HEADER OXIDOREDUCTASE 21-DEC-09 3ABT TITLE CRYSTAL STRUCTURE OF LSD1 IN COMPLEX WITH TRANS-2- TITLE 2 PENTAFLUOROPHENYLCYCLOPROPYLAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: AMINE OXIDASE (FLAVIN CONTAINING) DOMAIN 2, RESIDUES 172- COMPND 5 833; COMPND 6 SYNONYM: LSD1, FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING COMPND 7 PROTEIN 2, BRAF35-HDAC COMPLEX PROTEIN BHC110; COMPND 8 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: KAZUSA DNA KIAA 0601; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL-21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-HS KEYWDS AMINE OXIDASE, HISTONE DEMETHYLASE, TOWER DOMAIN, H3K4, STRUCTURAL KEYWDS 2 GENOMICS, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, KEYWDS 3 CHROMATIN REGULATOR, DEVELOPMENTAL PROTEIN, FAD, NUCLEUS, KEYWDS 4 OXIDOREDUCTASE, PHOSPHOPROTEIN, REPRESSOR, TRANSCRIPTION, KEYWDS 5 TRANSCRIPTION REGULATION, NPPSFA, NATIONAL PROJECT ON PROTEIN KEYWDS 6 STRUCTURAL AND FUNCTIONAL ANALYSES EXPDTA X-RAY DIFFRACTION AUTHOR S.MIMASU,N.UMEZAWA,S.SATO,T.HIGUCHI,T.UMEHARA,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 01-NOV-23 3ABT 1 REMARK REVDAT 2 11-AUG-10 3ABT 1 JRNL REVDAT 1 07-JUL-10 3ABT 0 JRNL AUTH S.MIMASU,N.UMEZAWA,S.SATO,T.HIGUCHI,T.UMEHARA,S.YOKOYAMA JRNL TITL STRUCTURALLY DESIGNED TRANS-2-PHENYLCYCLOPROPYLAMINE JRNL TITL 2 DERIVATIVES POTENTLY INHIBIT HISTONE DEMETHYLASE LSD1/KDM1 JRNL REF BIOCHEMISTRY V. 49 6494 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20568732 JRNL DOI 10.1021/BI100299R REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN 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) : 47.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 3724656.610 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 18396 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 SET) : 0.231 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 893 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.40 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2820 REMARK 3 BIN R VALUE (WORKING SET) : 0.3320 REMARK 3 BIN FREE R VALUE : 0.3610 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 150 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.029 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5049 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 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) : 58.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.78000 REMARK 3 B22 (A**2) : 9.78000 REMARK 3 B33 (A**2) : -19.57000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM SIGMAA (A) : 0.61 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.49 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.62 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.003 REMARK 3 BOND ANGLES (DEGREES) : 0.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.700 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.570 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.070 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.470 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 0.860 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 16.93 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DRGMSOXFLU3.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DRGMSOXFLU3.TOP REMARK 3 TOPOLOGY FILE 3 : WATER_REP.PARAM REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3ABT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000029059. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-08; 03-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SPRING-8; SPRING-8 REMARK 200 BEAMLINE : BL41XU; BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000000; 1.000000 REMARK 200 MONOCHROMATOR : NATIVE; NATIVE REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315; MARMOSAIC 225 REMARK 200 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18396 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.22600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.61200 REMARK 200 R SYM FOR SHELL (I) : 0.61200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.110 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2DW4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3-10% PEG 2000 MONOMETHYL ETHER, 0.1M REMARK 280 HEPES PH 7.5, 0.2M MAGNESIUM CHLORIDE, 0.1M CACODYLATE, 5MM REMARK 280 TRANYLCYPROMINE-DERIVATIVE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 278K 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 36.38333 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 72.76667 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 54.57500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 90.95833 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 18.19167 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 36.38333 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 72.76667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 90.95833 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 54.57500 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 18.19167 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 465 REMARK 465 SER A 466 REMARK 465 GLU A 467 REMARK 465 VAL A 468 REMARK 465 LYS A 469 REMARK 465 PRO A 470 REMARK 465 PRO A 471 REMARK 465 ARG A 472 REMARK 465 GLY A 783 REMARK 465 PRO A 784 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 ALA A 832 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 ASP A 473 CG OD1 OD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS A 699 NZ LYS A 699 9555 2.14 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 ARG A 187 145.32 -178.13 REMARK 500 ASN A 224 72.42 -174.47 REMARK 500 ARG A 316 18.27 -69.74 REMARK 500 MET A 332 -7.57 -158.73 REMARK 500 THR A 335 84.24 -65.89 REMARK 500 GLU A 364 -171.07 -66.04 REMARK 500 PHE A 398 58.83 -103.20 REMARK 500 ASN A 403 -5.13 68.73 REMARK 500 GLN A 461 -6.81 79.70 REMARK 500 LEU A 479 -72.20 -72.06 REMARK 500 TYR A 494 -72.34 -52.68 REMARK 500 LYS A 503 4.38 -66.79 REMARK 500 GLU A 512 7.14 -67.21 REMARK 500 ASP A 557 21.49 -72.53 REMARK 500 SER A 609 80.69 -155.94 REMARK 500 THR A 610 -1.75 -56.18 REMARK 500 PRO A 644 156.42 -48.17 REMARK 500 LEU A 659 121.83 -172.17 REMARK 500 PRO A 701 85.99 -59.52 REMARK 500 MET A 715 -16.68 -49.56 REMARK 500 SER A 737 -179.23 -58.10 REMARK 500 SER A 738 -8.20 60.23 REMARK 500 ARG A 750 59.90 -150.99 REMARK 500 ALA A 757 -52.86 -131.32 REMARK 500 SER A 760 -61.69 -90.03 REMARK 500 SER A 762 170.86 -57.54 REMARK 500 TYR A 763 146.48 -172.11 REMARK 500 GLU A 801 -8.08 -56.36 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 2PF A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DW4 RELATED DB: PDB REMARK 900 HUMAN LSD1 AT 2.3 A RESOLUTION REMARK 900 RELATED ID: 2Z5U RELATED DB: PDB REMARK 900 HUMAN LSD1 COMPLEXED WITH ANOTHER DRAG REMARK 900 RELATED ID: 2UXX RELATED DB: PDB REMARK 900 HUMAN LSD1 COMPLEXED WITH ANOTHER DRAG REMARK 900 RELATED ID: 3ABU RELATED DB: PDB REMARK 900 HUMAN LSD1 COMPLEXED WITH ANOTHER DRAG DBREF 3ABT A 172 833 UNP O60341 KDM1_HUMAN 172 833 SEQRES 1 A 662 SER GLY VAL GLU GLY ALA ALA PHE GLN SER ARG LEU PRO SEQRES 2 A 662 HIS ASP ARG MET THR SER GLN GLU ALA ALA CYS PHE PRO SEQRES 3 A 662 ASP ILE ILE SER GLY PRO GLN GLN THR GLN LYS VAL PHE SEQRES 4 A 662 LEU PHE ILE ARG ASN ARG THR LEU GLN LEU TRP LEU ASP SEQRES 5 A 662 ASN PRO LYS ILE GLN LEU THR PHE GLU ALA THR LEU GLN SEQRES 6 A 662 GLN LEU GLU ALA PRO TYR ASN SER ASP THR VAL LEU VAL SEQRES 7 A 662 HIS ARG VAL HIS SER TYR LEU GLU ARG HIS GLY LEU ILE SEQRES 8 A 662 ASN PHE GLY ILE TYR LYS ARG ILE LYS PRO LEU PRO THR SEQRES 9 A 662 LYS LYS THR GLY LYS VAL ILE ILE ILE GLY SER GLY VAL SEQRES 10 A 662 SER GLY LEU ALA ALA ALA ARG GLN LEU GLN SER PHE GLY SEQRES 11 A 662 MET ASP VAL THR LEU LEU GLU ALA ARG ASP ARG VAL GLY SEQRES 12 A 662 GLY ARG VAL ALA THR PHE ARG LYS GLY ASN TYR VAL ALA SEQRES 13 A 662 ASP LEU GLY ALA MET VAL VAL THR GLY LEU GLY GLY ASN SEQRES 14 A 662 PRO MET ALA VAL VAL SER LYS GLN VAL ASN MET GLU LEU SEQRES 15 A 662 ALA LYS ILE LYS GLN LYS CYS PRO LEU TYR GLU ALA ASN SEQRES 16 A 662 GLY GLN ALA VAL PRO LYS GLU LYS ASP GLU MET VAL GLU SEQRES 17 A 662 GLN GLU PHE ASN ARG LEU LEU GLU ALA THR SER TYR LEU SEQRES 18 A 662 SER HIS GLN LEU ASP PHE ASN VAL LEU ASN ASN LYS PRO SEQRES 19 A 662 VAL SER LEU GLY GLN ALA LEU GLU VAL VAL ILE GLN LEU SEQRES 20 A 662 GLN GLU LYS HIS VAL LYS ASP GLU GLN ILE GLU HIS TRP SEQRES 21 A 662 LYS LYS ILE VAL LYS THR GLN GLU GLU LEU LYS GLU LEU SEQRES 22 A 662 LEU ASN LYS MET VAL ASN LEU LYS GLU LYS ILE LYS GLU SEQRES 23 A 662 LEU HIS GLN GLN TYR LYS GLU ALA SER GLU VAL LYS PRO SEQRES 24 A 662 PRO ARG ASP ILE THR ALA GLU PHE LEU VAL LYS SER LYS SEQRES 25 A 662 HIS ARG ASP LEU THR ALA LEU CYS LYS GLU TYR ASP GLU SEQRES 26 A 662 LEU ALA GLU THR GLN GLY LYS LEU GLU GLU LYS LEU GLN SEQRES 27 A 662 GLU LEU GLU ALA ASN PRO PRO SER ASP VAL TYR LEU SER SEQRES 28 A 662 SER ARG ASP ARG GLN ILE LEU ASP TRP HIS PHE ALA ASN SEQRES 29 A 662 LEU GLU PHE ALA ASN ALA THR PRO LEU SER THR LEU SER SEQRES 30 A 662 LEU LYS HIS TRP ASP GLN ASP ASP ASP PHE GLU PHE THR SEQRES 31 A 662 GLY SER HIS LEU THR VAL ARG ASN GLY TYR SER CYS VAL SEQRES 32 A 662 PRO VAL ALA LEU ALA GLU GLY LEU ASP ILE LYS LEU ASN SEQRES 33 A 662 THR ALA VAL ARG GLN VAL ARG TYR THR ALA SER GLY CYS SEQRES 34 A 662 GLU VAL ILE ALA VAL ASN THR ARG SER THR SER GLN THR SEQRES 35 A 662 PHE ILE TYR LYS CYS ASP ALA VAL LEU CYS THR LEU PRO SEQRES 36 A 662 LEU GLY VAL LEU LYS GLN GLN PRO PRO ALA VAL GLN PHE SEQRES 37 A 662 VAL PRO PRO LEU PRO GLU TRP LYS THR SER ALA VAL GLN SEQRES 38 A 662 ARG MET GLY PHE GLY ASN LEU ASN LYS VAL VAL LEU CYS SEQRES 39 A 662 PHE ASP ARG VAL PHE TRP ASP PRO SER VAL ASN LEU PHE SEQRES 40 A 662 GLY HIS VAL GLY SER THR THR ALA SER ARG GLY GLU LEU SEQRES 41 A 662 PHE LEU PHE TRP ASN LEU TYR LYS ALA PRO ILE LEU LEU SEQRES 42 A 662 ALA LEU VAL ALA GLY GLU ALA ALA GLY ILE MET GLU ASN SEQRES 43 A 662 ILE SER ASP ASP VAL ILE VAL GLY ARG CYS LEU ALA ILE SEQRES 44 A 662 LEU LYS GLY ILE PHE GLY SER SER ALA VAL PRO GLN PRO SEQRES 45 A 662 LYS GLU THR VAL VAL SER ARG TRP ARG ALA ASP PRO TRP SEQRES 46 A 662 ALA ARG GLY SER TYR SER TYR VAL ALA ALA GLY SER SER SEQRES 47 A 662 GLY ASN ASP TYR ASP LEU MET ALA GLN PRO ILE THR PRO SEQRES 48 A 662 GLY PRO SER ILE PRO GLY ALA PRO GLN PRO ILE PRO ARG SEQRES 49 A 662 LEU PHE PHE ALA GLY GLU HIS THR ILE ARG ASN TYR PRO SEQRES 50 A 662 ALA THR VAL HIS GLY ALA LEU LEU SER GLY LEU ARG GLU SEQRES 51 A 662 ALA GLY ARG ILE ALA ASP GLN PHE LEU GLY ALA MET HET 2PF A 1 68 HETNAM 2PF [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4- HETNAM 2 2PF DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4S)-2,3,4- HETNAM 3 2PF TRIHYDROXY-5-[(1R,3R,3AS)-1-HYDROXY-10,11-DIMETHYL-4, HETNAM 4 2PF 6-DIOXO-3-(PENTAFLUOROPHENYL)-2,3,5,6-TETRAHYDRO-1H- HETNAM 5 2PF BENZO[G]PYRROLO[2,1-E]PTERIDIN-8(4H)-YL]PENTYL HETNAM 6 2PF DIHYDROGEN DIPHOSPHATE FORMUL 2 2PF C36 H38 F5 N9 O16 P2 HELIX 1 1 SER A 172 SER A 181 1 10 HELIX 2 2 THR A 189 PHE A 196 1 8 HELIX 3 3 PHE A 196 SER A 201 1 6 HELIX 4 4 PRO A 203 ASP A 223 1 21 HELIX 5 5 THR A 230 GLN A 236 1 7 HELIX 6 6 PRO A 241 SER A 244 5 4 HELIX 7 7 ASP A 245 HIS A 259 1 15 HELIX 8 8 GLY A 287 PHE A 300 1 14 HELIX 9 9 PRO A 341 ASN A 350 1 10 HELIX 10 10 PRO A 371 GLN A 395 1 25 HELIX 11 11 SER A 407 GLU A 457 1 51 HELIX 12 12 THR A 475 THR A 488 1 14 HELIX 13 13 LEU A 490 GLU A 512 1 23 HELIX 14 14 SER A 522 ASN A 540 1 19 HELIX 15 15 PRO A 543 LEU A 547 5 5 HELIX 16 16 ASP A 553 GLU A 559 5 7 HELIX 17 17 SER A 572 ALA A 579 1 8 HELIX 18 18 PRO A 626 GLN A 632 1 7 HELIX 19 19 PRO A 644 MET A 654 1 11 HELIX 20 20 ALA A 708 MET A 715 1 8 HELIX 21 21 GLU A 716 ILE A 718 5 3 HELIX 22 22 SER A 719 PHE A 735 1 17 HELIX 23 23 ASN A 771 MET A 776 1 6 HELIX 24 24 THR A 810 LEU A 830 1 21 SHEET 1 A 5 ILE A 584 LYS A 585 0 SHEET 2 A 5 ASP A 303 LEU A 307 1 N LEU A 306 O LYS A 585 SHEET 3 A 5 LYS A 280 ILE A 284 1 N ILE A 283 O THR A 305 SHEET 4 A 5 ALA A 620 CYS A 623 1 O LEU A 622 N ILE A 284 SHEET 5 A 5 LEU A 796 PHE A 798 1 O PHE A 797 N VAL A 621 SHEET 1 B 2 THR A 319 LYS A 322 0 SHEET 2 B 2 TYR A 325 ASP A 328 -1 O ALA A 327 N PHE A 320 SHEET 1 C 3 VAL A 333 VAL A 334 0 SHEET 2 C 3 LEU A 565 VAL A 567 -1 O LEU A 565 N VAL A 334 SHEET 3 C 3 LEU A 353 LYS A 355 -1 N ALA A 354 O THR A 566 SHEET 1 D 6 LEU A 362 TYR A 363 0 SHEET 2 D 6 LEU A 677 HIS A 680 1 O GLY A 679 N TYR A 363 SHEET 3 D 6 LEU A 693 TRP A 695 -1 O PHE A 694 N PHE A 678 SHEET 4 D 6 ILE A 702 VAL A 707 -1 O LEU A 706 N LEU A 693 SHEET 5 D 6 ASN A 660 CYS A 665 -1 N LEU A 664 O LEU A 703 SHEET 6 D 6 GLU A 745 VAL A 748 -1 O VAL A 747 N VAL A 663 SHEET 1 E 2 VAL A 400 LEU A 401 0 SHEET 2 E 2 LYS A 404 PRO A 405 -1 O LYS A 404 N LEU A 401 SHEET 1 F 4 THR A 613 CYS A 618 0 SHEET 2 F 4 CYS A 600 ASN A 606 -1 N VAL A 602 O TYR A 616 SHEET 3 F 4 THR A 588 TYR A 595 -1 N ARG A 594 O GLU A 601 SHEET 4 F 4 GLN A 638 VAL A 640 1 O GLN A 638 N VAL A 593 SHEET 1 G 2 GLY A 655 PHE A 656 0 SHEET 2 G 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 -0.12 CISPEP 2 GLN A 633 PRO A 634 0 -0.13 CISPEP 3 VAL A 640 PRO A 641 0 0.00 SITE 1 AC1 36 GLY A 285 SER A 286 GLY A 287 VAL A 288 SITE 2 AC1 36 SER A 289 LEU A 307 GLU A 308 ALA A 309 SITE 3 AC1 36 ARG A 310 GLY A 314 GLY A 315 ARG A 316 SITE 4 AC1 36 LEU A 329 GLY A 330 ALA A 331 MET A 332 SITE 5 AC1 36 VAL A 333 THR A 335 THR A 588 ALA A 589 SITE 6 AC1 36 VAL A 590 THR A 624 LEU A 625 PRO A 626 SITE 7 AC1 36 LEU A 659 LYS A 661 TRP A 751 TRP A 756 SITE 8 AC1 36 SER A 760 TYR A 761 GLY A 800 GLU A 801 SITE 9 AC1 36 ALA A 809 THR A 810 VAL A 811 ALA A 814 CRYST1 183.840 183.840 109.150 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 0.005440 0.003141 0.000000 0.00000 SCALE2 0.000000 0.006281 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009162 0.00000