PDB Short entry for 5LGU HEADER OXIDOREDUCTASE 08-JUL-16 5LGU TITLE THIENO[3,2-B]PYRROLE-5-CARBOXAMIDES AS NOVEL REVERSIBLE INHIBITORS OF TITLE 2 HISTONE LYSINE DEMETHYLASE KDM1A/LSD1: COMPOUND 34 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 MOL_ID: 2; COMPND 9 MOLECULE: REST COREPRESSOR 1; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: PROTEIN COREST; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KDM1A, AOF2, KDM1, KIAA0601, LSD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: RCOR1, KIAA0071, RCOR; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.MATTEVI,G.CIOSSANI REVDAT 3 10-JAN-24 5LGU 1 REMARK REVDAT 2 22-MAR-17 5LGU 1 JRNL REVDAT 1 22-FEB-17 5LGU 0 JRNL AUTH P.VIANELLO,L.SARTORI,F.AMIGONI,A.CAPPA,G.FAGA,R.FATTORI, JRNL AUTH 2 E.LEGNAGHI,G.CIOSSANI,A.MATTEVI,G.MERONI,L.MORETTI, JRNL AUTH 3 V.CECATIELLO,S.PASQUALATO,A.ROMUSSI,F.THALER,P.TRIFIRO, JRNL AUTH 4 M.VILLA,O.A.BOTRUGNO,P.DESSANTI,S.MINUCCI,S.VULTAGGIO, JRNL AUTH 5 E.ZAGARRI,M.VARASI,C.MERCURIO JRNL TITL THIENO[3,2-B]PYRROLE-5-CARBOXAMIDES AS NEW REVERSIBLE JRNL TITL 2 INHIBITORS OF HISTONE LYSINE DEMETHYLASE KDM1A/LSD1. PART 2: JRNL TITL 3 STRUCTURE-BASED DRUG DESIGN AND STRUCTURE-ACTIVITY JRNL TITL 4 RELATIONSHIP. JRNL REF J. MED. CHEM. V. 60 1693 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 28186757 JRNL DOI 10.1021/ACS.JMEDCHEM.6B01019 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 42378 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.900 REMARK 3 FREE R VALUE TEST SET COUNT : 835 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3036 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.57 REMARK 3 BIN R VALUE (WORKING SET) : 0.3570 REMARK 3 BIN FREE R VALUE SET COUNT : 61 REMARK 3 BIN FREE R VALUE : 0.3320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6293 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 101.4 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.04000 REMARK 3 B22 (A**2) : -5.32000 REMARK 3 B33 (A**2) : -1.73000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.366 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.259 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.241 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.396 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6517 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6300 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8839 ; 1.359 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14486 ; 0.782 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 797 ; 6.115 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 295 ;38.731 ;24.475 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1130 ;20.568 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;17.013 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 985 ; 0.062 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7332 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1484 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3195 ; 5.085 ; 9.755 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3196 ; 5.085 ; 9.754 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3989 ; 7.983 ;14.630 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3990 ; 7.982 ;14.629 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3322 ; 5.187 ;10.443 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3323 ; 5.186 ;10.442 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4851 ; 8.632 ;15.377 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7770 ;12.375 ;79.100 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7771 ;12.374 ;79.100 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5LGU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1200000714. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00004 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43214 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.92600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 2V1D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 80.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 6.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE HANGING-DROP VAPOR DIFFUSION REMARK 280 METHOD AT 20 C BY MIXING EQUAL VOLUMES OF 100 MICROM LSD1-COREST REMARK 280 SOLUTION IN 5% (W/V) GLYCEROL, 25 MM POTASSIUM PHOSPHATE, PH 7.2, REMARK 280 WITH RESERVOIR SOLUTIONS CONTAINING 1.2 M SODIUM/POTASSIUM REMARK 280 TARTRATE AND 100 MMN-(2-ACETAMIDO)-2-IMINODIACETIC ACID, PH 6.5., REMARK 280 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 60.70450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 90.57750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 118.72800 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 60.70450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 90.57750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 118.72800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 60.70450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 90.57750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 118.72800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 60.70450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 90.57750 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 118.72800 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 MET A 123 REMARK 465 ASP A 124 REMARK 465 GLU A 125 REMARK 465 SER A 126 REMARK 465 LEU A 127 REMARK 465 ALA A 128 REMARK 465 ASN A 129 REMARK 465 LEU A 130 REMARK 465 SER A 131 REMARK 465 GLU A 132 REMARK 465 ASP A 133 REMARK 465 GLU A 134 REMARK 465 TYR A 135 REMARK 465 TYR A 136 REMARK 465 SER A 137 REMARK 465 GLU A 138 REMARK 465 GLU A 139 REMARK 465 GLU A 140 REMARK 465 ARG A 141 REMARK 465 ASN A 142 REMARK 465 ALA A 143 REMARK 465 LYS A 144 REMARK 465 ALA A 145 REMARK 465 GLU A 146 REMARK 465 LYS A 147 REMARK 465 GLU A 148 REMARK 465 LYS A 149 REMARK 465 LYS A 150 REMARK 465 LEU A 151 REMARK 465 PRO A 152 REMARK 465 PRO A 153 REMARK 465 PRO A 154 REMARK 465 PRO A 155 REMARK 465 PRO A 156 REMARK 465 GLN A 157 REMARK 465 ALA A 158 REMARK 465 PRO A 159 REMARK 465 PRO A 160 REMARK 465 GLU A 161 REMARK 465 GLU A 162 REMARK 465 GLU A 163 REMARK 465 ASN A 164 REMARK 465 GLU A 165 REMARK 465 SER A 166 REMARK 465 GLU A 167 REMARK 465 PRO A 168 REMARK 465 GLU A 169 REMARK 465 GLU A 170 REMARK 465 PRO A 837 REMARK 465 ARG A 838 REMARK 465 GLN A 839 REMARK 465 ALA A 840 REMARK 465 THR A 841 REMARK 465 PRO A 842 REMARK 465 GLY A 843 REMARK 465 VAL A 844 REMARK 465 PRO A 845 REMARK 465 ALA A 846 REMARK 465 GLN A 847 REMARK 465 GLN A 848 REMARK 465 SER A 849 REMARK 465 PRO A 850 REMARK 465 SER A 851 REMARK 465 MET A 852 REMARK 465 ARG B 305 REMARK 465 ALA B 306 REMARK 465 LYS B 307 REMARK 465 HIS B 441 REMARK 465 GLY B 442 REMARK 465 LYS B 443 REMARK 465 GLU B 444 REMARK 465 GLU B 445 REMARK 465 THR B 446 REMARK 465 ASN B 447 REMARK 465 GLY B 448 REMARK 465 PRO B 449 REMARK 465 SER B 450 REMARK 465 ASN B 451 REMARK 465 GLN B 452 REMARK 465 LYS B 453 REMARK 465 PRO B 454 REMARK 465 VAL B 455 REMARK 465 LYS B 456 REMARK 465 SER B 457 REMARK 465 PRO B 458 REMARK 465 ASP B 459 REMARK 465 ASN B 460 REMARK 465 SER B 461 REMARK 465 ILE B 462 REMARK 465 LYS B 463 REMARK 465 MET B 464 REMARK 465 PRO B 465 REMARK 465 GLU B 466 REMARK 465 GLU B 467 REMARK 465 GLU B 468 REMARK 465 ASP B 469 REMARK 465 GLU B 470 REMARK 465 ALA B 471 REMARK 465 PRO B 472 REMARK 465 VAL B 473 REMARK 465 LEU B 474 REMARK 465 ASP B 475 REMARK 465 VAL B 476 REMARK 465 ARG B 477 REMARK 465 TYR B 478 REMARK 465 ALA B 479 REMARK 465 SER B 480 REMARK 465 ALA B 481 REMARK 465 SER B 482 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ALA A 343 OG SER A 346 2.12 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 SER A 244 -63.76 -28.32 REMARK 500 HIS A 259 40.00 -91.31 REMARK 500 ILE A 270 -71.94 -83.52 REMARK 500 PRO A 272 157.83 -46.43 REMARK 500 MET A 332 -15.34 -140.53 REMARK 500 GLU A 364 170.01 -57.00 REMARK 500 ASN A 403 40.50 36.73 REMARK 500 VAL A 468 99.27 -64.71 REMARK 500 PRO A 516 152.30 -39.55 REMARK 500 SER A 522 -153.41 -68.34 REMARK 500 ALA A 700 -176.10 -56.66 REMARK 500 ARG A 750 62.26 -150.85 REMARK 500 ALA A 757 -55.05 -161.92 REMARK 500 ILE A 793 129.68 -14.68 REMARK 500 PRO B 311 172.33 -59.36 REMARK 500 ALA B 326 -79.92 -19.70 REMARK 500 ALA B 331 -78.13 -28.77 REMARK 500 PRO B 373 145.39 -38.58 REMARK 500 CYS B 379 117.26 -37.89 REMARK 500 ALA B 439 55.86 -67.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 792 ILE A 793 137.39 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 6W1 A 902 DBREF 5LGU A 123 852 UNP O60341 KDM1A_HUMAN 123 852 DBREF 5LGU B 305 482 UNP Q9UKL0 RCOR1_HUMAN 305 482 SEQRES 1 A 730 MET ASP GLU SER LEU ALA ASN LEU SER GLU ASP GLU TYR SEQRES 2 A 730 TYR SER GLU GLU GLU ARG ASN ALA LYS ALA GLU LYS GLU SEQRES 3 A 730 LYS LYS LEU PRO PRO PRO PRO PRO GLN ALA PRO PRO GLU SEQRES 4 A 730 GLU GLU ASN GLU SER GLU PRO GLU GLU PRO SER GLY VAL SEQRES 5 A 730 GLU GLY ALA ALA PHE GLN SER ARG LEU PRO HIS ASP ARG SEQRES 6 A 730 MET THR SER GLN GLU ALA ALA CYS PHE PRO ASP ILE ILE SEQRES 7 A 730 SER GLY PRO GLN GLN THR GLN LYS VAL PHE LEU PHE ILE SEQRES 8 A 730 ARG ASN ARG THR LEU GLN LEU TRP LEU ASP ASN PRO LYS SEQRES 9 A 730 ILE GLN LEU THR PHE GLU ALA THR LEU GLN GLN LEU GLU SEQRES 10 A 730 ALA PRO TYR ASN SER ASP THR VAL LEU VAL HIS ARG VAL SEQRES 11 A 730 HIS SER TYR LEU GLU ARG HIS GLY LEU ILE ASN PHE GLY SEQRES 12 A 730 ILE TYR LYS ARG ILE LYS PRO LEU PRO THR LYS LYS THR SEQRES 13 A 730 GLY LYS VAL ILE ILE ILE GLY SER GLY VAL SER GLY LEU SEQRES 14 A 730 ALA ALA ALA ARG GLN LEU GLN SER PHE GLY MET ASP VAL SEQRES 15 A 730 THR LEU LEU GLU ALA ARG ASP ARG VAL GLY GLY ARG VAL SEQRES 16 A 730 ALA THR PHE ARG LYS GLY ASN TYR VAL ALA ASP LEU GLY SEQRES 17 A 730 ALA MET VAL VAL THR GLY LEU GLY GLY ASN PRO MET ALA SEQRES 18 A 730 VAL VAL SER LYS GLN VAL ASN MET GLU LEU ALA LYS ILE SEQRES 19 A 730 LYS GLN LYS CYS PRO LEU TYR GLU ALA ASN GLY GLN ALA SEQRES 20 A 730 VAL PRO LYS GLU LYS ASP GLU MET VAL GLU GLN GLU PHE SEQRES 21 A 730 ASN ARG LEU LEU GLU ALA THR SER TYR LEU SER HIS GLN SEQRES 22 A 730 LEU ASP PHE ASN VAL LEU ASN ASN LYS PRO VAL SER LEU SEQRES 23 A 730 GLY GLN ALA LEU GLU VAL VAL ILE GLN LEU GLN GLU LYS SEQRES 24 A 730 HIS VAL LYS ASP GLU GLN ILE GLU HIS TRP LYS LYS ILE SEQRES 25 A 730 VAL LYS THR GLN GLU GLU LEU LYS GLU LEU LEU ASN LYS SEQRES 26 A 730 MET VAL ASN LEU LYS GLU LYS ILE LYS GLU LEU HIS GLN SEQRES 27 A 730 GLN TYR LYS GLU ALA SER GLU VAL LYS PRO PRO ARG ASP SEQRES 28 A 730 ILE THR ALA GLU PHE LEU VAL LYS SER LYS HIS ARG ASP SEQRES 29 A 730 LEU THR ALA LEU CYS LYS GLU TYR ASP GLU LEU ALA GLU SEQRES 30 A 730 THR GLN GLY LYS LEU GLU GLU LYS LEU GLN GLU LEU GLU SEQRES 31 A 730 ALA ASN PRO PRO SER ASP VAL TYR LEU SER SER ARG ASP SEQRES 32 A 730 ARG GLN ILE LEU ASP TRP HIS PHE ALA ASN LEU GLU PHE SEQRES 33 A 730 ALA ASN ALA THR PRO LEU SER THR LEU SER LEU LYS HIS SEQRES 34 A 730 TRP ASP GLN ASP ASP ASP PHE GLU PHE THR GLY SER HIS SEQRES 35 A 730 LEU THR VAL ARG ASN GLY TYR SER CYS VAL PRO VAL ALA SEQRES 36 A 730 LEU ALA GLU GLY LEU ASP ILE LYS LEU ASN THR ALA VAL SEQRES 37 A 730 ARG GLN VAL ARG TYR THR ALA SER GLY CYS GLU VAL ILE SEQRES 38 A 730 ALA VAL ASN THR ARG SER THR SER GLN THR PHE ILE TYR SEQRES 39 A 730 LYS CYS ASP ALA VAL LEU CYS THR LEU PRO LEU GLY VAL SEQRES 40 A 730 LEU LYS GLN GLN PRO PRO ALA VAL GLN PHE VAL PRO PRO SEQRES 41 A 730 LEU PRO GLU TRP LYS THR SER ALA VAL GLN ARG MET GLY SEQRES 42 A 730 PHE GLY ASN LEU ASN LYS VAL VAL LEU CYS PHE ASP ARG SEQRES 43 A 730 VAL PHE TRP ASP PRO SER VAL ASN LEU PHE GLY HIS VAL SEQRES 44 A 730 GLY SER THR THR ALA SER ARG GLY GLU LEU PHE LEU PHE SEQRES 45 A 730 TRP ASN LEU TYR LYS ALA PRO ILE LEU LEU ALA LEU VAL SEQRES 46 A 730 ALA GLY GLU ALA ALA GLY ILE MET GLU ASN ILE SER ASP SEQRES 47 A 730 ASP VAL ILE VAL GLY ARG CYS LEU ALA ILE LEU LYS GLY SEQRES 48 A 730 ILE PHE GLY SER SER ALA VAL PRO GLN PRO LYS GLU THR SEQRES 49 A 730 VAL VAL SER ARG TRP ARG ALA ASP PRO TRP ALA ARG GLY SEQRES 50 A 730 SER TYR SER TYR VAL ALA ALA GLY SER SER GLY ASN ASP SEQRES 51 A 730 TYR ASP LEU MET ALA GLN PRO ILE THR PRO GLY PRO SER SEQRES 52 A 730 ILE PRO GLY ALA PRO GLN PRO ILE PRO ARG LEU PHE PHE SEQRES 53 A 730 ALA GLY GLU HIS THR ILE ARG ASN TYR PRO ALA THR VAL SEQRES 54 A 730 HIS GLY ALA LEU LEU SER GLY LEU ARG GLU ALA GLY ARG SEQRES 55 A 730 ILE ALA ASP GLN PHE LEU GLY ALA MET TYR THR LEU PRO SEQRES 56 A 730 ARG GLN ALA THR PRO GLY VAL PRO ALA GLN GLN SER PRO SEQRES 57 A 730 SER MET SEQRES 1 B 178 ARG ALA LYS ARG LYS PRO PRO LYS GLY MET PHE LEU SER SEQRES 2 B 178 GLN GLU ASP VAL GLU ALA VAL SER ALA ASN ALA THR ALA SEQRES 3 B 178 ALA THR THR VAL LEU ARG GLN LEU ASP MET GLU LEU VAL SEQRES 4 B 178 SER VAL LYS ARG GLN ILE GLN ASN ILE LYS GLN THR ASN SEQRES 5 B 178 SER ALA LEU LYS GLU LYS LEU ASP GLY GLY ILE GLU PRO SEQRES 6 B 178 TYR ARG LEU PRO GLU VAL ILE GLN LYS CYS ASN ALA ARG SEQRES 7 B 178 TRP THR THR GLU GLU GLN LEU LEU ALA VAL GLN ALA ILE SEQRES 8 B 178 ARG LYS TYR GLY ARG ASP PHE GLN ALA ILE SER ASP VAL SEQRES 9 B 178 ILE GLY ASN LYS SER VAL VAL GLN VAL LYS ASN PHE PHE SEQRES 10 B 178 VAL ASN TYR ARG ARG ARG PHE ASN ILE ASP GLU VAL LEU SEQRES 11 B 178 GLN GLU TRP GLU ALA GLU HIS GLY LYS GLU GLU THR ASN SEQRES 12 B 178 GLY PRO SER ASN GLN LYS PRO VAL LYS SER PRO ASP ASN SEQRES 13 B 178 SER ILE LYS MET PRO GLU GLU GLU ASP GLU ALA PRO VAL SEQRES 14 B 178 LEU ASP VAL ARG TYR ALA SER ALA SER HET FAD A 901 53 HET 6W1 A 902 33 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM 6W1 4-METHYL-~{N}-[2-[[4-[[(3~{R})-PYRROLIDIN-3- HETNAM 2 6W1 YL]METHOXY]PHENOXY]METHYL]PHENYL]THIENO[3,2-B]PYRROLE- HETNAM 3 6W1 5-CARBOXAMIDE FORMUL 3 FAD C27 H33 N9 O15 P2 FORMUL 4 6W1 C26 H27 N3 O3 S HELIX 1 AA1 VAL A 174 SER A 181 1 8 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 ASP A 223 1 21 HELIX 5 AA5 THR A 230 GLN A 237 1 8 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 ASP A 553 GLU A 559 5 7 HELIX 14 AB5 SER A 572 ALA A 579 1 8 HELIX 15 AB6 PRO A 626 GLN A 632 1 7 HELIX 16 AB7 PRO A 644 MET A 654 1 11 HELIX 17 AB8 ALA A 708 GLU A 716 1 9 HELIX 18 AB9 SER A 719 GLY A 736 1 18 HELIX 19 AC1 SER A 769 GLN A 778 1 10 HELIX 20 AC2 THR A 810 GLY A 831 1 22 HELIX 21 AC3 SER B 317 ALA B 323 1 7 HELIX 22 AC4 THR B 329 LEU B 363 1 35 HELIX 23 AC5 ILE B 367 ARG B 371 5 5 HELIX 24 AC6 THR B 384 GLY B 399 1 16 HELIX 25 AC7 ASP B 401 GLY B 410 1 10 HELIX 26 AC8 SER B 413 ARG B 425 1 13 HELIX 27 AC9 ASN B 429 ALA B 439 1 11 SHEET 1 AA1 5 ILE A 584 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 THR A 335 0 SHEET 2 AA3 3 HIS A 564 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 4 THR A 613 CYS A 618 0 SHEET 2 AA4 4 GLY A 599 ASN A 606 -1 N CYS A 600 O CYS A 618 SHEET 3 AA4 4 THR A 588 THR A 596 -1 N ARG A 591 O ILE A 603 SHEET 4 AA4 4 GLN A 638 VAL A 640 1 O VAL A 640 N VAL A 593 SHEET 1 AA5 2 GLY A 655 PHE A 656 0 SHEET 2 AA5 2 SER A 762 TYR A 763 -1 O TYR A 763 N GLY A 655 SHEET 1 AA6 5 LEU A 677 GLY A 679 0 SHEET 2 AA6 5 GLU A 690 ASN A 696 -1 O PHE A 694 N PHE A 678 SHEET 3 AA6 5 ILE A 702 VAL A 707 -1 O LEU A 704 N TRP A 695 SHEET 4 AA6 5 ASN A 660 CYS A 665 -1 N ASN A 660 O VAL A 707 SHEET 5 AA6 5 GLU A 745 VAL A 748 -1 O VAL A 747 N VAL A 663 CISPEP 1 ALA A 240 PRO A 241 0 -0.38 CISPEP 2 PRO A 470 PRO A 471 0 -0.72 CISPEP 3 GLN A 633 PRO A 634 0 -1.55 CISPEP 4 VAL A 640 PRO A 641 0 8.23 SITE 1 AC1 32 GLY A 285 GLY A 287 VAL A 288 SER A 289 SITE 2 AC1 32 LEU A 307 GLU A 308 ALA A 309 ARG A 310 SITE 3 AC1 32 GLY A 314 GLY A 315 ARG A 316 LEU A 329 SITE 4 AC1 32 GLY A 330 ALA A 331 MET A 332 VAL A 333 SITE 5 AC1 32 THR A 588 ALA A 589 VAL A 590 THR A 624 SITE 6 AC1 32 LEU A 625 PRO A 626 TRP A 756 SER A 760 SITE 7 AC1 32 TYR A 761 GLY A 800 GLU A 801 ALA A 809 SITE 8 AC1 32 THR A 810 VAL A 811 ALA A 814 6W1 A 902 SITE 1 AC2 7 THR A 335 ALA A 539 ASP A 555 TRP A 695 SITE 2 AC2 7 TYR A 761 ALA A 809 FAD A 901 CRYST1 121.409 181.155 237.456 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 0.008237 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005520 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004211 0.00000