HEADER OXIDOREDUCTASE 17-JUL-07 2Z5U
TITLE CRYSTAL STRUCTURE OF LYSINE-SPECIFIC HISTONE DEMETHYLASE 1
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: LSD1, RESIDUES 172-833;
COMPND 5 SYNONYM: FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING PROTEIN 2,
COMPND 6 BRAF35-HDAC COMPLEX PROTEIN BHC110;
COMPND 7 EC: 1.-.-.-;
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: KIAA0601, LSD1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-HS-6P
KEYWDS CHROMATIN, HISTONE DEMETHYLASE, NUCLEOSOME, TRANSCRIPTION, LSD1,
KEYWDS 2 LYSINE-SPECIFIC, CHROMATIN REGULATOR, FAD, NUCLEUS, OXIDOREDUCTASE,
KEYWDS 3 PHOSPHORYLATION, REPRESSOR, TRANSCRIPTION REGULATION, STRUCTURAL
KEYWDS 4 GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND
KEYWDS 5 FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS
KEYWDS 6 INITIATIVE, RSGI
EXPDTA X-RAY DIFFRACTION
AUTHOR S.MIMASU,T.SENGOKU,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS
AUTHOR 2 INITIATIVE (RSGI)
REVDAT 7 01-NOV-23 2Z5U 1 REMARK
REVDAT 6 25-DEC-19 2Z5U 1 REMARK
REVDAT 5 27-MAR-13 2Z5U 1 HET HETATM HETNAM VERSN
REVDAT 4 24-FEB-09 2Z5U 1 VERSN
REVDAT 3 24-JUN-08 2Z5U 1 JRNL
REVDAT 2 15-APR-08 2Z5U 1 HETATM
REVDAT 1 01-APR-08 2Z5U 0
JRNL AUTH S.MIMASU,T.SENGOKU,S.FUKUZAWA,T.UMEHARA,S.YOKOYAMA
JRNL TITL CRYSTAL STRUCTURE OF HISTONE DEMETHYLASE LSD1 AND
JRNL TITL 2 TRANYLCYPROMINE AT 2.25 A
JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 366 15 2008
JRNL REFN ISSN 0006-291X
JRNL PMID 18039463
JRNL DOI 10.1016/J.BBRC.2007.11.066
REMARK 2
REMARK 2 RESOLUTION. 2.25 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS
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) : 2.25
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.36
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.7
REMARK 3 NUMBER OF REFLECTIONS : 48969
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) : 0.225
REMARK 3 FREE R VALUE : 0.254
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 2551
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
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) : 2.25
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.39
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.10
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.3130
REMARK 3 BIN FREE R VALUE : 0.3220
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 381
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5044
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 63
REMARK 3 SOLVENT ATOMS : 130
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 31.40
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.32
REMARK 3 ESD FROM SIGMAA (A) : 0.34
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) : 0.33
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.007
REMARK 3 BOND ANGLES (DEGREES) : 1.300
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.50
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.950
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 1.350 ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : NULL
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 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2Z5U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUL-07.
REMARK 100 THE DEPOSITION ID IS D_1000027558.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 28-MAY-07
REMARK 200 TEMPERATURE (KELVIN) : 298
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SPRING-8
REMARK 200 BEAMLINE : BL41XU
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51520
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7
REMARK 200 DATA REDUNDANCY : 3.600
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.07500
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.9100
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39
REMARK 200 COMPLETENESS FOR SHELL (%) : 91.1
REMARK 200 DATA REDUNDANCY IN SHELL : 3.20
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.32000
REMARK 200 <I/SIGMA(I)> FOR SHELL : 11.30
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: CNS
REMARK 200 STARTING MODEL: PDB ENTRY 2EJR
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 66.55
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.68
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1MM HEPES-NA, 5% MPD, 3-4.5% PEG
REMARK 280 MONOMETHYLETHER 2000, 1MM DTT, PH 7.5, VAPOR DIFFUSION, HANGING
REMARK 280 DROP, TEMPERATURE 277.0K
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 36.24733
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 72.49467
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 54.37100
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 90.61833
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 18.12367
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 36.24733
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 72.49467
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 90.61833
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 54.37100
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 18.12367
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 ASP A 473
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 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 PRO A 782 C - N - CA ANGL. DEV. = -10.3 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 SER A 201 68.80 -100.01
REMARK 500 ASN A 224 74.28 -153.20
REMARK 500 LYS A 271 79.76 -106.87
REMARK 500 THR A 335 45.62 -85.75
REMARK 500 HIS A 394 49.62 -98.19
REMARK 500 GLN A 395 -53.49 -169.88
REMARK 500 ASP A 397 49.99 37.04
REMARK 500 ASN A 403 -0.56 66.32
REMARK 500 GLN A 460 147.08 169.86
REMARK 500 GLN A 461 -57.27 81.07
REMARK 500 TYR A 462 93.21 -59.33
REMARK 500 LYS A 463 48.47 158.29
REMARK 500 ALA A 476 -30.64 -39.60
REMARK 500 TYR A 494 -78.28 -59.59
REMARK 500 ASP A 495 -9.25 -53.33
REMARK 500 THR A 500 1.93 -69.85
REMARK 500 GLU A 512 6.08 -67.74
REMARK 500 GLU A 559 150.58 -49.95
REMARK 500 SER A 598 34.92 -141.69
REMARK 500 SER A 609 78.25 -157.51
REMARK 500 THR A 610 -0.33 -52.21
REMARK 500 PRO A 701 81.39 -67.28
REMARK 500 SER A 738 -21.46 79.98
REMARK 500 ALA A 757 -53.97 -133.15
REMARK 500 PRO A 794 120.39 -35.07
REMARK 500 TYR A 807 47.53 -142.02
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 FAJ A 1
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2EJR RELATED DB: PDB
REMARK 900 THE SAME PROTEIN COMPLEXED WITH ANOTHER DRAG
REMARK 900 RELATED ID: 2Z3Y RELATED DB: PDB
REMARK 900 THE SAME PROTEIN COMPLEXED WITH ANOTHER DRAG
DBREF 2Z5U A 172 833 UNP O60341 LSD1_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 FAJ A 1 63
HETNAM FAJ FAD-TRANS-2-PHENYLCYCLOPROPYLAMINE ADDUCT
HETSYN FAJ FAD-PCPA ADDUCT
FORMUL 2 FAJ C36 H43 N9 O16 P2
FORMUL 3 HOH *130(H2 O)
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 LEU A 238 1 9
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 ASN A 340 ASN A 350 1 11
HELIX 10 10 PRO A 371 HIS A 394 1 24
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 ALA A 498 1 9
HELIX 14 14 ALA A 498 GLU A 512 1 15
HELIX 15 15 SER A 522 ALA A 541 1 20
HELIX 16 16 PRO A 543 LEU A 547 5 5
HELIX 17 17 ASP A 555 GLU A 559 5 5
HELIX 18 18 SER A 572 ALA A 579 1 8
HELIX 19 19 PRO A 626 GLN A 632 1 7
HELIX 20 20 PRO A 644 MET A 654 1 11
HELIX 21 21 ALA A 708 GLU A 716 1 9
HELIX 22 22 SER A 719 GLY A 736 1 18
HELIX 23 23 GLY A 770 GLN A 778 1 9
HELIX 24 24 GLY A 800 ILE A 804 5 5
HELIX 25 25 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 VAL A 281 O ASP A 303
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 ASN A 696 -1 O PHE A 694 N PHE A 678
SHEET 4 D 6 ILE A 702 VAL A 707 -1 O LEU A 704 N TRP A 695
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 GLY A 599 ASN A 606 -1 N CYS A 600 O CYS A 618
SHEET 3 F 4 THR A 588 THR A 596 -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 ARG A 591
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 -0.02
CISPEP 2 GLN A 633 PRO A 634 0 -0.18
CISPEP 3 VAL A 640 PRO A 641 0 0.01
SITE 1 AC1 38 ILE A 284 GLY A 285 GLY A 287 VAL A 288
SITE 2 AC1 38 SER A 289 LEU A 307 GLU A 308 ALA A 309
SITE 3 AC1 38 ARG A 310 GLY A 314 GLY A 315 ARG A 316
SITE 4 AC1 38 LEU A 329 GLY A 330 ALA A 331 MET A 332
SITE 5 AC1 38 VAL A 333 THR A 335 THR A 588 VAL A 590
SITE 6 AC1 38 THR A 624 LEU A 625 PRO A 626 VAL A 637
SITE 7 AC1 38 TRP A 751 TRP A 756 TYR A 761 GLY A 800
SITE 8 AC1 38 GLU A 801 ALA A 809 THR A 810 VAL A 811
SITE 9 AC1 38 ALA A 814 HOH A 839 HOH A 847 HOH A 891
SITE 10 AC1 38 HOH A 892 HOH A 916
CRYST1 185.759 185.759 108.742 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 0.005383 0.003108 0.000000 0.00000
SCALE2 0.000000 0.006216 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009196 0.00000
(ATOM LINES ARE NOT SHOWN.)
END