2COM - Header Asymmetric Unit

HEADER OXIDOREDUCTASE 18-MAY-05 2COM

TITLE THE SOLUTION STRUCTURE OF THE SWIRM DOMAIN OF HUMAN LSD1

COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SWIRM DOMAIN; COMPND 5 SYNONYM: AMINE OXIDASE FLAVIN CONTAINING DOMAIN PROTEIN 2, COMPND 6 AOF2 PROTEIN, 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: LSD1; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P040401-21; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS

KEYWDS SWIRM DOMAIN, LSD1, AOF2, KIAA0601, HISTONE MODULATION, KEYWDS 2 STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN KEYWDS 3 STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 4 GENOMICS/PROTEOMICS INITIATIVE, RSGI, OXIDOREDUCTASE

EXPDTA SOLUTION NMR

NUMMDL 20

AUTHOR N.TOCHIO,T.UMEHARA,S.KOSHIBA,M.INOUE,A.TANAKA,T.KIGAWA, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE AUTHOR 3 (RSGI)

REVDAT 4 24-FEB-09 2COM 1 VERSN REVDAT 3 18-APR-06 2COM 1 JRNL REVDAT 2 10-JAN-06 2COM 1 JRNL TITLE REVDAT 1 18-NOV-05 2COM 0

JRNL AUTH N.TOCHIO,T.UMEHARA,S.KOSHIBA,M.INOUE,T.YABUKI, JRNL AUTH 2 M.AOKI,E.SEKI,S.WATANABE,Y.TOMO,M.HANADA,M.IKARI, JRNL AUTH 3 M.SATO,T.TERADA,T.NAGASE,O.OHARA,M.SHIROUZU, JRNL AUTH 4 A.TANAKA,T.KIGAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE SWIRM DOMAIN OF HUMAN JRNL TITL 2 HISTONE DEMETHYLASE LSD1 JRNL REF STRUCTURE V. 14 457 2006 JRNL REFN ISSN 0969-2126 JRNL PMID 16531230 JRNL DOI 10.1016/J.STR.2005.12.004

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.0.17 REMARK 3 AUTHORS : GUNTERT, P. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 2COM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-MAY-05. REMARK 100 THE RCSB ID CODE IS RCSB024454.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2MM SWIRM DOMAIN U-15N,13C; REMARK 210 20MM D-TRIS HCL; 100MM NACL; REMARK 210 1MM D-DTT; 0.02% NAN3; 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 3D_ REMARK 210 13C-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, NMRPIPE REMARK 210 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.8994, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION,STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL

REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS.

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 1 PRO A 10 -177.74 -69.71 REMARK 500 1 ARG A 21 78.16 -69.44 REMARK 500 1 SER A 40 35.47 -99.09 REMARK 500 1 GLN A 43 -36.25 -37.33 REMARK 500 1 ALA A 79 165.12 -47.37 REMARK 500 1 TYR A 94 -36.06 -38.46 REMARK 500 1 ILE A 105 -36.80 -132.46 REMARK 500 1 ILE A 109 112.75 -33.78 REMARK 500 1 LYS A 110 140.32 -171.41 REMARK 500 1 PRO A 113 94.97 -69.82 REMARK 500 1 LYS A 115 75.67 -60.86 REMARK 500 1 SER A 123 46.99 34.34 REMARK 500 2 GLU A 9 74.75 -115.40 REMARK 500 2 PRO A 10 4.38 -69.76 REMARK 500 2 ARG A 21 44.03 31.50 REMARK 500 2 SER A 40 33.28 -94.62 REMARK 500 2 ALA A 79 161.69 -44.83 REMARK 500 2 TYR A 94 -38.00 -39.54 REMARK 500 2 ILE A 105 -33.15 -39.18 REMARK 500 2 ARG A 108 151.99 -44.71 REMARK 500 2 SER A 119 95.21 -63.28 REMARK 500 3 SER A 3 108.66 -172.91 REMARK 500 3 PRO A 10 91.32 -69.80 REMARK 500 3 ALA A 17 -36.60 -33.90 REMARK 500 3 ARG A 21 41.20 -82.91 REMARK 500 3 ALA A 79 156.66 -41.33 REMARK 500 3 ILE A 105 -37.80 -33.54 REMARK 500 3 ILE A 109 111.40 -38.74 REMARK 500 3 PRO A 111 -173.82 -69.79 REMARK 500 3 PRO A 113 97.12 -69.76 REMARK 500 3 LYS A 115 43.64 34.25 REMARK 500 3 LYS A 116 46.91 -77.62 REMARK 500 4 ALA A 16 -34.24 -38.28 REMARK 500 4 GLN A 19 -35.51 -39.22 REMARK 500 4 ARG A 21 72.44 -69.76 REMARK 500 4 ALA A 79 163.80 -46.08 REMARK 500 4 TYR A 94 -37.47 -39.91 REMARK 500 4 ILE A 105 -33.38 -133.97 REMARK 500 4 ARG A 108 -55.53 -123.74 REMARK 500 4 PRO A 121 3.74 -69.74 REMARK 500 4 SER A 122 162.53 -41.87 REMARK 500 5 SER A 11 132.12 -170.45 REMARK 500 5 ALA A 17 -32.56 -35.49 REMARK 500 5 GLN A 30 -70.87 -59.59 REMARK 500 5 GLU A 31 -38.51 -37.77 REMARK 500 5 SER A 40 36.67 -95.27 REMARK 500 5 PRO A 64 4.46 -69.76 REMARK 500 5 ALA A 79 160.10 -43.77 REMARK 500 5 ILE A 105 -37.26 -134.11 REMARK 500 5 PRO A 111 -176.78 -69.78 REMARK 500 5 THR A 114 108.03 -48.18 REMARK 500 5 LYS A 116 97.93 -32.69 REMARK 500 5 PRO A 121 94.37 -69.77 REMARK 500 6 ALA A 17 -38.12 -38.29 REMARK 500 6 ALA A 79 157.41 -41.45 REMARK 500 6 ILE A 105 -34.31 -34.76 REMARK 500 6 ARG A 108 141.65 -35.46 REMARK 500 6 THR A 114 48.94 -78.55 REMARK 500 7 PRO A 10 86.55 -69.71 REMARK 500 7 ALA A 17 -35.17 -33.99 REMARK 500 7 GLN A 19 -33.44 -38.98 REMARK 500 7 SER A 40 33.84 -97.05 REMARK 500 7 PRO A 64 3.54 -69.67 REMARK 500 7 ALA A 79 164.65 -45.84 REMARK 500 7 ILE A 109 105.13 -39.18 REMARK 500 7 LYS A 115 126.48 -172.40 REMARK 500 7 SER A 119 -61.53 -129.89 REMARK 500 8 SER A 2 -43.66 -131.82 REMARK 500 8 SER A 3 93.97 -58.71 REMARK 500 8 SER A 5 81.30 -63.87 REMARK 500 8 GLU A 9 153.72 -42.59 REMARK 500 8 PRO A 10 4.39 -69.73 REMARK 500 8 ALA A 17 -32.35 -35.18 REMARK 500 8 ARG A 21 47.45 -79.62 REMARK 500 8 GLN A 43 -38.95 -38.74 REMARK 500 8 ALA A 79 163.13 -45.50 REMARK 500 8 ILE A 105 -39.26 -33.85 REMARK 500 8 PRO A 113 4.06 -69.73 REMARK 500 8 THR A 114 168.17 -43.84 REMARK 500 8 LYS A 115 146.44 -34.31 REMARK 500 8 PRO A 121 95.14 -69.73 REMARK 500 9 GLU A 14 43.72 -81.61 REMARK 500 9 SER A 20 34.67 -99.29 REMARK 500 9 ARG A 21 45.55 34.66 REMARK 500 9 PRO A 64 3.53 -69.73 REMARK 500 9 ALA A 79 162.12 -45.32 REMARK 500 9 ARG A 108 52.48 37.54 REMARK 500 9 PRO A 113 95.48 -69.73 REMARK 500 9 LYS A 116 45.61 -81.43 REMARK 500 9 PRO A 121 -174.93 -69.80 REMARK 500 10 ALA A 17 -33.61 -33.62 REMARK 500 10 GLN A 19 -39.62 -38.67 REMARK 500 10 ARG A 21 41.32 -89.85 REMARK 500 10 SER A 40 33.10 -94.88 REMARK 500 10 PRO A 64 4.50 -69.80 REMARK 500 10 ALA A 79 159.31 -43.78 REMARK 500 10 ILE A 105 -39.58 -130.73 REMARK 500 10 LYS A 107 44.07 -79.10 REMARK 500 10 PRO A 113 0.31 -69.78 REMARK 500 10 SER A 123 107.23 -44.12 REMARK 500 11 SER A 6 111.76 -167.98 REMARK 500 11 ALA A 17 -36.48 -37.33 REMARK 500 11 SER A 29 -36.01 -35.73 REMARK 500 11 PRO A 64 3.59 -69.74 REMARK 500 11 ALA A 79 158.27 -45.55 REMARK 500 11 ILE A 105 -36.96 -132.20 REMARK 500 11 ARG A 108 -70.11 -115.93 REMARK 500 11 PRO A 113 82.08 -69.78 REMARK 500 11 SER A 123 153.17 -43.29 REMARK 500 12 SER A 3 42.16 34.93 REMARK 500 12 GLN A 19 -36.91 -39.28 REMARK 500 12 ARG A 21 42.21 -83.03 REMARK 500 12 SER A 40 32.27 -93.47 REMARK 500 12 PRO A 64 2.04 -69.74 REMARK 500 12 ALA A 79 163.18 -48.34 REMARK 500 12 ILE A 105 -34.96 -39.40 REMARK 500 12 LYS A 110 140.26 -34.33 REMARK 500 12 LYS A 115 105.31 -34.33 REMARK 500 12 PRO A 121 -176.45 -69.74 REMARK 500 12 SER A 123 42.23 -83.20 REMARK 500 13 PRO A 10 96.56 -69.80 REMARK 500 13 GLN A 19 -35.97 -38.80 REMARK 500 13 SER A 40 32.06 -96.76 REMARK 500 13 ARG A 53 -71.14 -63.61 REMARK 500 13 PRO A 64 3.93 -69.77 REMARK 500 13 ALA A 79 160.48 -46.28 REMARK 500 13 ILE A 105 -34.95 -35.62 REMARK 500 13 LYS A 107 99.71 -60.59 REMARK 500 13 PRO A 121 91.19 -69.80 REMARK 500 14 PRO A 10 4.39 -69.76 REMARK 500 14 ALA A 17 -33.30 -34.09 REMARK 500 14 GLN A 19 -35.39 -34.42 REMARK 500 14 ARG A 21 47.71 -78.00 REMARK 500 14 SER A 40 37.18 -89.83 REMARK 500 14 PRO A 64 2.60 -69.73 REMARK 500 14 ALA A 79 153.55 -44.71 REMARK 500 14 ILE A 105 -26.05 -38.38 REMARK 500 14 LYS A 110 134.69 -34.42 REMARK 500 14 PRO A 111 -174.66 -69.74 REMARK 500 15 PHE A 18 -30.17 -36.24 REMARK 500 15 GLN A 19 31.75 -84.68 REMARK 500 15 SER A 40 35.24 -91.74 REMARK 500 15 GLN A 43 -38.40 -39.61 REMARK 500 15 PRO A 64 5.09 -69.75 REMARK 500 15 ALA A 79 158.54 -43.97 REMARK 500 15 ILE A 105 -34.45 -34.51 REMARK 500 15 LYS A 107 80.32 -67.13 REMARK 500 15 ILE A 109 112.41 -34.10 REMARK 500 15 PRO A 111 -173.07 -69.81 REMARK 500 15 SER A 119 -71.04 -97.55 REMARK 500 15 SER A 123 42.18 37.70 REMARK 500 16 GLU A 8 48.44 -82.61 REMARK 500 16 THR A 56 -38.71 -39.71 REMARK 500 16 PRO A 64 2.90 -69.74 REMARK 500 16 LEU A 77 170.70 -49.37 REMARK 500 16 ALA A 79 153.98 -41.39 REMARK 500 16 TYR A 94 -32.31 -39.74 REMARK 500 16 LEU A 95 -70.72 -72.89 REMARK 500 16 ILE A 105 -39.75 -135.01 REMARK 500 16 LYS A 107 -30.08 -35.08 REMARK 500 16 ARG A 108 150.62 -34.08 REMARK 500 16 ILE A 109 110.28 -38.65 REMARK 500 16 LYS A 110 135.98 -36.20 REMARK 500 16 PRO A 113 92.25 -69.76 REMARK 500 16 SER A 119 40.67 36.88 REMARK 500 17 GLU A 8 46.30 -80.27 REMARK 500 17 PRO A 10 3.87 -69.78 REMARK 500 17 ALA A 17 -35.58 -33.82 REMARK 500 17 GLN A 19 -33.27 -37.35 REMARK 500 17 SER A 40 31.78 -95.52 REMARK 500 17 PRO A 64 3.17 -69.78 REMARK 500 17 ALA A 79 152.95 -43.10 REMARK 500 17 ILE A 105 -36.35 -134.96 REMARK 500 17 PRO A 113 -179.23 -69.76 REMARK 500 17 LYS A 116 86.22 -67.50 REMARK 500 18 SER A 2 100.94 -46.82 REMARK 500 18 ARG A 21 54.56 -100.90 REMARK 500 18 GLN A 30 -70.40 -57.02 REMARK 500 18 PRO A 64 1.38 -69.74 REMARK 500 18 ALA A 79 155.88 -44.19 REMARK 500 18 ILE A 105 -38.04 -131.40 REMARK 500 18 ARG A 108 -57.10 -126.09 REMARK 500 18 LYS A 110 154.93 -37.98 REMARK 500 19 SER A 6 108.59 -44.94 REMARK 500 19 GLU A 9 143.72 -39.58 REMARK 500 19 PRO A 10 92.19 -69.79 REMARK 500 19 ALA A 17 -35.79 -34.18 REMARK 500 19 GLN A 19 -27.73 -37.92 REMARK 500 19 ARG A 21 75.04 -68.92 REMARK 500 19 PRO A 64 2.88 -69.80 REMARK 500 19 ALA A 79 157.10 -46.10 REMARK 500 19 ILE A 105 -38.13 -134.04 REMARK 500 19 LYS A 110 143.29 -172.42 REMARK 500 19 LEU A 112 147.48 -34.19 REMARK 500 19 PRO A 113 -175.19 -69.77 REMARK 500 19 THR A 117 157.55 -43.20 REMARK 500 19 PRO A 121 -179.38 -69.80 REMARK 500 20 SER A 5 47.00 -82.36 REMARK 500 20 PRO A 10 82.69 -69.71 REMARK 500 20 ARG A 21 39.40 36.55 REMARK 500 20 PRO A 64 2.75 -69.75 REMARK 500 20 ALA A 79 165.85 -46.24 REMARK 500 20 ILE A 105 -33.51 -35.79 REMARK 500 20 PRO A 113 -176.40 -69.81 REMARK 500 20 LYS A 116 87.65 -66.28 REMARK 500 20 SER A 122 101.21 -40.00 REMARK 500 REMARK 500 REMARK: NULL

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSK002000585.1 RELATED DB: TARGETDB

DBREF 2COM A 8 118 UNP O60341 LSD1_HUMAN 169 279

SEQADV 2COM GLY A 1 UNP O60341 CLONING ARTIFACT SEQADV 2COM SER A 2 UNP O60341 CLONING ARTIFACT SEQADV 2COM SER A 3 UNP O60341 CLONING ARTIFACT SEQADV 2COM GLY A 4 UNP O60341 CLONING ARTIFACT SEQADV 2COM SER A 5 UNP O60341 CLONING ARTIFACT SEQADV 2COM SER A 6 UNP O60341 CLONING ARTIFACT SEQADV 2COM GLY A 7 UNP O60341 CLONING ARTIFACT SEQADV 2COM SER A 119 UNP O60341 CLONING ARTIFACT SEQADV 2COM GLY A 120 UNP O60341 CLONING ARTIFACT SEQADV 2COM PRO A 121 UNP O60341 CLONING ARTIFACT SEQADV 2COM SER A 122 UNP O60341 CLONING ARTIFACT SEQADV 2COM SER A 123 UNP O60341 CLONING ARTIFACT SEQADV 2COM GLY A 124 UNP O60341 CLONING ARTIFACT

SEQRES 1 A 124 GLY SER SER GLY SER SER GLY GLU GLU PRO SER GLY VAL SEQRES 2 A 124 GLU GLY ALA ALA PHE GLN SER ARG LEU PRO HIS ASP ARG SEQRES 3 A 124 MET THR SER GLN GLU ALA ALA CYS PHE PRO ASP ILE ILE SEQRES 4 A 124 SER GLY PRO GLN GLN THR GLN LYS VAL PHE LEU PHE ILE SEQRES 5 A 124 ARG ASN ARG THR LEU GLN LEU TRP LEU ASP ASN PRO LYS SEQRES 6 A 124 ILE GLN LEU THR PHE GLU ALA THR LEU GLN GLN LEU GLU SEQRES 7 A 124 ALA PRO TYR ASN SER ASP THR VAL LEU VAL HIS ARG VAL SEQRES 8 A 124 HIS SER TYR LEU GLU ARG HIS GLY LEU ILE ASN PHE GLY SEQRES 9 A 124 ILE TYR LYS ARG ILE LYS PRO LEU PRO THR LYS LYS THR SEQRES 10 A 124 GLY SER GLY PRO SER SER GLY

HELIX 1 1 GLY A 12 GLN A 19 1 8 HELIX 2 2 THR A 28 PHE A 35 1 8 HELIX 3 3 PHE A 35 SER A 40 1 6 HELIX 4 4 PRO A 42 ASN A 63 1 22 HELIX 5 5 THR A 69 LEU A 77 1 9 HELIX 6 6 ASP A 84 HIS A 98 1 15

CISPEP 1 ALA A 79 PRO A 80 1 -0.04 CISPEP 2 ALA A 79 PRO A 80 2 -0.02 CISPEP 3 ALA A 79 PRO A 80 3 0.06 CISPEP 4 ALA A 79 PRO A 80 4 -0.01 CISPEP 5 ALA A 79 PRO A 80 5 -0.01 CISPEP 6 ALA A 79 PRO A 80 6 0.02 CISPEP 7 ALA A 79 PRO A 80 7 -0.03 CISPEP 8 ALA A 79 PRO A 80 8 0.03 CISPEP 9 ALA A 79 PRO A 80 9 -0.01 CISPEP 10 ALA A 79 PRO A 80 10 0.01 CISPEP 11 ALA A 79 PRO A 80 11 0.03 CISPEP 12 ALA A 79 PRO A 80 12 0.05 CISPEP 13 ALA A 79 PRO A 80 13 0.05 CISPEP 14 ALA A 79 PRO A 80 14 0.02 CISPEP 15 ALA A 79 PRO A 80 15 -0.03 CISPEP 16 ALA A 79 PRO A 80 16 0.08 CISPEP 17 ALA A 79 PRO A 80 17 0.05 CISPEP 18 ALA A 79 PRO A 80 18 0.03 CISPEP 19 ALA A 79 PRO A 80 19 -0.05 CISPEP 20 ALA A 79 PRO A 80 20 0.04

CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1

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 1.000000 0.000000 0.000000 0.00000

SCALE2 0.000000 1.000000 0.000000 0.00000

SCALE3 0.000000 0.000000 1.000000 0.00000