HEADER OXIDOREDUCTASE 12-JUL-19 6KGP TITLE LSD1-S2157 N5 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. 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 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 6KGP 1 REMARK REVDAT 2 20-MAY-20 6KGP 1 JRNL REVDAT 1 25-MAR-20 6KGP 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. 2.25 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 52484 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 5004 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 44.6000 - 6.9800 0.99 3155 130 0.1389 0.1336 REMARK 3 2 6.9800 - 5.5500 1.00 3135 178 0.1596 0.1958 REMARK 3 3 5.5500 - 4.8500 1.00 3123 178 0.1444 0.1482 REMARK 3 4 4.8500 - 4.4000 1.00 3103 189 0.1292 0.1680 REMARK 3 5 4.4000 - 4.0900 1.00 3128 206 0.1328 0.1418 REMARK 3 6 4.0900 - 3.8500 1.00 3133 169 0.1359 0.1849 REMARK 3 7 3.8500 - 3.6500 1.00 3149 157 0.1569 0.2137 REMARK 3 8 3.6500 - 3.5000 1.00 3125 192 0.1705 0.1740 REMARK 3 9 3.5000 - 3.3600 1.00 3140 156 0.1729 0.2232 REMARK 3 10 3.3600 - 3.2400 1.00 3169 157 0.1735 0.2316 REMARK 3 11 3.2400 - 3.1400 1.00 3106 197 0.1853 0.2229 REMARK 3 12 3.1400 - 3.0500 1.00 3144 180 0.1871 0.2585 REMARK 3 13 3.0500 - 2.9700 1.00 3172 141 0.2040 0.2369 REMARK 3 14 2.9700 - 2.9000 1.00 3125 178 0.1981 0.2200 REMARK 3 15 2.9000 - 2.8300 1.00 3165 149 0.1924 0.2500 REMARK 3 16 2.8300 - 2.7700 1.00 3158 143 0.1902 0.1891 REMARK 3 17 2.7700 - 2.7200 1.00 3150 147 0.1963 0.2404 REMARK 3 18 2.7200 - 2.6700 1.00 3201 136 0.2020 0.2635 REMARK 3 19 2.6700 - 2.6200 1.00 3097 178 0.2111 0.2517 REMARK 3 20 2.6200 - 2.5800 1.00 3134 198 0.2127 0.2675 REMARK 3 21 2.5800 - 2.5300 1.00 3172 123 0.2317 0.3104 REMARK 3 22 2.5300 - 2.5000 1.00 3158 176 0.2376 0.2856 REMARK 3 23 2.5000 - 2.4600 1.00 3139 168 0.2453 0.2716 REMARK 3 24 2.4600 - 2.4200 1.00 3152 137 0.2575 0.3322 REMARK 3 25 2.4200 - 2.3900 1.00 3140 166 0.2625 0.3065 REMARK 3 26 2.3900 - 2.3600 1.00 3097 196 0.2698 0.3118 REMARK 3 27 2.3600 - 2.3300 1.00 3152 182 0.2889 0.3341 REMARK 3 28 2.3300 - 2.3000 1.00 3169 150 0.3018 0.3601 REMARK 3 29 2.3000 - 2.2800 1.00 3138 166 0.3098 0.3447 REMARK 3 30 2.2800 - 2.2500 1.00 3111 181 0.3234 0.3714 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.406 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.58 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 : 0.007 5303 REMARK 3 ANGLE : 0.839 7189 REMARK 3 CHIRALITY : 0.051 799 REMARK 3 PLANARITY : 0.006 968 REMARK 3 DIHEDRAL : 13.897 3209 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 172 THROUGH 371 ) REMARK 3 ORIGIN FOR THE GROUP (A): 44.4802 38.1671 -22.2192 REMARK 3 T TENSOR REMARK 3 T11: 0.4288 T22: 0.3847 REMARK 3 T33: 0.3177 T12: -0.0523 REMARK 3 T13: -0.0313 T23: -0.0251 REMARK 3 L TENSOR REMARK 3 L11: 1.8324 L22: 2.8054 REMARK 3 L33: 0.9899 L12: -1.3816 REMARK 3 L13: -0.4155 L23: 0.3573 REMARK 3 S TENSOR REMARK 3 S11: -0.0599 S12: 0.0697 S13: 0.0428 REMARK 3 S21: 0.1969 S22: 0.0731 S23: -0.3008 REMARK 3 S31: 0.1534 S32: 0.1709 S33: -0.0149 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 372 THROUGH 513 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.3278 81.7940 29.5234 REMARK 3 T TENSOR REMARK 3 T11: 0.8961 T22: 0.5668 REMARK 3 T33: 0.5908 T12: -0.1761 REMARK 3 T13: 0.0208 T23: -0.0895 REMARK 3 L TENSOR REMARK 3 L11: 0.5327 L22: 4.2831 REMARK 3 L33: 7.1669 L12: 0.5881 REMARK 3 L13: 0.5816 L23: 5.7646 REMARK 3 S TENSOR REMARK 3 S11: 0.0826 S12: -0.1339 S13: 0.2673 REMARK 3 S21: -0.0427 S22: 0.1798 S23: -0.1990 REMARK 3 S31: -0.6050 S32: 0.5698 S33: -0.1580 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 514 THROUGH 832 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.5796 47.2813 -14.5271 REMARK 3 T TENSOR REMARK 3 T11: 0.3229 T22: 0.3532 REMARK 3 T33: 0.2960 T12: -0.0817 REMARK 3 T13: 0.0167 T23: -0.0057 REMARK 3 L TENSOR REMARK 3 L11: 1.1404 L22: 2.1611 REMARK 3 L33: 2.0798 L12: -0.4282 REMARK 3 L13: 0.0493 L23: 0.7353 REMARK 3 S TENSOR REMARK 3 S11: 0.0163 S12: -0.0216 S13: -0.0256 REMARK 3 S21: 0.2029 S22: -0.0254 S23: 0.0725 REMARK 3 S31: 0.0811 S32: -0.1898 S33: 0.0041 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 6KGP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300012854. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-15 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 : 52531 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 48.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10700 REMARK 200 FOR THE DATA SET : 22.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 2.47400 REMARK 200 FOR SHELL : 1.800 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 (%): 67.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES (PH 6.2-6.3), 0.2M DIAMMONIUM REMARK 280 TARTRATE, 0.0005M TCEP, 10% PEG3350, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 36.16667 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 72.33333 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 54.25000 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 90.41667 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 18.08333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 36.16667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 72.33333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 90.41667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 54.25000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 18.08333 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL 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 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 SER A 466 REMARK 465 GLU A 467 REMARK 465 VAL A 468 REMARK 465 LYS A 469 REMARK 465 PRO A 470 REMARK 465 PRO A 471 REMARK 465 ARG A 472 REMARK 465 SER A 785 REMARK 465 ILE A 786 REMARK 465 PRO A 787 REMARK 465 GLY A 788 REMARK 465 ALA A 789 REMARK 465 PRO A 790 REMARK 465 GLN A 791 REMARK 465 MET A 833 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 ILE A 474 CG1 CG2 CD1 REMARK 470 GLU A 477 CG CD OE1 OE2 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 908 N5 FAD A 909 1.43 REMARK 500 NZ LYS A 347 O HOH A 1001 2.18 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 77.11 -154.63 REMARK 500 MET A 332 -11.43 -141.63 REMARK 500 ASN A 514 51.33 -118.21 REMARK 500 SER A 609 76.59 -155.70 REMARK 500 THR A 610 2.38 -63.10 REMARK 500 ALA A 757 -50.46 -134.99 REMARK 500 ALA A 757 -50.04 -134.99 REMARK 500 TYR A 807 44.92 -140.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 6KGO AND 6KGP 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 residue GOL A 906 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TLA A 907 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues DJ0 A 908 and FAD A REMARK 800 909 DBREF 6KGP A 172 833 UNP O60341 KDM1A_HUMAN 172 833 SEQADV 6KGP GLY A 165 UNP O60341 EXPRESSION TAG SEQADV 6KGP PRO A 166 UNP O60341 EXPRESSION TAG SEQADV 6KGP LEU A 167 UNP O60341 EXPRESSION TAG SEQADV 6KGP GLY A 168 UNP O60341 EXPRESSION TAG SEQADV 6KGP SER A 169 UNP O60341 EXPRESSION TAG SEQADV 6KGP HIS A 170 UNP O60341 EXPRESSION TAG SEQADV 6KGP MET A 171 UNP O60341 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 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 GOL A 906 6 HET TLA A 907 10 HET DJ0 A 908 20 HET FAD A 909 53 HETNAM GOL GLYCEROL HETNAM TLA L(+)-TARTARIC ACID 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 2 GOL 6(C3 H8 O3) FORMUL 8 TLA C4 H6 O6 FORMUL 9 DJ0 C16 H14 F2 O2 FORMUL 10 FAD C27 H33 N9 O15 P2 FORMUL 11 HOH *190(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 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 PRO A 341 ASN A 350 1 10 HELIX 10 AB1 PRO A 371 GLN A 395 1 25 HELIX 11 AB2 SER A 407 TYR A 462 1 56 HELIX 12 AB3 ILE A 474 ASN A 514 1 41 HELIX 13 AB4 SER A 522 ALA A 541 1 20 HELIX 14 AB5 PRO A 543 LEU A 547 5 5 HELIX 15 AB6 ASP A 555 GLU A 559 5 5 HELIX 16 AB7 SER A 572 ALA A 579 1 8 HELIX 17 AB8 PRO A 626 LYS A 631 1 6 HELIX 18 AB9 PRO A 644 MET A 654 1 11 HELIX 19 AC1 GLY A 709 GLU A 716 1 8 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 GLY A 831 1 22 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 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 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 GLU A 690 TRP A 695 -1 O PHE A 692 N HIS A 680 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 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 SER A 609 CYS A 618 0 SHEET 2 AA6 4 GLY A 599 ASN A 606 -1 N CYS A 600 O CYS A 618 SHEET 3 AA6 4 THR A 588 THR A 596 -1 N ARG A 591 O ILE A 603 SHEET 4 AA6 4 GLN A 638 VAL A 640 1 O GLN A 638 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 4.23 CISPEP 2 GLN A 633 PRO A 634 0 -5.03 CISPEP 3 VAL A 640 PRO A 641 0 -0.53 SITE 1 AC1 5 GLU A 413 ARG A 526 LEU A 544 ARG A 688 SITE 2 AC1 5 HOH A1086 SITE 1 AC2 6 ARG A 310 ARG A 312 SER A 749 ARG A 750 SITE 2 AC2 6 TRP A 751 ASP A 754 SITE 1 AC3 4 LYS A 277 GLN A 298 ARG A 608 HOH A1031 SITE 1 AC4 4 GLN A 358 CYS A 360 ASN A 535 HOH A1155 SITE 1 AC5 2 ARG A 312 VAL A 313 SITE 1 AC6 5 CYS A 360 ASP A 375 GLU A 379 TRP A 531 SITE 2 AC6 5 HOH A1003 SITE 1 AC7 10 THR A 230 PHE A 231 HIS A 250 HIS A 253 SITE 2 AC7 10 GLU A 257 LYS A 271 ASN A 717 HOH A1027 SITE 3 AC7 10 HOH A1034 HOH A1045 SITE 1 AC8 42 GLY A 285 GLY A 287 VAL A 288 SER A 289 SITE 2 AC8 42 LEU A 307 GLU A 308 ALA A 309 ARG A 310 SITE 3 AC8 42 GLY A 314 GLY A 315 ARG A 316 LEU A 329 SITE 4 AC8 42 GLY A 330 ALA A 331 MET A 332 VAL A 333 SITE 5 AC8 42 THR A 335 PHE A 538 ALA A 539 THR A 588 SITE 6 AC8 42 VAL A 590 THR A 624 LEU A 625 PRO A 626 SITE 7 AC8 42 VAL A 637 LEU A 659 TRP A 751 TRP A 756 SITE 8 AC8 42 TYR A 761 GLY A 800 GLU A 801 ALA A 809 SITE 9 AC8 42 THR A 810 VAL A 811 ALA A 814 HOH A1013 SITE 10 AC8 42 HOH A1021 HOH A1035 HOH A1069 HOH A1079 SITE 11 AC8 42 HOH A1090 HOH A1129 CRYST1 185.703 185.703 108.500 90.00 90.00 120.00 P 61 2 2 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 0.005385 0.003109 0.000000 0.00000 SCALE2 0.000000 0.006218 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009217 0.00000