HEADER FLAVOPROTEIN 11-MAR-20 6W4K TITLE CRYSTAL STRUCTURE OF LYSINE SPECIFIC DEMETHYLASE 1 (LSD1) WITH CC- TITLE 2 90011 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 HUMAN LSD1 INHIBITOR-COMPLEX, FLAVOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.J.HOSFIELD REVDAT 3 18-OCT-23 6W4K 1 REMARK REVDAT 2 03-NOV-21 6W4K 1 JRNL REVDAT 1 21-OCT-20 6W4K 0 JRNL AUTH T.KANOUNI,C.SEVERIN,R.W.CHO,N.Y.YUEN,J.XU,L.SHI,C.LAI, JRNL AUTH 2 J.R.DEL ROSARIO,R.K.STANSFIELD,L.N.LAWTON,D.HOSFIELD, JRNL AUTH 3 S.O'CONNELL,M.M.KREILEIN,P.TAVARES-GRECO,Z.NIE,S.W.KALDOR, JRNL AUTH 4 J.M.VEAL,J.A.STAFFORD,Y.K.CHEN JRNL TITL DISCOVERY OF CC-90011: A POTENT AND SELECTIVE REVERSIBLE JRNL TITL 2 INHIBITOR OF LYSINE SPECIFIC DEMETHYLASE 1 (LSD1). JRNL REF J.MED.CHEM. V. 63 14522 2020 JRNL REFN ISSN 0022-2623 JRNL PMID 33034194 JRNL DOI 10.1021/ACS.JMEDCHEM.0C00978 REMARK 2 REMARK 2 RESOLUTION. 2.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 52530 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2723 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3639 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.4020 REMARK 3 BIN FREE R VALUE SET COUNT : 206 REMARK 3 BIN FREE R VALUE : 0.4130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6115 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 22 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 89.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.99000 REMARK 3 B22 (A**2) : -5.79000 REMARK 3 B33 (A**2) : -4.21000 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): 0.271 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.242 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.211 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.550 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6333 ; 0.010 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 5916 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8593 ; 1.941 ; 1.651 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13737 ; 1.316 ; 1.578 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 772 ; 9.365 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 330 ;35.426 ;22.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1095 ;20.663 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 41 ;22.102 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 813 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7030 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1285 ; 0.002 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : MASK 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6W4K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1000247568. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55358 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.930 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.90200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3ZMU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 83.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 7.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3M NA TARTRATE, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 60.82750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 89.25500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 118.02450 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 60.82750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 89.25500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 118.02450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 60.82750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 89.25500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 118.02450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 60.82750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 89.25500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 118.02450 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: 6530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 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 ALA A 343 REMARK 465 VAL A 344 REMARK 465 VAL A 345 REMARK 465 SER A 346 REMARK 465 LYS A 347 REMARK 465 GLN A 348 REMARK 465 VAL A 349 REMARK 465 ASN A 350 REMARK 465 LEU B 372 REMARK 465 PRO B 373 REMARK 465 GLU B 374 REMARK 465 VAL B 375 REMARK 465 ILE B 376 REMARK 465 GLN B 377 REMARK 465 LYS B 378 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 OG SER A 762 OE2 GLU A 801 2.04 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 MET A 342 C MET A 342 O 0.130 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ARG A 251 CG - CD - NE ANGL. DEV. = 12.9 DEGREES REMARK 500 ARG A 251 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 795 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 426 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES 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 PHE A 196 53.30 -149.97 REMARK 500 GLU A 232 -82.75 -39.19 REMARK 500 ALA A 240 -152.73 51.87 REMARK 500 PRO A 241 22.32 -79.18 REMARK 500 ASN A 243 3.81 -66.61 REMARK 500 SER A 244 -83.36 -50.83 REMARK 500 ILE A 270 -64.15 -99.26 REMARK 500 PRO A 274 104.70 -25.76 REMARK 500 THR A 275 -70.70 -11.81 REMARK 500 THR A 335 62.88 -59.81 REMARK 500 PRO A 341 1.44 -49.71 REMARK 500 GLN A 358 44.78 -90.07 REMARK 500 TYR A 363 85.88 -159.02 REMARK 500 GLU A 364 162.23 -42.11 REMARK 500 ALA A 369 171.93 -49.76 REMARK 500 PHE A 398 75.33 -116.18 REMARK 500 LEU A 401 101.16 -178.77 REMARK 500 ASN A 402 37.42 90.01 REMARK 500 ASN A 403 -57.48 69.02 REMARK 500 ILE A 428 -81.36 -58.84 REMARK 500 GLU A 429 -26.31 -38.00 REMARK 500 LYS A 454 -19.70 -48.77 REMARK 500 GLU A 457 -74.26 -29.53 REMARK 500 GLN A 460 -83.51 -45.02 REMARK 500 GLN A 461 -34.01 -30.11 REMARK 500 VAL A 468 100.41 -40.65 REMARK 500 PRO A 471 83.51 -64.24 REMARK 500 SER A 482 -64.55 -29.40 REMARK 500 ARG A 485 -71.57 -59.07 REMARK 500 GLU A 510 -71.93 -60.07 REMARK 500 SER A 522 -147.79 -51.82 REMARK 500 THR A 610 -50.24 -14.50 REMARK 500 PRO A 626 151.40 -48.53 REMARK 500 GLN A 632 124.20 -39.71 REMARK 500 GLU A 645 -59.98 -27.90 REMARK 500 LEU A 659 122.12 -173.35 REMARK 500 ALA A 686 -8.26 -58.23 REMARK 500 ALA A 729 -70.32 -33.78 REMARK 500 SER A 737 11.95 -64.53 REMARK 500 SER A 738 -10.52 -154.20 REMARK 500 ALA A 757 -49.60 -136.77 REMARK 500 SER A 760 -61.55 -98.18 REMARK 500 GLN A 791 116.84 -29.25 REMARK 500 ILE A 793 138.21 2.84 REMARK 500 GLU A 801 -50.70 -18.85 REMARK 500 TYR A 807 38.05 -141.73 REMARK 500 LEU B 316 86.46 -157.78 REMARK 500 ASN B 327 -157.97 -134.80 REMARK 500 THR B 329 -0.58 -144.58 REMARK 500 ALA B 331 -84.00 -14.84 REMARK 500 REMARK 500 THIS ENTRY HAS 59 RAMACHANDRAN OUTLIERS. 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 LYS A 469 PRO A 470 -145.94 REMARK 500 LEU A 697 TYR A 698 -147.69 REMARK 500 PRO A 792 ILE A 793 123.98 REMARK 500 GLU B 438 ALA B 439 -144.31 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 V0Y A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FAD A 902 DBREF 6W4K A 174 832 UNP O60341 KDM1A_HUMAN 174 832 DBREF 6W4K B 309 440 UNP Q9UKL0 RCOR1_HUMAN 312 443 SEQRES 1 A 659 VAL GLU GLY ALA ALA PHE GLN SER ARG LEU PRO HIS ASP SEQRES 2 A 659 ARG MET THR SER GLN GLU ALA ALA CYS PHE PRO ASP ILE SEQRES 3 A 659 ILE SER GLY PRO GLN GLN THR GLN LYS VAL PHE LEU PHE SEQRES 4 A 659 ILE ARG ASN ARG THR LEU GLN LEU TRP LEU ASP ASN PRO SEQRES 5 A 659 LYS ILE GLN LEU THR PHE GLU ALA THR LEU GLN GLN LEU SEQRES 6 A 659 GLU ALA PRO TYR ASN SER ASP THR VAL LEU VAL HIS ARG SEQRES 7 A 659 VAL HIS SER TYR LEU GLU ARG HIS GLY LEU ILE ASN PHE SEQRES 8 A 659 GLY ILE TYR LYS ARG ILE LYS PRO LEU PRO THR LYS LYS SEQRES 9 A 659 THR GLY LYS VAL ILE ILE ILE GLY SER GLY VAL SER GLY SEQRES 10 A 659 LEU ALA ALA ALA ARG GLN LEU GLN SER PHE GLY MET ASP SEQRES 11 A 659 VAL THR LEU LEU GLU ALA ARG ASP ARG VAL GLY GLY ARG SEQRES 12 A 659 VAL ALA THR PHE ARG LYS GLY ASN TYR VAL ALA ASP LEU SEQRES 13 A 659 GLY ALA MET VAL VAL THR GLY LEU GLY GLY ASN PRO MET SEQRES 14 A 659 ALA VAL VAL SER LYS GLN VAL ASN MET GLU LEU ALA LYS SEQRES 15 A 659 ILE LYS GLN LYS CYS PRO LEU TYR GLU ALA ASN GLY GLN SEQRES 16 A 659 ALA VAL PRO LYS GLU LYS ASP GLU MET VAL GLU GLN GLU SEQRES 17 A 659 PHE ASN ARG LEU LEU GLU ALA THR SER TYR LEU SER HIS SEQRES 18 A 659 GLN LEU ASP PHE ASN VAL LEU ASN ASN LYS PRO VAL SER SEQRES 19 A 659 LEU GLY GLN ALA LEU GLU VAL VAL ILE GLN LEU GLN GLU SEQRES 20 A 659 LYS HIS VAL LYS ASP GLU GLN ILE GLU HIS TRP LYS LYS SEQRES 21 A 659 ILE VAL LYS THR GLN GLU GLU LEU LYS GLU LEU LEU ASN SEQRES 22 A 659 LYS MET VAL ASN LEU LYS GLU LYS ILE LYS GLU LEU HIS SEQRES 23 A 659 GLN GLN TYR LYS GLU ALA SER GLU VAL LYS PRO PRO ARG SEQRES 24 A 659 ASP ILE THR ALA GLU PHE LEU VAL LYS SER LYS HIS ARG SEQRES 25 A 659 ASP LEU THR ALA LEU CYS LYS GLU TYR ASP GLU LEU ALA SEQRES 26 A 659 GLU THR GLN GLY LYS LEU GLU GLU LYS LEU GLN GLU LEU SEQRES 27 A 659 GLU ALA ASN PRO PRO SER ASP VAL TYR LEU SER SER ARG SEQRES 28 A 659 ASP ARG GLN ILE LEU ASP TRP HIS PHE ALA ASN LEU GLU SEQRES 29 A 659 PHE ALA ASN ALA THR PRO LEU SER THR LEU SER LEU LYS SEQRES 30 A 659 HIS TRP ASP GLN ASP ASP ASP PHE GLU PHE THR GLY SER SEQRES 31 A 659 HIS LEU THR VAL ARG ASN GLY TYR SER CYS VAL PRO VAL SEQRES 32 A 659 ALA LEU ALA GLU GLY LEU ASP ILE LYS LEU ASN THR ALA SEQRES 33 A 659 VAL ARG GLN VAL ARG TYR THR ALA SER GLY CYS GLU VAL SEQRES 34 A 659 ILE ALA VAL ASN THR ARG SER THR SER GLN THR PHE ILE SEQRES 35 A 659 TYR LYS CYS ASP ALA VAL LEU CYS THR LEU PRO LEU GLY SEQRES 36 A 659 VAL LEU LYS GLN GLN PRO PRO ALA VAL GLN PHE VAL PRO SEQRES 37 A 659 PRO LEU PRO GLU TRP LYS THR SER ALA VAL GLN ARG MET SEQRES 38 A 659 GLY PHE GLY ASN LEU ASN LYS VAL VAL LEU CYS PHE ASP SEQRES 39 A 659 ARG VAL PHE TRP ASP PRO SER VAL ASN LEU PHE GLY HIS SEQRES 40 A 659 VAL GLY SER THR THR ALA SER ARG GLY GLU LEU PHE LEU SEQRES 41 A 659 PHE TRP ASN LEU TYR LYS ALA PRO ILE LEU LEU ALA LEU SEQRES 42 A 659 VAL ALA GLY GLU ALA ALA GLY ILE MET GLU ASN ILE SER SEQRES 43 A 659 ASP ASP VAL ILE VAL GLY ARG CYS LEU ALA ILE LEU LYS SEQRES 44 A 659 GLY ILE PHE GLY SER SER ALA VAL PRO GLN PRO LYS GLU SEQRES 45 A 659 THR VAL VAL SER ARG TRP ARG ALA ASP PRO TRP ALA ARG SEQRES 46 A 659 GLY SER TYR SER TYR VAL ALA ALA GLY SER SER GLY ASN SEQRES 47 A 659 ASP TYR ASP LEU MET ALA GLN PRO ILE THR PRO GLY PRO SEQRES 48 A 659 SER ILE PRO GLY ALA PRO GLN PRO ILE PRO ARG LEU PHE SEQRES 49 A 659 PHE ALA GLY GLU HIS THR ILE ARG ASN TYR PRO ALA THR SEQRES 50 A 659 VAL HIS GLY ALA LEU LEU SER GLY LEU ARG GLU ALA GLY SEQRES 51 A 659 ARG ILE ALA ASP GLN PHE LEU GLY ALA SEQRES 1 B 132 LYS PRO PRO LYS GLY MET PHE LEU SER GLN GLU ASP VAL SEQRES 2 B 132 GLU ALA VAL SER ALA ASN ALA THR ALA ALA THR THR VAL SEQRES 3 B 132 LEU ARG GLN LEU ASP MET GLU LEU VAL SER VAL LYS ARG SEQRES 4 B 132 GLN ILE GLN ASN ILE LYS GLN THR ASN SER ALA LEU LYS SEQRES 5 B 132 GLU LYS LEU ASP GLY GLY ILE GLU PRO TYR ARG LEU PRO SEQRES 6 B 132 GLU VAL ILE GLN LYS CYS ASN ALA ARG TRP THR THR GLU SEQRES 7 B 132 GLU GLN LEU LEU ALA VAL GLN ALA ILE ARG LYS TYR GLY SEQRES 8 B 132 ARG ASP PHE GLN ALA ILE SER ASP VAL ILE GLY ASN LYS SEQRES 9 B 132 SER VAL VAL GLN VAL LYS ASN PHE PHE VAL ASN TYR ARG SEQRES 10 B 132 ARG ARG PHE ASN ILE ASP GLU VAL LEU GLN GLU TRP GLU SEQRES 11 B 132 ALA GLU HET V0Y A 901 33 HET FAD A 902 53 HETNAM V0Y 4-[2-(4-AMINOPIPERIDIN-1-YL)-5-(3-FLUORO-4- HETNAM 2 V0Y METHOXYPHENYL)-1-METHYL-6-OXO-1,6-DIHYDROPYRIMIDIN-4- HETNAM 3 V0Y YL]-2-FLUOROBENZONITRILE HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 3 V0Y C24 H23 F2 N5 O2 FORMUL 4 FAD C27 H33 N9 O15 P2 FORMUL 5 HOH *22(H2 O) HELIX 1 AA1 VAL A 174 PHE A 179 1 6 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 GLN A 237 1 8 HELIX 6 AA6 THR A 246 HIS A 259 1 14 HELIX 7 AA7 GLY A 287 PHE A 300 1 14 HELIX 8 AA8 PRO A 371 GLN A 395 1 25 HELIX 9 AA9 SER A 407 VAL A 468 1 62 HELIX 10 AB1 ASP A 473 GLU A 512 1 40 HELIX 11 AB2 SER A 523 ASN A 540 1 18 HELIX 12 AB3 ASP A 555 GLU A 559 5 5 HELIX 13 AB4 SER A 572 GLU A 580 1 9 HELIX 14 AB5 PRO A 626 GLN A 632 1 7 HELIX 15 AB6 PRO A 644 MET A 654 1 11 HELIX 16 AB7 THR A 684 ARG A 688 5 5 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 GLY A 770 GLN A 778 1 9 HELIX 20 AC2 GLY A 800 ILE A 804 5 5 HELIX 21 AC3 THR A 810 LEU A 830 1 21 HELIX 22 AC4 SER B 317 ALA B 326 1 10 HELIX 23 AC5 THR B 329 LEU B 363 1 35 HELIX 24 AC6 ILE B 367 ARG B 371 5 5 HELIX 25 AC7 THR B 384 LYS B 397 1 14 HELIX 26 AC8 ASP B 401 GLY B 410 1 10 HELIX 27 AC9 SER B 413 TYR B 424 1 12 HELIX 28 AD1 ASN B 429 GLU B 438 1 10 SHEET 1 AA1 5 ASP A 583 LYS A 585 0 SHEET 2 AA1 5 ASP A 303 LEU A 307 1 N LEU A 306 O LYS A 585 SHEET 3 AA1 5 LYS A 280 ILE A 284 1 N VAL A 281 O ASP A 303 SHEET 4 AA1 5 ALA A 620 CYS A 623 1 O LEU A 622 N ILE A 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 VAL A 602 O TYR A 616 SHEET 3 AA4 4 THR A 588 THR A 596 -1 N GLN A 592 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 LEU A 693 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 LEU A 664 O LEU A 703 SHEET 5 AA6 5 GLU A 745 VAL A 748 -1 O VAL A 747 N VAL A 663 CISPEP 1 VAL A 640 PRO A 641 0 1.17 SITE 1 AC1 14 MET A 332 VAL A 333 THR A 335 ILE A 356 SITE 2 AC1 14 GLN A 358 PHE A 538 ALA A 539 ASP A 555 SITE 3 AC1 14 HIS A 564 LEU A 659 LYS A 661 TRP A 695 SITE 4 AC1 14 TYR A 761 FAD A 902 SITE 1 AC2 40 GLY A 285 GLY A 287 VAL A 288 SER A 289 SITE 2 AC2 40 LEU A 307 GLU A 308 ALA A 309 ARG A 310 SITE 3 AC2 40 GLY A 314 GLY A 315 ARG A 316 VAL A 317 SITE 4 AC2 40 LEU A 329 GLY A 330 ALA A 331 MET A 332 SITE 5 AC2 40 VAL A 333 THR A 588 ALA A 589 VAL A 590 SITE 6 AC2 40 THR A 624 LEU A 625 PRO A 626 TRP A 751 SITE 7 AC2 40 TRP A 756 SER A 760 TYR A 761 GLY A 800 SITE 8 AC2 40 GLU A 801 ALA A 809 THR A 810 VAL A 811 SITE 9 AC2 40 ALA A 814 V0Y A 901 HOH A1003 HOH A1005 SITE 10 AC2 40 HOH A1006 HOH A1007 HOH A1010 HOH A1011 CRYST1 121.655 178.510 236.049 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 0.008220 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005602 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004236 0.00000