HEADER OXIDOREDUCTASE 12-JUL-19 6KGM TITLE LSD1-COREST-S2116 FIVE-MEMBERED RING ADDUCT MODEL 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; COMPND 6 EC: 1.-.-.-; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: SF FILE CONTAINS FRIEDEL PAIRS.; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: REST COREPRESSOR 1; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: PROTEIN COREST; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: SF FILE CONTAINS FRIEDEL PAIRS. 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, MECHANISM-BASED KEYWDS 2 INHIBITOR, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.NIWA,S.SATO,T.UMEHARA REVDAT 3 27-MAR-24 6KGM 1 REMARK REVDAT 2 20-MAY-20 6KGM 1 JRNL REVDAT 1 25-MAR-20 6KGM 0 JRNL AUTH H.NIWA,S.SATO,N.HANDA,T.SENGOKU,T.UMEHARA,S.YOKOYAMA JRNL TITL DEVELOPMENT AND STRUCTURAL EVALUATION OF N-ALKYLATED JRNL TITL 2 TRANS-2-PHENYLCYCLOPROPYLAMINE-BASED LSD1 INHIBITORS. JRNL REF CHEMMEDCHEM V. 15 787 2020 JRNL REFN ESSN 1860-7187 JRNL PMID 32166890 JRNL DOI 10.1002/CMDC.202000014 REMARK 2 REMARK 2 RESOLUTION. 2.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998+SVN 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.280 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 76234 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.950 REMARK 3 FREE R VALUE TEST SET COUNT : 2866 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 49.1300 - 7.1100 0.99 7215 132 0.1559 0.1752 REMARK 3 2 7.1100 - 5.6400 1.00 7225 147 0.1752 0.1653 REMARK 3 3 5.6400 - 4.9300 1.00 7266 138 0.1486 0.1689 REMARK 3 4 4.9300 - 4.4800 1.00 7214 122 0.1242 0.1889 REMARK 3 5 4.4800 - 4.1600 1.00 7232 116 0.1270 0.1486 REMARK 3 6 4.1600 - 3.9100 1.00 7261 151 0.1372 0.1477 REMARK 3 7 3.9100 - 3.7200 1.00 7188 155 0.1586 0.1660 REMARK 3 8 3.7200 - 3.5600 1.00 7174 172 0.1757 0.2143 REMARK 3 9 3.5600 - 3.4200 1.00 7244 158 0.1799 0.2128 REMARK 3 10 3.4200 - 3.3000 1.00 7244 160 0.1866 0.2140 REMARK 3 11 3.3000 - 3.2000 1.00 7196 131 0.1927 0.2102 REMARK 3 12 3.2000 - 3.1100 1.00 7237 130 0.2238 0.1822 REMARK 3 13 3.1100 - 3.0200 1.00 7192 171 0.2318 0.2478 REMARK 3 14 3.0200 - 2.9500 1.00 7199 146 0.2453 0.2572 REMARK 3 15 2.9500 - 2.8800 1.00 7209 152 0.2518 0.2733 REMARK 3 16 2.8800 - 2.8200 1.00 7292 135 0.2791 0.3156 REMARK 3 17 2.8200 - 2.7700 1.00 7164 148 0.2927 0.3185 REMARK 3 18 2.7700 - 2.7100 1.00 7238 127 0.3181 0.3258 REMARK 3 19 2.7100 - 2.6700 1.00 7220 121 0.3471 0.2823 REMARK 3 20 2.6700 - 2.6200 1.00 7133 154 0.3810 0.3647 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.364 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 68.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 90.42 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 6472 REMARK 3 ANGLE : 0.904 8777 REMARK 3 CHIRALITY : 0.054 978 REMARK 3 PLANARITY : 0.006 1174 REMARK 3 DIHEDRAL : 12.783 3943 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 172 THROUGH 371 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.3618 -56.2372 -16.8055 REMARK 3 T TENSOR REMARK 3 T11: 0.5746 T22: 0.6493 REMARK 3 T33: 0.7042 T12: -0.0969 REMARK 3 T13: -0.2142 T23: 0.1711 REMARK 3 L TENSOR REMARK 3 L11: 1.7869 L22: 1.7566 REMARK 3 L33: 3.4836 L12: 0.0079 REMARK 3 L13: -0.7982 L23: -0.2832 REMARK 3 S TENSOR REMARK 3 S11: -0.0780 S12: -0.3193 S13: 0.2335 REMARK 3 S21: 0.1925 S22: -0.1580 S23: -0.5712 REMARK 3 S31: -0.3941 S32: 0.8020 S33: 0.2089 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 372 THROUGH 513 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.7413 -14.5510 -57.0451 REMARK 3 T TENSOR REMARK 3 T11: 1.0469 T22: 0.7800 REMARK 3 T33: 1.2314 T12: 0.0470 REMARK 3 T13: -0.3388 T23: 0.3145 REMARK 3 L TENSOR REMARK 3 L11: 2.3314 L22: 7.3751 REMARK 3 L33: 2.0722 L12: -5.5241 REMARK 3 L13: 2.9089 L23: -4.2554 REMARK 3 S TENSOR REMARK 3 S11: -0.0258 S12: 0.1931 S13: 0.2628 REMARK 3 S21: 0.2911 S22: -0.1364 S23: -0.1962 REMARK 3 S31: -0.3233 S32: 0.0891 S33: 0.1721 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 514 THROUGH 832 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.7990 -62.4796 -33.5931 REMARK 3 T TENSOR REMARK 3 T11: 0.5940 T22: 0.4396 REMARK 3 T33: 0.4709 T12: 0.0222 REMARK 3 T13: -0.0401 T23: 0.0563 REMARK 3 L TENSOR REMARK 3 L11: 1.8686 L22: 3.2370 REMARK 3 L33: 2.4986 L12: 0.0290 REMARK 3 L13: -0.2578 L23: -0.8886 REMARK 3 S TENSOR REMARK 3 S11: -0.1105 S12: 0.3099 S13: 0.0752 REMARK 3 S21: -0.3787 S22: -0.2190 S23: -0.1624 REMARK 3 S31: 0.0997 S32: 0.1673 S33: 0.3184 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 309 THROUGH 370 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.3091 -26.3850 -56.5376 REMARK 3 T TENSOR REMARK 3 T11: 0.8892 T22: 0.8370 REMARK 3 T33: 1.0904 T12: 0.0536 REMARK 3 T13: -0.1890 T23: 0.2235 REMARK 3 L TENSOR REMARK 3 L11: 3.2898 L22: 6.3848 REMARK 3 L33: 4.2109 L12: -4.4713 REMARK 3 L13: 3.8546 L23: -5.0789 REMARK 3 S TENSOR REMARK 3 S11: 0.3532 S12: 0.2025 S13: -0.0199 REMARK 3 S21: -0.2674 S22: -0.0439 S23: 0.3677 REMARK 3 S31: 0.1212 S32: -0.2392 S33: -0.3166 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 371 THROUGH 439 ) REMARK 3 ORIGIN FOR THE GROUP (A): -44.4287 25.0780 -60.2127 REMARK 3 T TENSOR REMARK 3 T11: 1.3206 T22: 1.0087 REMARK 3 T33: 0.7917 T12: -0.0402 REMARK 3 T13: -0.4525 T23: 0.0859 REMARK 3 L TENSOR REMARK 3 L11: 6.1871 L22: 6.9240 REMARK 3 L33: 3.9041 L12: -2.0396 REMARK 3 L13: -1.4218 L23: 2.4232 REMARK 3 S TENSOR REMARK 3 S11: -0.2889 S12: -1.7034 S13: 0.2037 REMARK 3 S21: 1.6891 S22: 0.1315 S23: -1.0240 REMARK 3 S31: 0.0384 S32: 0.2293 S33: 0.1316 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 6KGM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1300012846. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-16 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 MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76266 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.620 REMARK 200 RESOLUTION RANGE LOW (A) : 49.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 15.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.45800 REMARK 200 FOR SHELL : 1.600 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 (%): 82.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 7.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M N-(CARBAMOYLMETHYL)IMINODIACETIC REMARK 280 ACID (PH 5.5), 1.28 M POTASSIUM SODIUM TARTRATE, VAPOR DIFFUSION, REMARK 280 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 60.22550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 89.34800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 117.62800 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 60.22550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 89.34800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 117.62800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 60.22550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 89.34800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 117.62800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 60.22550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 89.34800 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 117.62800 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: 7870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 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 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 ALA B 328 CB 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 C27 DJ0 A 906 N5 FAD A 907 1.48 REMARK 500 C29 DJ0 A 906 C4X FAD A 907 1.60 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 ASN A 224 76.48 -167.28 REMARK 500 THR A 335 -175.70 -66.29 REMARK 500 ASN A 350 87.94 -69.58 REMARK 500 PRO A 516 173.11 -55.87 REMARK 500 ASP A 557 4.71 -64.11 REMARK 500 PRO A 701 91.95 -66.24 REMARK 500 ALA A 757 -55.68 -134.30 REMARK 500 SER A 768 -166.60 -107.80 REMARK 500 SER A 785 -74.33 -67.48 REMARK 500 LEU B 316 73.11 -157.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 6KGM AND 6KGN USE THE SAME DATA BUT HAVE LIGAND MODELS WITH REMARK 600 POSSIBLE DIFFERENT CONFIGURATIONS. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues DJ0 A 906 and FAD A REMARK 800 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues DJ0 A 906 and FAD A REMARK 800 907 DBREF 6KGM A 172 833 UNP O60341 KDM1A_HUMAN 172 833 DBREF 6KGM B 308 440 UNP Q9UKL0 RCOR1_HUMAN 311 443 SEQADV 6KGM GLY A 165 UNP O60341 EXPRESSION TAG SEQADV 6KGM PRO A 166 UNP O60341 EXPRESSION TAG SEQADV 6KGM LEU A 167 UNP O60341 EXPRESSION TAG SEQADV 6KGM GLY A 168 UNP O60341 EXPRESSION TAG SEQADV 6KGM SER A 169 UNP O60341 EXPRESSION TAG SEQADV 6KGM HIS A 170 UNP O60341 EXPRESSION TAG SEQADV 6KGM MET A 171 UNP O60341 EXPRESSION TAG SEQADV 6KGM GLY B 301 UNP Q9UKL0 EXPRESSION TAG SEQADV 6KGM SER B 302 UNP Q9UKL0 EXPRESSION TAG SEQADV 6KGM SER B 303 UNP Q9UKL0 EXPRESSION TAG SEQADV 6KGM GLY B 304 UNP Q9UKL0 EXPRESSION TAG SEQADV 6KGM SER B 305 UNP Q9UKL0 EXPRESSION TAG SEQADV 6KGM ALA B 306 UNP Q9UKL0 EXPRESSION TAG SEQADV 6KGM 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 GOL A 901 6 HET GOL A 902 6 HET GOL A 903 6 HET GOL A 904 6 HET GOL A 905 6 HET DJ0 A 906 20 HET FAD A 907 53 HETNAM GOL GLYCEROL HETNAM DJ0 3-[3,5-BIS(FLUORANYL)-2-PHENYLMETHOXY-PHENYL]PROPANAL HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 5(C3 H8 O3) FORMUL 8 DJ0 C16 H14 F2 O2 FORMUL 9 FAD C27 H33 N9 O15 P2 FORMUL 10 HOH *54(H2 O) 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 VAL A 349 1 10 HELIX 9 AA9 PRO A 371 GLN A 395 1 25 HELIX 10 AB1 SER A 407 VAL A 468 1 62 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 555 GLU A 559 5 5 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 GLY A 709 GLU A 716 1 8 HELIX 19 AC1 SER A 719 GLY A 736 1 18 HELIX 20 AC2 SER A 737 VAL A 740 5 4 HELIX 21 AC3 SER A 769 GLN A 778 1 10 HELIX 22 AC4 GLY A 800 ILE A 804 5 5 HELIX 23 AC5 THR A 810 GLY A 831 1 22 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 ALA B 439 1 11 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 GLU A 364 0 SHEET 2 AA4 6 LEU A 677 VAL A 681 1 O VAL A 681 N TYR A 363 SHEET 3 AA4 6 GLU A 690 TRP A 695 -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 LEU A 664 O LEU A 703 SHEET 6 AA4 6 GLU A 745 VAL A 748 -1 O GLU A 745 N CYS A 665 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 VAL A 602 O TYR A 616 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 0.39 CISPEP 2 PRO A 470 PRO A 471 0 4.27 CISPEP 3 GLN A 633 PRO A 634 0 -2.23 CISPEP 4 VAL A 640 PRO A 641 0 -7.66 SITE 1 AC1 5 GLY A 409 GLU A 413 ARG A 526 LEU A 544 SITE 2 AC1 5 ARG A 688 SITE 1 AC2 3 LYS A 374 SER A 522 ARG A 524 SITE 1 AC3 1 ARG A 182 SITE 1 AC4 5 ARG A 312 SER A 749 ARG A 750 TRP A 751 SITE 2 AC4 5 ASP A 754 SITE 1 AC5 3 GLN A 358 ASN A 535 HIS A 564 SITE 1 AC6 42 GLY A 285 GLY A 287 VAL A 288 SER A 289 SITE 2 AC6 42 LEU A 307 GLU A 308 ALA A 309 ARG A 310 SITE 3 AC6 42 GLY A 314 GLY A 315 ARG A 316 VAL A 317 SITE 4 AC6 42 LEU A 329 GLY A 330 ALA A 331 MET A 332 SITE 5 AC6 42 VAL A 333 THR A 335 PHE A 538 ALA A 539 SITE 6 AC6 42 THR A 588 ALA A 589 VAL A 590 THR A 624 SITE 7 AC6 42 LEU A 625 PRO A 626 LYS A 661 TRP A 751 SITE 8 AC6 42 TRP A 756 SER A 760 TYR A 761 GLY A 800 SITE 9 AC6 42 GLU A 801 ALA A 809 THR A 810 VAL A 811 SITE 10 AC6 42 ALA A 814 HOH A1005 HOH A1007 HOH A1018 SITE 11 AC6 42 HOH A1020 HOH A1022 SITE 1 AC7 42 GLY A 285 GLY A 287 VAL A 288 SER A 289 SITE 2 AC7 42 LEU A 307 GLU A 308 ALA A 309 ARG A 310 SITE 3 AC7 42 GLY A 314 GLY A 315 ARG A 316 VAL A 317 SITE 4 AC7 42 LEU A 329 GLY A 330 ALA A 331 MET A 332 SITE 5 AC7 42 VAL A 333 THR A 335 PHE A 538 ALA A 539 SITE 6 AC7 42 THR A 588 ALA A 589 VAL A 590 THR A 624 SITE 7 AC7 42 LEU A 625 PRO A 626 LYS A 661 TRP A 751 SITE 8 AC7 42 TRP A 756 SER A 760 TYR A 761 GLY A 800 SITE 9 AC7 42 GLU A 801 ALA A 809 THR A 810 VAL A 811 SITE 10 AC7 42 ALA A 814 HOH A1005 HOH A1007 HOH A1018 SITE 11 AC7 42 HOH A1020 HOH A1022 CRYST1 120.451 178.696 235.256 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 0.008302 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005596 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004251 0.00000