HEADER OXIDOREDUCTASE 12-JUL-19 6KGR TITLE LSD1-FCPA-MPE 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,N.HANDA,T.UMEHARA REVDAT 3 27-MAR-24 6KGR 1 REMARK REVDAT 2 20-MAY-20 6KGR 1 JRNL REVDAT 1 25-MAR-20 6KGR 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. 2.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549+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) : 2.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.320 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 48129 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 4559 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 34.8800 - 7.1900 0.99 2902 118 0.1280 0.1475 REMARK 3 2 7.1900 - 5.7100 1.00 2885 145 0.1621 0.1913 REMARK 3 3 5.7100 - 4.9900 1.00 2842 183 0.1493 0.1533 REMARK 3 4 4.9900 - 4.5400 1.00 2875 160 0.1322 0.1695 REMARK 3 5 4.5400 - 4.2100 1.00 2838 184 0.1316 0.1465 REMARK 3 6 4.2100 - 3.9700 1.00 2868 176 0.1361 0.1880 REMARK 3 7 3.9700 - 3.7700 1.00 2853 154 0.1444 0.1553 REMARK 3 8 3.7700 - 3.6000 1.00 2913 151 0.1573 0.1819 REMARK 3 9 3.6000 - 3.4600 1.00 2852 164 0.1701 0.2023 REMARK 3 10 3.4600 - 3.3500 1.00 2889 145 0.1777 0.2436 REMARK 3 11 3.3500 - 3.2400 1.00 2891 137 0.1840 0.2495 REMARK 3 12 3.2400 - 3.1500 1.00 2837 192 0.1854 0.2124 REMARK 3 13 3.1500 - 3.0700 1.00 2872 157 0.1973 0.2585 REMARK 3 14 3.0700 - 2.9900 1.00 2857 146 0.2036 0.2456 REMARK 3 15 2.9900 - 2.9200 1.00 2908 149 0.2090 0.2124 REMARK 3 16 2.9200 - 2.8600 1.00 2880 145 0.2018 0.2625 REMARK 3 17 2.8600 - 2.8000 1.00 2866 145 0.1992 0.2195 REMARK 3 18 2.8000 - 2.7500 1.00 2957 106 0.2080 0.2745 REMARK 3 19 2.7500 - 2.7000 1.00 2879 138 0.2043 0.2335 REMARK 3 20 2.7000 - 2.6600 1.00 2858 127 0.1961 0.2480 REMARK 3 21 2.6600 - 2.6100 1.00 2879 188 0.2128 0.2446 REMARK 3 22 2.6100 - 2.5700 1.00 2857 159 0.2187 0.2079 REMARK 3 23 2.5700 - 2.5300 1.00 2887 115 0.2139 0.2602 REMARK 3 24 2.5300 - 2.5000 1.00 2892 143 0.2173 0.2711 REMARK 3 25 2.5000 - 2.4700 1.00 2886 168 0.2180 0.2565 REMARK 3 26 2.4700 - 2.4300 1.00 2881 142 0.2255 0.2450 REMARK 3 27 2.4300 - 2.4000 1.00 2876 144 0.2401 0.2693 REMARK 3 28 2.4000 - 2.3700 1.00 2843 167 0.2484 0.2958 REMARK 3 29 2.3700 - 2.3500 1.00 2884 165 0.2684 0.2857 REMARK 3 30 2.3500 - 2.3200 1.00 2878 146 0.2874 0.3217 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) : 0.248 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.027 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.02 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 5288 REMARK 3 ANGLE : 0.875 7183 REMARK 3 CHIRALITY : 0.050 804 REMARK 3 PLANARITY : 0.006 969 REMARK 3 DIHEDRAL : 13.062 3203 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): 44.1286 -38.3663 22.0942 REMARK 3 T TENSOR REMARK 3 T11: 0.3812 T22: 0.4198 REMARK 3 T33: 0.3029 T12: -0.0188 REMARK 3 T13: 0.0317 T23: -0.0662 REMARK 3 L TENSOR REMARK 3 L11: 2.4838 L22: 3.2167 REMARK 3 L33: 0.9718 L12: 1.6182 REMARK 3 L13: 0.6390 L23: 0.2189 REMARK 3 S TENSOR REMARK 3 S11: 0.0459 S12: -0.2387 S13: 0.0948 REMARK 3 S21: -0.0675 S22: -0.0467 S23: -0.3301 REMARK 3 S31: -0.1537 S32: 0.1614 S33: -0.0056 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 372 THROUGH 513 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.4190 -82.5637 -30.6654 REMARK 3 T TENSOR REMARK 3 T11: 0.7532 T22: 0.6306 REMARK 3 T33: 0.6925 T12: 0.1004 REMARK 3 T13: 0.0348 T23: -0.1529 REMARK 3 L TENSOR REMARK 3 L11: 0.8784 L22: 5.7483 REMARK 3 L33: 6.6628 L12: -1.3461 REMARK 3 L13: -1.2386 L23: 5.9889 REMARK 3 S TENSOR REMARK 3 S11: 0.0433 S12: 0.2435 S13: -0.4488 REMARK 3 S21: -0.0902 S22: 0.0179 S23: -0.0651 REMARK 3 S31: 0.4641 S32: 0.3040 S33: -0.0393 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 514 THROUGH 832 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.2024 -47.0761 14.5432 REMARK 3 T TENSOR REMARK 3 T11: 0.2591 T22: 0.3483 REMARK 3 T33: 0.2438 T12: -0.0004 REMARK 3 T13: 0.0035 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 1.5825 L22: 2.7937 REMARK 3 L33: 1.9039 L12: 0.2745 REMARK 3 L13: 0.0888 L23: 0.7410 REMARK 3 S TENSOR REMARK 3 S11: 0.0904 S12: -0.1766 S13: 0.0651 REMARK 3 S21: -0.1756 S22: -0.0634 S23: 0.0273 REMARK 3 S31: -0.0855 S32: -0.1651 S33: -0.0287 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 6KGR 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_1300012888. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-10 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 : BL41XU 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 : 48179 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.320 REMARK 200 RESOLUTION RANGE LOW (A) : 48.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 18.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09800 REMARK 200 FOR THE DATA SET : 24.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 18.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.32600 REMARK 200 FOR SHELL : 3.000 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 (%): 67.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES (PH 7.5), 5% MPD, 3.5-4.0% REMARK 280 PEG MME 2000, VAPOR DIFFUSION, HANGING 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 36.44233 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 72.88467 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 54.66350 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 91.10583 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 18.22117 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 36.44233 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 72.88467 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 91.10583 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 54.66350 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 18.22117 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: 1790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1260 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1261 LIES ON A SPECIAL POSITION. 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 LYS A 469 REMARK 465 PRO A 470 REMARK 465 PRO A 471 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 LYS A 404 CG CD CE NZ REMARK 470 GLU A 467 CG CD OE1 OE2 REMARK 470 GLU A 506 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 DJC A 902 N5 FAD A 903 1.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 727 CB CYS A 727 SG -0.101 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 -169.09 -74.97 REMARK 500 PRO A 516 -177.15 -67.86 REMARK 500 ALA A 597 9.00 -63.86 REMARK 500 ALA A 757 -48.39 -134.70 REMARK 500 TYR A 807 44.72 -142.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 6KGQ AND 6KGR 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 MPD A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues DJC A 902 and FAD A REMARK 800 903 DBREF 6KGR A 172 833 UNP O60341 KDM1A_HUMAN 172 833 SEQADV 6KGR GLY A 165 UNP O60341 EXPRESSION TAG SEQADV 6KGR PRO A 166 UNP O60341 EXPRESSION TAG SEQADV 6KGR LEU A 167 UNP O60341 EXPRESSION TAG SEQADV 6KGR GLY A 168 UNP O60341 EXPRESSION TAG SEQADV 6KGR SER A 169 UNP O60341 EXPRESSION TAG SEQADV 6KGR HIS A 170 UNP O60341 EXPRESSION TAG SEQADV 6KGR 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 MPD A 901 8 HET DJC A 902 21 HET FAD A 903 53 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM DJC 3-[4-[5-FLUORANYL-2-(TRIFLUOROMETHYL) HETNAM 2 DJC PHENYL]PHENYL]PROPANAL HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 2 MPD C6 H14 O2 FORMUL 3 DJC C16 H12 F4 O FORMUL 4 FAD C27 H33 N9 O15 P2 FORMUL 5 HOH *164(H2 O) 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 SER A 201 1 6 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 ASN A 350 1 11 HELIX 10 AB1 PRO A 371 GLN A 395 1 25 HELIX 11 AB2 SER A 407 VAL A 468 1 62 HELIX 12 AB3 ASP A 473 GLU A 512 1 40 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 LEU A 830 1 21 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 LEU A 693 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 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 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 0.54 CISPEP 2 GLN A 633 PRO A 634 0 -2.81 CISPEP 3 VAL A 640 PRO A 641 0 0.45 SITE 1 AC1 5 ILE A 356 ASN A 535 HIS A 564 TRP A 695 SITE 2 AC1 5 DJC A 902 SITE 1 AC2 45 GLY A 285 GLY A 287 VAL A 288 SER A 289 SITE 2 AC2 45 LEU A 307 GLU A 308 ALA A 309 ARG A 310 SITE 3 AC2 45 GLY A 314 GLY A 315 ARG A 316 LEU A 329 SITE 4 AC2 45 GLY A 330 ALA A 331 MET A 332 VAL A 333 SITE 5 AC2 45 THR A 335 ALA A 539 GLU A 559 HIS A 564 SITE 6 AC2 45 ALA A 589 VAL A 590 THR A 624 LEU A 625 SITE 7 AC2 45 PRO A 626 LEU A 659 TRP A 751 TRP A 756 SITE 8 AC2 45 SER A 760 TYR A 761 GLY A 800 GLU A 801 SITE 9 AC2 45 ALA A 809 THR A 810 VAL A 811 ALA A 814 SITE 10 AC2 45 MPD A 901 HOH A1102 HOH A1133 HOH A1166 SITE 11 AC2 45 HOH A1175 HOH A1178 HOH A1197 HOH A1213 SITE 12 AC2 45 HOH A1243 CRYST1 185.268 185.268 109.327 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 0.005398 0.003116 0.000000 0.00000 SCALE2 0.000000 0.006233 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009147 0.00000