEP 4 VAL A 640 PRO A 641 0 3.21 CRYST1 118.681 178.655 235.702 90.00 90.00 90.00 I 2 2 2 8 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 0.008426 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005597 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004243 0.00000