HEADER OXIDOREDUCTASE/TRANSCRIPTION/INHIBITOR 10-OCT-17 5YJB TITLE LSD1-COREST IN COMPLEX WITH 4-[5-(PIPERIDIN-4-YLMETHOXY)-2-(P-TOLYL) TITLE 2 PYRIDIN-3-YL]BENZONITRILE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 172-833; COMPND 5 SYNONYM: BRAF35-HDAC COMPLEX PROTEIN BHC110,FLAVIN-CONTAINING AMINE COMPND 6 OXIDASE DOMAIN-CONTAINING PROTEIN 2; COMPND 7 EC: 1.-.-.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: REST COREPRESSOR 1; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: UNP RESIDUES 311-443; COMPND 13 SYNONYM: PROTEIN COREST; COMPND 14 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 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETDUET-1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: RCOR1, KIAA0071, RCOR; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI KRX; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 1452720; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: KRX KEYWDS DEMETHYLASE, AMINE OXIDASE, CHROMATIN, HISTONE, FAD, COREPRESSOR, KEYWDS 2 OXIDOREDUCTASE-TRANSCRIPTION-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.NIWA,S.SATO,T.HASHIMOTO,K.MATSUNO,T.UMEHARA REVDAT 3 22-NOV-23 5YJB 1 REMARK REVDAT 2 01-AUG-18 5YJB 1 JRNL REVDAT 1 04-JUL-18 5YJB 0 JRNL AUTH H.NIWA,S.SATO,T.HASHIMOTO,K.MATSUNO,T.UMEHARA JRNL TITL CRYSTAL STRUCTURE OF LSD1 IN COMPLEX WITH JRNL TITL 2 4-[5-(PIPERIDIN-4-YLMETHOXY)-2-(P-TOLYL) JRNL TITL 3 PYRIDIN-3-YL]BENZONITRILE. JRNL REF MOLECULES V. 23 2018 JRNL REFN ESSN 1420-3049 JRNL PMID 29949906 JRNL DOI 10.3390/MOLECULES23071538 REMARK 2 REMARK 2 RESOLUTION. 2.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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) : 2.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.220 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 53614 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1053 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 48.8283 - 7.2924 1.00 6756 124 0.1649 0.1820 REMARK 3 2 7.2924 - 5.7912 1.00 6746 142 0.1870 0.2195 REMARK 3 3 5.7912 - 5.0600 1.00 6787 125 0.1594 0.1983 REMARK 3 4 5.0600 - 4.5978 1.00 6742 124 0.1309 0.1802 REMARK 3 5 4.5978 - 4.2684 1.00 6750 111 0.1236 0.1579 REMARK 3 6 4.2684 - 4.0169 1.00 6714 134 0.1399 0.1448 REMARK 3 7 4.0169 - 3.8158 1.00 6774 127 0.1686 0.1787 REMARK 3 8 3.8158 - 3.6498 1.00 6718 145 0.2020 0.2321 REMARK 3 9 3.6498 - 3.5093 1.00 6705 177 0.2197 0.2284 REMARK 3 10 3.5093 - 3.3882 1.00 6710 129 0.2385 0.2555 REMARK 3 11 3.3882 - 3.2823 1.00 6764 142 0.2381 0.2932 REMARK 3 12 3.2823 - 3.1885 1.00 6701 147 0.2838 0.3179 REMARK 3 13 3.1885 - 3.1046 1.00 6804 111 0.3224 0.3866 REMARK 3 14 3.1046 - 3.0289 1.00 6715 159 0.3584 0.4082 REMARK 3 15 3.0289 - 2.9600 1.00 6660 135 0.3977 0.3832 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) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.230 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 : 0.008 6446 REMARK 3 ANGLE : 0.945 8746 REMARK 3 CHIRALITY : 0.048 976 REMARK 3 PLANARITY : 0.006 1150 REMARK 3 DIHEDRAL : 13.803 3892 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 172 THROUGH 371 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2127 -56.5947 -17.0409 REMARK 3 T TENSOR REMARK 3 T11: 0.6174 T22: 0.4661 REMARK 3 T33: 0.6009 T12: -0.1225 REMARK 3 T13: -0.1916 T23: 0.1194 REMARK 3 L TENSOR REMARK 3 L11: 1.8195 L22: 1.8655 REMARK 3 L33: 3.6041 L12: -0.2100 REMARK 3 L13: -0.9109 L23: -0.4834 REMARK 3 S TENSOR REMARK 3 S11: -0.0950 S12: -0.2390 S13: 0.3385 REMARK 3 S21: 0.0446 S22: -0.0402 S23: -0.5134 REMARK 3 S31: -0.4017 S32: 0.6014 S33: 0.1575 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 372 THROUGH 513 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.8694 -14.8152 -56.9416 REMARK 3 T TENSOR REMARK 3 T11: 1.1812 T22: 0.7729 REMARK 3 T33: 1.0864 T12: 0.0296 REMARK 3 T13: -0.3705 T23: 0.3033 REMARK 3 L TENSOR REMARK 3 L11: 2.9016 L22: 8.3048 REMARK 3 L33: 2.6027 L12: -6.1237 REMARK 3 L13: 3.4278 L23: -4.8317 REMARK 3 S TENSOR REMARK 3 S11: -0.1648 S12: 0.1765 S13: 0.3799 REMARK 3 S21: 0.4356 S22: -0.0735 S23: -0.4680 REMARK 3 S31: -0.4190 S32: -0.0131 S33: 0.2049 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 514 THROUGH 832 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.6730 -62.9560 -33.7827 REMARK 3 T TENSOR REMARK 3 T11: 0.8322 T22: 0.3984 REMARK 3 T33: 0.4246 T12: 0.0127 REMARK 3 T13: -0.0233 T23: 0.0874 REMARK 3 L TENSOR REMARK 3 L11: 1.7976 L22: 3.2785 REMARK 3 L33: 1.7875 L12: -0.1138 REMARK 3 L13: -0.0337 L23: -0.1288 REMARK 3 S TENSOR REMARK 3 S11: -0.0720 S12: 0.3738 S13: 0.0944 REMARK 3 S21: -0.6112 S22: -0.2293 S23: -0.1933 REMARK 3 S31: 0.0667 S32: 0.1065 S33: 0.2781 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 309 THROUGH 370 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.4831 -26.6262 -56.2624 REMARK 3 T TENSOR REMARK 3 T11: 0.7668 T22: 0.6225 REMARK 3 T33: 0.7601 T12: 0.0112 REMARK 3 T13: -0.1830 T23: 0.1777 REMARK 3 L TENSOR REMARK 3 L11: 3.2026 L22: 5.5562 REMARK 3 L33: 6.5251 L12: -3.2550 REMARK 3 L13: 3.5823 L23: -4.6319 REMARK 3 S TENSOR REMARK 3 S11: 0.2755 S12: 0.2420 S13: -0.1745 REMARK 3 S21: -0.0577 S22: -0.0817 S23: 0.2845 REMARK 3 S31: 0.1349 S32: -0.3797 S33: -0.1934 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 371 THROUGH 384 ) REMARK 3 ORIGIN FOR THE GROUP (A): -33.5982 26.2815 -66.3882 REMARK 3 T TENSOR REMARK 3 T11: 1.3505 T22: 1.1135 REMARK 3 T33: 1.6335 T12: -0.1726 REMARK 3 T13: -0.2629 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 4.7028 L22: 0.5890 REMARK 3 L33: 2.7017 L12: 1.5054 REMARK 3 L13: -0.6911 L23: -0.7494 REMARK 3 S TENSOR REMARK 3 S11: 0.3717 S12: -1.2301 S13: 0.3206 REMARK 3 S21: 0.6382 S22: -0.0266 S23: -0.8279 REMARK 3 S31: -0.6356 S32: 0.7918 S33: -0.3337 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 385 THROUGH 413 ) REMARK 3 ORIGIN FOR THE GROUP (A): -44.0182 23.3215 -61.8190 REMARK 3 T TENSOR REMARK 3 T11: 1.7315 T22: 1.0555 REMARK 3 T33: 0.8831 T12: 0.0259 REMARK 3 T13: -0.5469 T23: 0.1954 REMARK 3 L TENSOR REMARK 3 L11: 7.1637 L22: 1.9274 REMARK 3 L33: 4.7672 L12: -2.2213 REMARK 3 L13: -4.1113 L23: -0.0404 REMARK 3 S TENSOR REMARK 3 S11: -0.3980 S12: -2.2212 S13: -0.6664 REMARK 3 S21: 0.7164 S22: 0.3075 S23: -0.9129 REMARK 3 S31: 0.2517 S32: 0.3421 S33: 0.0537 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 414 THROUGH 439 ) REMARK 3 ORIGIN FOR THE GROUP (A): -50.4168 25.6474 -54.7992 REMARK 3 T TENSOR REMARK 3 T11: 1.8403 T22: 1.2486 REMARK 3 T33: 0.7590 T12: 0.1702 REMARK 3 T13: -0.2606 T23: -0.0382 REMARK 3 L TENSOR REMARK 3 L11: 6.8039 L22: 4.0737 REMARK 3 L33: 9.7084 L12: 1.0258 REMARK 3 L13: 5.3872 L23: 0.2817 REMARK 3 S TENSOR REMARK 3 S11: 0.2042 S12: -1.4690 S13: -0.0329 REMARK 3 S21: 2.4537 S22: -0.2242 S23: -0.3171 REMARK 3 S31: -0.1502 S32: -0.0613 S33: 0.0414 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 5YJB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1300005391. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53652 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.960 REMARK 200 RESOLUTION RANGE LOW (A) : 49.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 1.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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: 5H6Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 82.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 7.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M N-(2-ACETAMIDO)IMINODIACETIC ACID REMARK 280 (PH 5.5), 1.23M POTASSIUM SODIUM TARTRATE TETRAHYDRATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 60.57200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 89.81200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 117.47650 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 60.57200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 89.81200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 117.47650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 60.57200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 89.81200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 117.47650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 60.57200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 89.81200 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 117.47650 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: 7210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 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 165 REMARK 465 PRO A 166 REMARK 465 LEU A 167 REMARK 465 GLY A 168 REMARK 465 SER A 169 REMARK 465 HIS A 170 REMARK 465 MET A 171 REMARK 465 MET A 833 REMARK 465 GLY B 301 REMARK 465 SER B 302 REMARK 465 SER B 303 REMARK 465 GLY B 304 REMARK 465 SER B 305 REMARK 465 ALA B 306 REMARK 465 SER B 307 REMARK 465 ARG B 308 REMARK 465 GLU B 440 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 239 CG CD OE1 OE2 REMARK 470 LYS A 276 CG CD CE NZ REMARK 470 LYS A 359 CG 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 224 83.10 -167.54 REMARK 500 MET A 332 -17.56 -146.60 REMARK 500 LEU A 697 -7.36 -158.89 REMARK 500 PRO A 701 96.88 -65.35 REMARK 500 ASN A 717 31.62 -84.50 REMARK 500 ALA A 757 -55.38 -138.40 REMARK 500 SER A 760 -70.57 -100.01 REMARK 500 SER A 785 -70.38 -58.54 REMARK 500 PRO A 790 152.60 -49.56 REMARK 500 TYR A 807 49.28 -145.84 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 FAD A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8WC A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 904 DBREF 5YJB A 172 833 UNP O60341 KDM1A_HUMAN 172 833 DBREF 5YJB B 308 440 UNP Q9UKL0 RCOR1_HUMAN 311 443 SEQADV 5YJB GLY A 165 UNP O60341 EXPRESSION TAG SEQADV 5YJB PRO A 166 UNP O60341 EXPRESSION TAG SEQADV 5YJB LEU A 167 UNP O60341 EXPRESSION TAG SEQADV 5YJB GLY A 168 UNP O60341 EXPRESSION TAG SEQADV 5YJB SER A 169 UNP O60341 EXPRESSION TAG SEQADV 5YJB HIS A 170 UNP O60341 EXPRESSION TAG SEQADV 5YJB MET A 171 UNP O60341 EXPRESSION TAG SEQADV 5YJB GLY B 301 UNP Q9UKL0 EXPRESSION TAG SEQADV 5YJB SER B 302 UNP Q9UKL0 EXPRESSION TAG SEQADV 5YJB SER B 303 UNP Q9UKL0 EXPRESSION TAG SEQADV 5YJB GLY B 304 UNP Q9UKL0 EXPRESSION TAG SEQADV 5YJB SER B 305 UNP Q9UKL0 EXPRESSION TAG SEQADV 5YJB ALA B 306 UNP Q9UKL0 EXPRESSION TAG SEQADV 5YJB SER B 307 UNP Q9UKL0 EXPRESSION TAG SEQRES 1 A 669 GLY PRO LEU GLY SER HIS MET SER GLY VAL GLU GLY ALA SEQRES 2 A 669 ALA PHE GLN SER ARG LEU PRO HIS ASP ARG MET THR SER SEQRES 3 A 669 GLN GLU ALA ALA CYS PHE PRO ASP ILE ILE SER GLY PRO SEQRES 4 A 669 GLN GLN THR GLN LYS VAL PHE LEU PHE ILE ARG ASN ARG SEQRES 5 A 669 THR LEU GLN LEU TRP LEU ASP ASN PRO LYS ILE GLN LEU SEQRES 6 A 669 THR PHE GLU ALA THR LEU GLN GLN LEU GLU ALA PRO TYR SEQRES 7 A 669 ASN SER ASP THR VAL LEU VAL HIS ARG VAL HIS SER TYR SEQRES 8 A 669 LEU GLU ARG HIS GLY LEU ILE ASN PHE GLY ILE TYR LYS SEQRES 9 A 669 ARG ILE LYS PRO LEU PRO THR LYS LYS THR GLY LYS VAL SEQRES 10 A 669 ILE ILE ILE GLY SER GLY VAL SER GLY LEU ALA ALA ALA SEQRES 11 A 669 ARG GLN LEU GLN SER PHE GLY MET ASP VAL THR LEU LEU SEQRES 12 A 669 GLU ALA ARG ASP ARG VAL GLY GLY ARG VAL ALA THR PHE SEQRES 13 A 669 ARG LYS GLY ASN TYR VAL ALA ASP LEU GLY ALA MET VAL SEQRES 14 A 669 VAL THR GLY LEU GLY GLY ASN PRO MET ALA VAL VAL SER SEQRES 15 A 669 LYS GLN VAL ASN MET GLU LEU ALA LYS ILE LYS GLN LYS SEQRES 16 A 669 CYS PRO LEU TYR GLU ALA ASN GLY GLN ALA VAL PRO LYS SEQRES 17 A 669 GLU LYS ASP GLU MET VAL GLU GLN GLU PHE ASN ARG LEU SEQRES 18 A 669 LEU GLU ALA THR SER TYR LEU SER HIS GLN LEU ASP PHE SEQRES 19 A 669 ASN VAL LEU ASN ASN LYS PRO VAL SER LEU GLY GLN ALA SEQRES 20 A 669 LEU GLU VAL VAL ILE GLN LEU GLN GLU LYS HIS VAL LYS SEQRES 21 A 669 ASP GLU GLN ILE GLU HIS TRP LYS LYS ILE VAL LYS THR SEQRES 22 A 669 GLN GLU GLU LEU LYS GLU LEU LEU ASN LYS MET VAL ASN SEQRES 23 A 669 LEU LYS GLU LYS ILE LYS GLU LEU HIS GLN GLN TYR LYS SEQRES 24 A 669 GLU ALA SER GLU VAL LYS PRO PRO ARG ASP ILE THR ALA SEQRES 25 A 669 GLU PHE LEU VAL LYS SER LYS HIS ARG ASP LEU THR ALA SEQRES 26 A 669 LEU CYS LYS GLU TYR ASP GLU LEU ALA GLU THR GLN GLY SEQRES 27 A 669 LYS LEU GLU GLU LYS LEU GLN GLU LEU GLU ALA ASN PRO SEQRES 28 A 669 PRO SER ASP VAL TYR LEU SER SER ARG ASP ARG GLN ILE SEQRES 29 A 669 LEU ASP TRP HIS PHE ALA ASN LEU GLU PHE ALA ASN ALA SEQRES 30 A 669 THR PRO LEU SER THR LEU SER LEU LYS HIS TRP ASP GLN SEQRES 31 A 669 ASP ASP ASP PHE GLU PHE THR GLY SER HIS LEU THR VAL SEQRES 32 A 669 ARG ASN GLY TYR SER CYS VAL PRO VAL ALA LEU ALA GLU SEQRES 33 A 669 GLY LEU ASP ILE LYS LEU ASN THR ALA VAL ARG GLN VAL SEQRES 34 A 669 ARG TYR THR ALA SER GLY CYS GLU VAL ILE ALA VAL ASN SEQRES 35 A 669 THR ARG SER THR SER GLN THR PHE ILE TYR LYS CYS ASP SEQRES 36 A 669 ALA VAL LEU CYS THR LEU PRO LEU GLY VAL LEU LYS GLN SEQRES 37 A 669 GLN PRO PRO ALA VAL GLN PHE VAL PRO PRO LEU PRO GLU SEQRES 38 A 669 TRP LYS THR SER ALA VAL GLN ARG MET GLY PHE GLY ASN SEQRES 39 A 669 LEU ASN LYS VAL VAL LEU CYS PHE ASP ARG VAL PHE TRP SEQRES 40 A 669 ASP PRO SER VAL ASN LEU PHE GLY HIS VAL GLY SER THR SEQRES 41 A 669 THR ALA SER ARG GLY GLU LEU PHE LEU PHE TRP ASN LEU SEQRES 42 A 669 TYR LYS ALA PRO ILE LEU LEU ALA LEU VAL ALA GLY GLU SEQRES 43 A 669 ALA ALA GLY ILE MET GLU ASN ILE SER ASP ASP VAL ILE SEQRES 44 A 669 VAL GLY ARG CYS LEU ALA ILE LEU LYS GLY ILE PHE GLY SEQRES 45 A 669 SER SER ALA VAL PRO GLN PRO LYS GLU THR VAL VAL SER SEQRES 46 A 669 ARG TRP ARG ALA ASP PRO TRP ALA ARG GLY SER TYR SER SEQRES 47 A 669 TYR VAL ALA ALA GLY SER SER GLY ASN ASP TYR ASP LEU SEQRES 48 A 669 MET ALA GLN PRO ILE THR PRO GLY PRO SER ILE PRO GLY SEQRES 49 A 669 ALA PRO GLN PRO ILE PRO ARG LEU PHE PHE ALA GLY GLU SEQRES 50 A 669 HIS THR ILE ARG ASN TYR PRO ALA THR VAL HIS GLY ALA SEQRES 51 A 669 LEU LEU SER GLY LEU ARG GLU ALA GLY ARG ILE ALA ASP SEQRES 52 A 669 GLN PHE LEU GLY ALA MET SEQRES 1 B 140 GLY SER SER GLY SER ALA SER ARG LYS PRO PRO LYS GLY SEQRES 2 B 140 MET PHE LEU SER GLN GLU ASP VAL GLU ALA VAL SER ALA SEQRES 3 B 140 ASN ALA THR ALA ALA THR THR VAL LEU ARG GLN LEU ASP SEQRES 4 B 140 MET GLU LEU VAL SER VAL LYS ARG GLN ILE GLN ASN ILE SEQRES 5 B 140 LYS GLN THR ASN SER ALA LEU LYS GLU LYS LEU ASP GLY SEQRES 6 B 140 GLY ILE GLU PRO TYR ARG LEU PRO GLU VAL ILE GLN LYS SEQRES 7 B 140 CYS ASN ALA ARG TRP THR THR GLU GLU GLN LEU LEU ALA SEQRES 8 B 140 VAL GLN ALA ILE ARG LYS TYR GLY ARG ASP PHE GLN ALA SEQRES 9 B 140 ILE SER ASP VAL ILE GLY ASN LYS SER VAL VAL GLN VAL SEQRES 10 B 140 LYS ASN PHE PHE VAL ASN TYR ARG ARG ARG PHE ASN ILE SEQRES 11 B 140 ASP GLU VAL LEU GLN GLU TRP GLU ALA GLU HET FAD A 901 53 HET 8WC A 902 29 HET GOL A 903 6 HET GOL A 904 6 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM 8WC 4-[2-(4-METHYLPHENYL)-5-(PIPERIDIN-4-YLMETHOXY)PYRIDIN- HETNAM 2 8WC 3-YL]BENZENECARBONITRILE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 FAD C27 H33 N9 O15 P2 FORMUL 4 8WC C25 H25 N3 O FORMUL 5 GOL 2(C3 H8 O3) HELIX 1 AA1 SER A 172 SER A 181 1 10 HELIX 2 AA2 THR A 189 PHE A 196 1 8 HELIX 3 AA3 PHE A 196 SER A 201 1 6 HELIX 4 AA4 PRO A 203 ASP A 223 1 21 HELIX 5 AA5 THR A 230 LEU A 238 1 9 HELIX 6 AA6 ASP A 245 HIS A 259 1 15 HELIX 7 AA7 GLY A 287 PHE A 300 1 14 HELIX 8 AA8 ASN A 340 ASN A 350 1 11 HELIX 9 AA9 PRO A 371 GLN A 395 1 25 HELIX 10 AB1 SER A 407 GLU A 467 1 61 HELIX 11 AB2 ASP A 473 GLU A 512 1 40 HELIX 12 AB3 SER A 522 ALA A 541 1 20 HELIX 13 AB4 PRO A 543 LEU A 547 5 5 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 THR A 685 GLU A 690 5 6 HELIX 19 AC1 ALA A 708 ASN A 717 1 10 HELIX 20 AC2 SER A 719 GLY A 736 1 18 HELIX 21 AC3 SER A 737 VAL A 740 5 4 HELIX 22 AC4 SER A 769 GLN A 778 1 10 HELIX 23 AC5 GLY A 800 ILE A 804 5 5 HELIX 24 AC6 THR A 810 LEU A 830 1 21 HELIX 25 AC7 SER B 317 ALA B 326 1 10 HELIX 26 AC8 THR B 329 LEU B 363 1 35 HELIX 27 AC9 ILE B 367 ARG B 371 5 5 HELIX 28 AD1 THR B 384 GLY B 399 1 16 HELIX 29 AD2 ASP B 401 GLY B 410 1 10 HELIX 30 AD3 SER B 413 TYR B 424 1 12 HELIX 31 AD4 ASN B 429 GLU B 438 1 10 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 VAL A 281 O ASP A 303 SHEET 4 AA1 5 ALA A 620 CYS A 623 1 O LEU A 622 N ILE A 282 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 6 LEU A 362 TYR A 363 0 SHEET 2 AA4 6 LEU A 677 HIS A 680 1 O GLY A 679 N TYR A 363 SHEET 3 AA4 6 LEU A 693 ASN A 696 -1 O PHE A 694 N PHE A 678 SHEET 4 AA4 6 ILE A 702 VAL A 707 -1 O LEU A 704 N TRP A 695 SHEET 5 AA4 6 ASN A 660 CYS A 665 -1 N ASN A 660 O VAL A 707 SHEET 6 AA4 6 GLU A 745 VAL A 748 -1 O VAL A 747 N VAL A 663 SHEET 1 AA5 2 VAL A 400 LEU A 401 0 SHEET 2 AA5 2 LYS A 404 PRO A 405 -1 O LYS A 404 N LEU A 401 SHEET 1 AA6 4 THR A 613 CYS A 618 0 SHEET 2 AA6 4 GLY A 599 ASN A 606 -1 N ALA A 604 O PHE A 614 SHEET 3 AA6 4 THR A 588 THR A 596 -1 N ARG A 594 O GLU A 601 SHEET 4 AA6 4 GLN A 638 VAL A 640 1 O VAL A 640 N VAL A 593 SHEET 1 AA7 2 GLY A 655 PHE A 656 0 SHEET 2 AA7 2 SER A 762 TYR A 763 -1 O TYR A 763 N GLY A 655 CISPEP 1 ALA A 240 PRO A 241 0 -1.27 CISPEP 2 PRO A 470 PRO A 471 0 5.46 CISPEP 3 GLN A 633 PRO A 634 0 -3.80 CISPEP 4 VAL A 640 PRO A 641 0 3.75 SITE 1 AC1 33 GLY A 285 GLY A 287 VAL A 288 SER A 289 SITE 2 AC1 33 LEU A 307 GLU A 308 ALA A 309 ARG A 310 SITE 3 AC1 33 GLY A 314 GLY A 315 ARG A 316 VAL A 317 SITE 4 AC1 33 GLY A 330 ALA A 331 MET A 332 VAL A 333 SITE 5 AC1 33 THR A 588 ALA A 589 VAL A 590 THR A 624 SITE 6 AC1 33 LEU A 625 PRO A 626 VAL A 637 LEU A 659 SITE 7 AC1 33 TRP A 751 TRP A 756 SER A 760 TYR A 761 SITE 8 AC1 33 GLY A 800 GLU A 801 THR A 810 VAL A 811 SITE 9 AC1 33 8WC A 902 SITE 1 AC2 11 MET A 332 PHE A 538 ALA A 539 ASN A 540 SITE 2 AC2 11 ASP A 555 LEU A 659 LYS A 661 TRP A 695 SITE 3 AC2 11 TYR A 761 ALA A 809 FAD A 901 SITE 1 AC3 2 ARG A 526 ARG A 688 SITE 1 AC4 6 ARG A 310 ARG A 312 SER A 749 ARG A 750 SITE 2 AC4 6 TRP A 751 ASP A 754 CRYST1 121.144 179.624 234.953 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 0.008255 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005567 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004256 0.00000