HEADER OXIDOREDUCTASE 17-SEP-12 4BAY TITLE PHOSPHOMIMETIC MUTANT OF LSD1-8A SPLICING VARIANT IN COMPLEX WITH TITLE 2 COREST COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 192-876; COMPND 5 SYNONYM: BRAF35-HDAC COMPLEX PROTEIN BHC110, FLAVIN-CONTAINING AMINE COMPND 6 OXIDASE DOMAIN-CONTAINING PROTEIN 2, LSD1; COMPND 7 EC: 1.-.-.-; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: REST COREPRESSOR 1; COMPND 12 CHAIN: B; COMPND 13 FRAGMENT: RESIDUES 308-440; COMPND 14 SYNONYM: PROTEIN COREST; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS OXIDOREDUCTASE, DEMETHYLASE SPLICING CHROMATIN EXPDTA X-RAY DIFFRACTION AUTHOR E.TOFFOLO,L.PAGANINI,F.RUSCONI,M.TORTORICI,S.PILOTTO,C.VERPELLI, AUTHOR 2 G.TEDESCHI,E.MAFFIOLI,C.SALA,A.MATTEVI,E.BATTAGLIOLI REVDAT 4 20-DEC-23 4BAY 1 REMARK REVDAT 3 08-MAY-19 4BAY 1 REMARK REVDAT 2 19-MAR-14 4BAY 1 JRNL REVDAT 1 27-NOV-13 4BAY 0 JRNL AUTH E.TOFFOLO,F.RUSCONI,L.PAGANINI,M.TORTORICI,S.PILOTTO, JRNL AUTH 2 C.HEISE,C.VERPELLI,G.TEDESCHI,E.MAFFIOLI,C.SALA,A.MATTEVI, JRNL AUTH 3 E.BATTAGLIOLI JRNL TITL PHOSPHORYLATION OF NEURONAL LYSINE-SPECIFIC DEMETHYLASE JRNL TITL 2 1LSD1/KDM1A IMPAIRS TRANSCRIPTIONAL REPRESSION BY REGULATING JRNL TITL 3 INTERACTION WITH COREST AND HISTONE DEACETYLASES HDAC1/2. JRNL REF J.NEUROCHEM. V. 128 616 2014 JRNL REFN ISSN 0022-3042 JRNL PMID 24111946 JRNL DOI 10.1111/JNC.12457 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0027 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 44180 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.900 REMARK 3 FREE R VALUE TEST SET COUNT : 874 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) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3227 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.3070 REMARK 3 BIN FREE R VALUE SET COUNT : 64 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6325 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 3 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 80.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.42000 REMARK 3 B22 (A**2) : -3.77000 REMARK 3 B33 (A**2) : -1.65000 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): 0.382 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.268 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.223 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.101 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6512 ; 0.005 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8835 ; 0.907 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 801 ; 4.492 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 297 ;36.198 ;24.512 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1137 ;16.161 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;13.896 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 989 ; 0.058 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4900 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U REMARK 3 VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4BAY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1290054136. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-11 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 : ESRF REMARK 200 BEAMLINE : ID14-1 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44180 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 65.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.60000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2X0L REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 6.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20DEG BY HANGING-DROP VAPOR DIFFUSION REMARK 280 METHOD BY MIXING EQUAL VOLUMES OF PROTEIN SAMPLES WITH RESERVOIR REMARK 280 SOLUTIONS CONTAINING 1.2 M SODIUM/POTASSIUM TARTRATE AND 100 MM REMARK 280 N-(2-ACETAMIDO)IMINODIACETIC ACID, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 58.99000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 89.56000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 116.82000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 58.99000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 89.56000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 116.82000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 58.99000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 89.56000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 116.82000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 58.99000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 89.56000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 116.82000 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: 6760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.1 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 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 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 286 42.41 -106.85 REMARK 500 MET A 332 -34.14 -136.50 REMARK 500 MET A 351 87.12 41.75 REMARK 500 ASN A 366 48.85 -141.76 REMARK 500 PHE A 398 68.42 -103.29 REMARK 500 ASN A 514 75.70 -118.95 REMARK 500 LEU A 697 -86.32 -129.46 REMARK 500 LYS A 699 -4.60 -57.86 REMARK 500 SER A 737 15.30 -64.19 REMARK 500 SER A 738 -33.00 -138.85 REMARK 500 ALA A 757 -54.92 -144.37 REMARK 500 SER A 785 -70.80 -68.44 REMARK 500 TYR A 807 45.85 -141.63 REMARK 500 PRO B 311 153.31 -48.31 REMARK 500 LYS B 312 102.02 -53.00 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 900 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2COM RELATED DB: PDB REMARK 900 THE SOLUTION STRUCTURE OF THE 33RD FIBRONECTIN TYPE IIIDOMAIN OF REMARK 900 HUMAN TENASCIN-X REMARK 900 RELATED ID: 2H94 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE AND MECHANISM OF HUMAN LYSINE- REMARK 900 SPECIFICDEMETHYLASE-1 REMARK 900 RELATED ID: 2IW5 RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR COREST-DEPENDENT DEMETHYLATION OF NUCLEOSOMES REMARK 900 BY THE HUMAN LSD1 HISTONE DEMETHYLASE REMARK 900 RELATED ID: 2UXN RELATED DB: PDB REMARK 900 STRUCTURAL BASIS OF HISTONE DEMETHYLATION BY LSD1 REVEALED BY REMARK 900 SUICIDE INACTIVATION REMARK 900 RELATED ID: 2UXX RELATED DB: PDB REMARK 900 HUMAN LSD1 HISTONE DEMETHYLASE-COREST IN COMPLEX WITH AN FAD- REMARK 900 TRANYLCYPROMINE ADDUCT REMARK 900 RELATED ID: 2V1D RELATED DB: PDB REMARK 900 STRUCTURAL BASIS OF LSD1-COREST SELECTIVITY IN HISTONE H3 REMARK 900 RECOGNITION REMARK 900 RELATED ID: 2X0L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A NEURO-SPECIFIC SPLICING VARIANT OF HUMAN REMARK 900 HISTONE LYSINE DEMETHYLASE LSD1. REMARK 900 RELATED ID: 2XAF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH PARA -BROMO-(+)- REMARK 900 CIS-2-PHENYLCYCLOPROPYL-1-AMINE REMARK 900 RELATED ID: 2XAG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH PARA -BROMO-(-)- REMARK 900 TRANS-2-PHENYLCYCLOPROPYL-1-AMINE REMARK 900 RELATED ID: 2XAH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH (+)- TRANS-2- REMARK 900 PHENYLCYCLOPROPYL-1-AMINE REMARK 900 RELATED ID: 2XAJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH (-)- TRANS-2- REMARK 900 PHENYLCYCLOPROPYL-1-AMINE REMARK 900 RELATED ID: 2XAQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH A TRANYLCYPROMINE REMARK 900 DERIVATIVE (MC2584, 13B) REMARK 900 RELATED ID: 2XAS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH A TRANYLCYPROMINE REMARK 900 DERIVATIVE (MC2580, 14E) REMARK 900 RELATED ID: 2Y48 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH A N -TERMINAL REMARK 900 SNAIL PEPTIDE REMARK 999 REMARK 999 SEQUENCE REMARK 999 MUTATION OF THREONINE 369B IN ASPARTATE DBREF 4BAY A 172 852 UNP O60341 KDM1A_HUMAN 192 876 DBREF 4BAY B 308 440 UNP Q9UKL0 RCOR1_HUMAN 308 440 SEQADV 4BAY PRO A 171 UNP O60341 EXPRESSION TAG SEQADV 4BAY ASP A 369B UNP O60341 THR 391 ENGINEERED MUTATION SEQRES 1 A 686 PRO SER GLY VAL GLU GLY ALA ALA PHE GLN SER ARG LEU SEQRES 2 A 686 PRO HIS ASP ARG MET THR SER GLN GLU ALA ALA CYS PHE SEQRES 3 A 686 PRO ASP ILE ILE SER GLY PRO GLN GLN THR GLN LYS VAL SEQRES 4 A 686 PHE LEU PHE ILE ARG ASN ARG THR LEU GLN LEU TRP LEU SEQRES 5 A 686 ASP ASN PRO LYS ILE GLN LEU THR PHE GLU ALA THR LEU SEQRES 6 A 686 GLN GLN LEU GLU ALA PRO TYR ASN SER ASP THR VAL LEU SEQRES 7 A 686 VAL HIS ARG VAL HIS SER TYR LEU GLU ARG HIS GLY LEU SEQRES 8 A 686 ILE ASN PHE GLY ILE TYR LYS ARG ILE LYS PRO LEU PRO SEQRES 9 A 686 THR LYS LYS THR GLY LYS VAL ILE ILE ILE GLY SER GLY SEQRES 10 A 686 VAL SER GLY LEU ALA ALA ALA ARG GLN LEU GLN SER PHE SEQRES 11 A 686 GLY MET ASP VAL THR LEU LEU GLU ALA ARG ASP ARG VAL SEQRES 12 A 686 GLY GLY ARG VAL ALA THR PHE ARG LYS GLY ASN TYR VAL SEQRES 13 A 686 ALA ASP LEU GLY ALA MET VAL VAL THR GLY LEU GLY GLY SEQRES 14 A 686 ASN PRO MET ALA VAL VAL SER LYS GLN VAL ASN MET GLU SEQRES 15 A 686 LEU ALA LYS ILE LYS GLN LYS CYS PRO LEU TYR GLU ALA SEQRES 16 A 686 ASN GLY GLN ALA ASP ASP VAL LYS VAL PRO LYS GLU LYS SEQRES 17 A 686 ASP GLU MET VAL GLU GLN GLU PHE ASN ARG LEU LEU GLU SEQRES 18 A 686 ALA THR SER TYR LEU SER HIS GLN LEU ASP PHE ASN VAL SEQRES 19 A 686 LEU ASN ASN LYS PRO VAL SER LEU GLY GLN ALA LEU GLU SEQRES 20 A 686 VAL VAL ILE GLN LEU GLN GLU LYS HIS VAL LYS ASP GLU SEQRES 21 A 686 GLN ILE GLU HIS TRP LYS LYS ILE VAL LYS THR GLN GLU SEQRES 22 A 686 GLU LEU LYS GLU LEU LEU ASN LYS MET VAL ASN LEU LYS SEQRES 23 A 686 GLU LYS ILE LYS GLU LEU HIS GLN GLN TYR LYS GLU ALA SEQRES 24 A 686 SER GLU VAL LYS PRO PRO ARG ASP ILE THR ALA GLU PHE SEQRES 25 A 686 LEU VAL LYS SER LYS HIS ARG ASP LEU THR ALA LEU CYS SEQRES 26 A 686 LYS GLU TYR ASP GLU LEU ALA GLU THR GLN GLY LYS LEU SEQRES 27 A 686 GLU GLU LYS LEU GLN GLU LEU GLU ALA ASN PRO PRO SER SEQRES 28 A 686 ASP VAL TYR LEU SER SER ARG ASP ARG GLN ILE LEU ASP SEQRES 29 A 686 TRP HIS PHE ALA ASN LEU GLU PHE ALA ASN ALA THR PRO SEQRES 30 A 686 LEU SER THR LEU SER LEU LYS HIS TRP ASP GLN ASP ASP SEQRES 31 A 686 ASP PHE GLU PHE THR GLY SER HIS LEU THR VAL ARG ASN SEQRES 32 A 686 GLY TYR SER CYS VAL PRO VAL ALA LEU ALA GLU GLY LEU SEQRES 33 A 686 ASP ILE LYS LEU ASN THR ALA VAL ARG GLN VAL ARG TYR SEQRES 34 A 686 THR ALA SER GLY CYS GLU VAL ILE ALA VAL ASN THR ARG SEQRES 35 A 686 SER THR SER GLN THR PHE ILE TYR LYS CYS ASP ALA VAL SEQRES 36 A 686 LEU CYS THR LEU PRO LEU GLY VAL LEU LYS GLN GLN PRO SEQRES 37 A 686 PRO ALA VAL GLN PHE VAL PRO PRO LEU PRO GLU TRP LYS SEQRES 38 A 686 THR SER ALA VAL GLN ARG MET GLY PHE GLY ASN LEU ASN SEQRES 39 A 686 LYS VAL VAL LEU CYS PHE ASP ARG VAL PHE TRP ASP PRO SEQRES 40 A 686 SER VAL ASN LEU PHE GLY HIS VAL GLY SER THR THR ALA SEQRES 41 A 686 SER ARG GLY GLU LEU PHE LEU PHE TRP ASN LEU TYR LYS SEQRES 42 A 686 ALA PRO ILE LEU LEU ALA LEU VAL ALA GLY GLU ALA ALA SEQRES 43 A 686 GLY ILE MET GLU ASN ILE SER ASP ASP VAL ILE VAL GLY SEQRES 44 A 686 ARG CYS LEU ALA ILE LEU LYS GLY ILE PHE GLY SER SER SEQRES 45 A 686 ALA VAL PRO GLN PRO LYS GLU THR VAL VAL SER ARG TRP SEQRES 46 A 686 ARG ALA ASP PRO TRP ALA ARG GLY SER TYR SER TYR VAL SEQRES 47 A 686 ALA ALA GLY SER SER GLY ASN ASP TYR ASP LEU MET ALA SEQRES 48 A 686 GLN PRO ILE THR PRO GLY PRO SER ILE PRO GLY ALA PRO SEQRES 49 A 686 GLN PRO ILE PRO ARG LEU PHE PHE ALA GLY GLU HIS THR SEQRES 50 A 686 ILE ARG ASN TYR PRO ALA THR VAL HIS GLY ALA LEU LEU SEQRES 51 A 686 SER GLY LEU ARG GLU ALA GLY ARG ILE ALA ASP GLN PHE SEQRES 52 A 686 LEU GLY ALA MET TYR THR LEU PRO ARG GLN ALA THR PRO SEQRES 53 A 686 GLY VAL PRO ALA GLN GLN SER PRO SER MET SEQRES 1 B 133 ARG LYS PRO PRO LYS GLY MET PHE LEU SER GLN GLU ASP SEQRES 2 B 133 VAL GLU ALA VAL SER ALA ASN ALA THR ALA ALA THR THR SEQRES 3 B 133 VAL LEU ARG GLN LEU ASP MET GLU LEU VAL SER VAL LYS SEQRES 4 B 133 ARG GLN ILE GLN ASN ILE LYS GLN THR ASN SER ALA LEU SEQRES 5 B 133 LYS GLU LYS LEU ASP GLY GLY ILE GLU PRO TYR ARG LEU SEQRES 6 B 133 PRO GLU VAL ILE GLN LYS CYS ASN ALA ARG TRP THR THR SEQRES 7 B 133 GLU GLU GLN LEU LEU ALA VAL GLN ALA ILE ARG LYS TYR SEQRES 8 B 133 GLY ARG ASP PHE GLN ALA ILE SER ASP VAL ILE GLY ASN SEQRES 9 B 133 LYS SER VAL VAL GLN VAL LYS ASN PHE PHE VAL ASN TYR SEQRES 10 B 133 ARG ARG ARG PHE ASN ILE ASP GLU VAL LEU GLN GLU TRP SEQRES 11 B 133 GLU ALA GLU HET FAD A 900 53 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 3 FAD C27 H33 N9 O15 P2 FORMUL 4 HOH *3(H2 O) HELIX 1 1 GLY A 173 SER A 181 1 9 HELIX 2 2 THR A 189 PHE A 196 1 8 HELIX 3 3 PHE A 196 GLY A 202 1 7 HELIX 4 4 PRO A 203 ASN A 224 1 22 HELIX 5 5 THR A 230 GLN A 237 1 8 HELIX 6 6 ASP A 245 HIS A 259 1 15 HELIX 7 7 GLY A 287 PHE A 300 1 14 HELIX 8 8 ASN A 340 VAL A 349 1 10 HELIX 9 9 PRO A 371 GLN A 395 1 25 HELIX 10 10 SER A 407 GLU A 467 1 61 HELIX 11 11 ASP A 473 ASN A 514 1 42 HELIX 12 12 SER A 522 ASN A 540 1 19 HELIX 13 13 ASP A 553 ASP A 557 5 5 HELIX 14 14 SER A 572 GLU A 580 1 9 HELIX 15 15 PRO A 626 GLN A 632 1 7 HELIX 16 16 PRO A 644 MET A 654 1 11 HELIX 17 17 ALA A 708 GLU A 716 1 9 HELIX 18 18 SER A 719 GLY A 736 1 18 HELIX 19 19 GLY A 770 GLN A 778 1 9 HELIX 20 20 GLY A 800 ILE A 804 5 5 HELIX 21 21 THR A 810 LEU A 830 1 21 HELIX 22 22 SER B 317 ALA B 326 1 10 HELIX 23 23 THR B 329 LEU B 363 1 35 HELIX 24 24 ILE B 367 ARG B 371 5 5 HELIX 25 25 THR B 384 GLY B 399 1 16 HELIX 26 26 ASP B 401 GLY B 410 1 10 HELIX 27 27 SER B 413 TYR B 424 1 12 HELIX 28 28 ASN B 429 ALA B 439 1 11 SHEET 1 AA 5 ILE A 584 LYS A 585 0 SHEET 2 AA 5 ASP A 303 LEU A 307 1 O LEU A 306 N LYS A 585 SHEET 3 AA 5 LYS A 280 ILE A 284 1 O VAL A 281 N THR A 305 SHEET 4 AA 5 ALA A 620 CYS A 623 1 O ALA A 620 N ILE A 282 SHEET 5 AA 5 LEU A 796 PHE A 798 1 O PHE A 797 N CYS A 623 SHEET 1 AB 2 THR A 319 LYS A 322 0 SHEET 2 AB 2 TYR A 325 ASP A 328 -1 O TYR A 325 N LYS A 322 SHEET 1 AC 3 VAL A 333 VAL A 334 0 SHEET 2 AC 3 LEU A 565 VAL A 567 -1 O LEU A 565 N VAL A 334 SHEET 3 AC 3 LEU A 353 LYS A 355 -1 O ALA A 354 N THR A 566 SHEET 1 AD 7 ALA A 369 LYS A 369D 0 SHEET 2 AD 7 LEU A 362 ASN A 366 -1 O GLU A 364 N VAL A 369C SHEET 3 AD 7 LEU A 677 HIS A 680 1 O GLY A 679 N TYR A 363 SHEET 4 AD 7 LEU A 693 TRP A 695 -1 O PHE A 694 N PHE A 678 SHEET 5 AD 7 ILE A 702 VAL A 707 -1 O LEU A 704 N TRP A 695 SHEET 6 AD 7 ASN A 660 CYS A 665 -1 O ASN A 660 N VAL A 707 SHEET 7 AD 7 GLU A 745 VAL A 748 -1 O GLU A 745 N CYS A 665 SHEET 1 AE 2 VAL A 400 LEU A 401 0 SHEET 2 AE 2 LYS A 404 PRO A 405 -1 O LYS A 404 N LEU A 401 SHEET 1 AF 4 THR A 613 CYS A 618 0 SHEET 2 AF 4 GLY A 599 ASN A 606 -1 O CYS A 600 N CYS A 618 SHEET 3 AF 4 THR A 588 THR A 596 -1 O ALA A 589 N VAL A 605 SHEET 4 AF 4 GLN A 638 VAL A 640 1 O GLN A 638 N VAL A 593 SHEET 1 AG 2 GLY A 655 PHE A 656 0 SHEET 2 AG 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 -3.31 CISPEP 2 PRO A 470 PRO A 471 0 5.89 CISPEP 3 GLN A 633 PRO A 634 0 -0.58 CISPEP 4 VAL A 640 PRO A 641 0 -1.35 SITE 1 AC1 34 GLY A 285 GLY A 287 VAL A 288 SER A 289 SITE 2 AC1 34 LEU A 307 GLU A 308 ALA A 309 ARG A 310 SITE 3 AC1 34 GLY A 314 GLY A 315 ARG A 316 VAL A 317 SITE 4 AC1 34 LEU A 329 GLY A 330 ALA A 331 MET A 332 SITE 5 AC1 34 VAL A 333 THR A 588 ALA A 589 VAL A 590 SITE 6 AC1 34 THR A 624 LEU A 625 PRO A 626 VAL A 637 SITE 7 AC1 34 LEU A 659 TRP A 751 TRP A 756 SER A 760 SITE 8 AC1 34 TYR A 761 GLY A 800 GLU A 801 THR A 810 SITE 9 AC1 34 VAL A 811 ALA A 814 CRYST1 117.980 179.120 233.640 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 0.008476 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005583 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004280 0.00000