HEADER OXIDOREDUCTASE 20-OCT-21 7VQS TITLE CRYSTAL STRUCTURE OF LSD1 IN COMPLEX WITH COMPOUND 4 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: 1.14.99.66; COMPND 7 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 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETDUET-1 KEYWDS DEMETHYLASE, AMINE OXIDASE, CHROMATIN, HISTONE, FAD, MECHANISM-BASED KEYWDS 2 INHIBITOR, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.NIWA,Y.KODA,S.SATO,H.YAMAMOTO,H.KOYAMA,T.UMEHARA REVDAT 2 29-NOV-23 7VQS 1 REMARK REVDAT 1 01-JUN-22 7VQS 0 JRNL AUTH Y.KODA,S.SATO,H.YAMAMOTO,H.NIWA,H.WATANABE,C.WATANABE, JRNL AUTH 2 T.SATO,K.NAKAMURA,A.TANAKA,M.SHIROUZU,T.HONMA,T.FUKAMI, JRNL AUTH 3 H.KOYAMA,T.UMEHARA JRNL TITL DESIGN AND SYNTHESIS OF TRANYLCYPROMINE-DERIVED LSD1 JRNL TITL 2 INHIBITORS WITH IMPROVED HERG AND MICROSOMAL STABILITY JRNL TITL 3 PROFILES. JRNL REF ACS MED.CHEM.LETT. V. 13 848 2022 JRNL REFN ISSN 1948-5875 JRNL PMID 35586426 JRNL DOI 10.1021/ACSMEDCHEMLETT.2C00120 REMARK 2 REMARK 2 RESOLUTION. 2.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874+SVN REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.310 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 23653 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.230 REMARK 3 FREE R VALUE TEST SET COUNT : 1238 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.0000 - 6.1100 1.00 2710 122 0.1833 0.2209 REMARK 3 2 6.1100 - 4.8500 1.00 2515 153 0.2048 0.2388 REMARK 3 3 4.8500 - 4.2400 1.00 2483 157 0.1844 0.2294 REMARK 3 4 4.2400 - 3.8500 1.00 2475 140 0.2034 0.2520 REMARK 3 5 3.8500 - 3.5800 1.00 2435 134 0.2313 0.2838 REMARK 3 6 3.5800 - 3.3700 1.00 2471 135 0.2649 0.3389 REMARK 3 7 3.3600 - 3.2000 1.00 2452 129 0.2673 0.3003 REMARK 3 8 3.2000 - 3.0600 1.00 2418 146 0.2890 0.3482 REMARK 3 9 3.0600 - 2.9400 1.00 2456 122 0.3345 0.3260 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.448 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.835 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 86.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 98.99 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 5289 REMARK 3 ANGLE : 1.422 7173 REMARK 3 CHIRALITY : 0.075 800 REMARK 3 PLANARITY : 0.010 964 REMARK 3 DIHEDRAL : 15.678 1995 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 172 THROUGH 371 ) REMARK 3 ORIGIN FOR THE GROUP (A): 44.7391 37.8034 -21.8093 REMARK 3 T TENSOR REMARK 3 T11: 0.9014 T22: 0.8763 REMARK 3 T33: 0.7072 T12: -0.1961 REMARK 3 T13: 0.1832 T23: -0.3029 REMARK 3 L TENSOR REMARK 3 L11: 2.5085 L22: 2.4369 REMARK 3 L33: 0.9441 L12: -1.3093 REMARK 3 L13: -0.1910 L23: 0.1303 REMARK 3 S TENSOR REMARK 3 S11: -0.0183 S12: 0.3060 S13: -0.1403 REMARK 3 S21: 0.3553 S22: 0.0735 S23: -0.1384 REMARK 3 S31: 0.2230 S32: 0.2565 S33: -0.0666 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 372 THROUGH 579 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.7504 74.1383 18.2304 REMARK 3 T TENSOR REMARK 3 T11: 1.2637 T22: 1.0189 REMARK 3 T33: 0.8895 T12: -0.2645 REMARK 3 T13: 0.1134 T23: -0.2992 REMARK 3 L TENSOR REMARK 3 L11: -0.3164 L22: 1.7333 REMARK 3 L33: 5.1199 L12: -0.2894 REMARK 3 L13: 0.0156 L23: 3.2661 REMARK 3 S TENSOR REMARK 3 S11: -0.1203 S12: -0.0158 S13: 0.0593 REMARK 3 S21: -0.1602 S22: 0.2056 S23: -0.3162 REMARK 3 S31: -0.6469 S32: 0.4014 S33: -0.0161 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 580 THROUGH 832 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.0339 44.6171 -16.4772 REMARK 3 T TENSOR REMARK 3 T11: 0.7626 T22: 0.7636 REMARK 3 T33: 0.7316 T12: -0.2571 REMARK 3 T13: 0.2780 T23: -0.2237 REMARK 3 L TENSOR REMARK 3 L11: 1.6478 L22: 1.8697 REMARK 3 L33: 2.4338 L12: -0.7237 REMARK 3 L13: 0.0174 L23: 0.3975 REMARK 3 S TENSOR REMARK 3 S11: 0.1074 S12: -0.0616 S13: -0.1213 REMARK 3 S21: 0.2008 S22: -0.1108 S23: 0.2370 REMARK 3 S31: 0.0275 S32: -0.3022 S33: 0.0062 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7VQS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1300025181. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23702 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.940 REMARK 200 RESOLUTION RANGE LOW (A) : 48.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 18.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.14600 REMARK 200 FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 18.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 2.27300 REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 6KGP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES (PH 6.2-6.3), 0.2M DIAMMONIUM REMARK 280 TARTRATE, 0.0005M TCEP, 10-12% PEG 3350, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K 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 35.51767 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 71.03533 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 53.27650 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 88.79417 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 17.75883 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 35.51767 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 71.03533 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 88.79417 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 53.27650 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 17.75883 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 TOTAL BURIED SURFACE AREA: 250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 GLY A 165 REMARK 465 PRO A 166 REMARK 465 LEU A 167 REMARK 465 GLY A 168 REMARK 465 SER A 169 REMARK 465 HIS A 170 REMARK 465 MET A 171 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 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 MET A 833 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 CYS A 600 CB CYS A 600 SG -0.099 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 LEU A 659 CB - CG - CD2 ANGL. DEV. = -11.1 DEGREES REMARK 500 LEU A 677 CB - CG - CD2 ANGL. DEV. = -13.9 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 ASN A 224 76.79 -154.06 REMARK 500 MET A 332 -1.77 -168.25 REMARK 500 ASN A 514 50.85 -118.11 REMARK 500 SER A 609 76.81 -156.10 REMARK 500 THR A 610 1.11 -63.12 REMARK 500 ALA A 757 -47.83 -135.69 REMARK 500 REMARK 500 REMARK: NULL DBREF 7VQS A 172 833 UNP O60341 KDM1A_HUMAN 172 833 SEQADV 7VQS GLY A 165 UNP O60341 EXPRESSION TAG SEQADV 7VQS PRO A 166 UNP O60341 EXPRESSION TAG SEQADV 7VQS LEU A 167 UNP O60341 EXPRESSION TAG SEQADV 7VQS GLY A 168 UNP O60341 EXPRESSION TAG SEQADV 7VQS SER A 169 UNP O60341 EXPRESSION TAG SEQADV 7VQS HIS A 170 UNP O60341 EXPRESSION TAG SEQADV 7VQS MET A 171 UNP O60341 EXPRESSION TAG SEQRES 1 A 669 GLY PRO LEU GLY SER HIS MET SER GLY VAL GLU GLY ALA SEQRES 2 A 669 ALA PHE GLN SER ARG LEU PRO HIS ASP ARG MET THR SER SEQRES 3 A 669 GLN GLU ALA ALA CYS PHE PRO ASP ILE ILE SER GLY PRO SEQRES 4 A 669 GLN GLN THR GLN LYS VAL PHE LEU PHE ILE ARG ASN ARG SEQRES 5 A 669 THR LEU GLN LEU TRP LEU ASP ASN PRO LYS ILE GLN LEU SEQRES 6 A 669 THR PHE GLU ALA THR LEU GLN GLN LEU GLU ALA PRO TYR SEQRES 7 A 669 ASN SER ASP THR VAL LEU VAL HIS ARG VAL HIS SER TYR SEQRES 8 A 669 LEU GLU ARG HIS GLY LEU ILE ASN PHE GLY ILE TYR LYS SEQRES 9 A 669 ARG ILE LYS PRO LEU PRO THR LYS LYS THR GLY LYS VAL SEQRES 10 A 669 ILE ILE ILE GLY SER GLY VAL SER GLY LEU ALA ALA ALA SEQRES 11 A 669 ARG GLN LEU GLN SER PHE GLY MET ASP VAL THR LEU LEU SEQRES 12 A 669 GLU ALA ARG ASP ARG VAL GLY GLY ARG VAL ALA THR PHE SEQRES 13 A 669 ARG LYS GLY ASN TYR VAL ALA ASP LEU GLY ALA MET VAL SEQRES 14 A 669 VAL THR GLY LEU GLY GLY ASN PRO MET ALA VAL VAL SER SEQRES 15 A 669 LYS GLN VAL ASN MET GLU LEU ALA LYS ILE LYS GLN LYS SEQRES 16 A 669 CYS PRO LEU TYR GLU ALA ASN GLY GLN ALA VAL PRO LYS SEQRES 17 A 669 GLU LYS ASP GLU MET VAL GLU GLN GLU PHE ASN ARG LEU SEQRES 18 A 669 LEU GLU ALA THR SER TYR LEU SER HIS GLN LEU ASP PHE SEQRES 19 A 669 ASN VAL LEU ASN ASN LYS PRO VAL SER LEU GLY GLN ALA SEQRES 20 A 669 LEU GLU VAL VAL ILE GLN LEU GLN GLU LYS HIS VAL LYS SEQRES 21 A 669 ASP GLU GLN ILE GLU HIS TRP LYS LYS ILE VAL LYS THR SEQRES 22 A 669 GLN GLU GLU LEU LYS GLU LEU LEU ASN LYS MET VAL ASN SEQRES 23 A 669 LEU LYS GLU LYS ILE LYS GLU LEU HIS GLN GLN TYR LYS SEQRES 24 A 669 GLU ALA SER GLU VAL LYS PRO PRO ARG ASP ILE THR ALA SEQRES 25 A 669 GLU PHE LEU VAL LYS SER LYS HIS ARG ASP LEU THR ALA SEQRES 26 A 669 LEU CYS LYS GLU TYR ASP GLU LEU ALA GLU THR GLN GLY SEQRES 27 A 669 LYS LEU GLU GLU LYS LEU GLN GLU LEU GLU ALA ASN PRO SEQRES 28 A 669 PRO SER ASP VAL TYR LEU SER SER ARG ASP ARG GLN ILE SEQRES 29 A 669 LEU ASP TRP HIS PHE ALA ASN LEU GLU PHE ALA ASN ALA SEQRES 30 A 669 THR PRO LEU SER THR LEU SER LEU LYS HIS TRP ASP GLN SEQRES 31 A 669 ASP ASP ASP PHE GLU PHE THR GLY SER HIS LEU THR VAL SEQRES 32 A 669 ARG ASN GLY TYR SER CYS VAL PRO VAL ALA LEU ALA GLU SEQRES 33 A 669 GLY LEU ASP ILE LYS LEU ASN THR ALA VAL ARG GLN VAL SEQRES 34 A 669 ARG TYR THR ALA SER GLY CYS GLU VAL ILE ALA VAL ASN SEQRES 35 A 669 THR ARG SER THR SER GLN THR PHE ILE TYR LYS CYS ASP SEQRES 36 A 669 ALA VAL LEU CYS THR LEU PRO LEU GLY VAL LEU LYS GLN SEQRES 37 A 669 GLN PRO PRO ALA VAL GLN PHE VAL PRO PRO LEU PRO GLU SEQRES 38 A 669 TRP LYS THR SER ALA VAL GLN ARG MET GLY PHE GLY ASN SEQRES 39 A 669 LEU ASN LYS VAL VAL LEU CYS PHE ASP ARG VAL PHE TRP SEQRES 40 A 669 ASP PRO SER VAL ASN LEU PHE GLY HIS VAL GLY SER THR SEQRES 41 A 669 THR ALA SER ARG GLY GLU LEU PHE LEU PHE TRP ASN LEU SEQRES 42 A 669 TYR LYS ALA PRO ILE LEU LEU ALA LEU VAL ALA GLY GLU SEQRES 43 A 669 ALA ALA GLY ILE MET GLU ASN ILE SER ASP ASP VAL ILE SEQRES 44 A 669 VAL GLY ARG CYS LEU ALA ILE LEU LYS GLY ILE PHE GLY SEQRES 45 A 669 SER SER ALA VAL PRO GLN PRO LYS GLU THR VAL VAL SER SEQRES 46 A 669 ARG TRP ARG ALA ASP PRO TRP ALA ARG GLY SER TYR SER SEQRES 47 A 669 TYR VAL ALA ALA GLY SER SER GLY ASN ASP TYR ASP LEU SEQRES 48 A 669 MET ALA GLN PRO ILE THR PRO GLY PRO SER ILE PRO GLY SEQRES 49 A 669 ALA PRO GLN PRO ILE PRO ARG LEU PHE PHE ALA GLY GLU SEQRES 50 A 669 HIS THR ILE ARG ASN TYR PRO ALA THR VAL HIS GLY ALA SEQRES 51 A 669 LEU LEU SER GLY LEU ARG GLU ALA GLY ARG ILE ALA ASP SEQRES 52 A 669 GLN PHE LEU GLY ALA MET HET GOL A 901 6 HET GOL A 902 6 HET GOL A 903 6 HET GOL A 904 6 HET TLA A 905 10 HET 7UQ A 906 21 HET FAD A 907 53 HETNAM GOL GLYCEROL HETNAM TLA L(+)-TARTARIC ACID HETNAM 7UQ 3-[3,5-BIS(FLUORANYL)-2-[(2-FLUORANYLPYRIDIN-3-YL) HETNAM 2 7UQ METHOXY]PHENYL]PROPANAL HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 4(C3 H8 O3) FORMUL 6 TLA C4 H6 O6 FORMUL 7 7UQ C15 H12 F3 N O2 FORMUL 8 FAD C27 H33 N9 O15 P2 HELIX 1 AA1 SER A 172 SER A 181 1 10 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 LEU A 238 1 9 HELIX 6 AA6 PRO A 241 SER A 244 5 4 HELIX 7 AA7 ASP A 245 HIS A 259 1 15 HELIX 8 AA8 GLY A 287 PHE A 300 1 14 HELIX 9 AA9 ASN A 340 ASN A 350 1 11 HELIX 10 AB1 PRO A 371 GLN A 395 1 25 HELIX 11 AB2 SER A 407 TYR A 462 1 56 HELIX 12 AB3 ILE A 474 ASN A 514 1 41 HELIX 13 AB4 SER A 522 ALA A 541 1 20 HELIX 14 AB5 PRO A 543 LEU A 547 5 5 HELIX 15 AB6 ASP A 555 GLU A 559 5 5 HELIX 16 AB7 SER A 572 ALA A 579 1 8 HELIX 17 AB8 PRO A 626 GLN A 632 1 7 HELIX 18 AB9 PRO A 644 MET A 654 1 11 HELIX 19 AC1 GLY A 709 GLU A 716 1 8 HELIX 20 AC2 SER A 719 GLY A 736 1 18 HELIX 21 AC3 SER A 737 VAL A 740 5 4 HELIX 22 AC4 SER A 769 GLN A 778 1 10 HELIX 23 AC5 GLY A 800 ILE A 804 5 5 HELIX 24 AC6 THR A 810 GLY A 831 1 22 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 ILE A 283 O THR A 305 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 VAL A 334 0 SHEET 2 AA3 3 LEU A 565 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 6 LEU A 362 TYR A 363 0 SHEET 2 AA4 6 LEU A 677 HIS A 680 1 O GLY A 679 N TYR A 363 SHEET 3 AA4 6 GLU A 690 TRP A 695 -1 O PHE A 692 N HIS A 680 SHEET 4 AA4 6 ILE A 702 VAL A 707 -1 O LEU A 704 N TRP A 695 SHEET 5 AA4 6 ASN A 660 CYS A 665 -1 N LEU A 664 O LEU A 703 SHEET 6 AA4 6 GLU A 745 VAL A 748 -1 O VAL A 747 N VAL A 663 SHEET 1 AA5 2 VAL A 400 LEU A 401 0 SHEET 2 AA5 2 LYS A 404 PRO A 405 -1 O LYS A 404 N LEU A 401 SHEET 1 AA6 4 SER A 609 CYS A 618 0 SHEET 2 AA6 4 GLY A 599 ASN A 606 -1 N VAL A 602 O TYR A 616 SHEET 3 AA6 4 THR A 588 THR A 596 -1 N ARG A 594 O GLU A 601 SHEET 4 AA6 4 GLN A 638 VAL A 640 1 O VAL A 640 N VAL A 593 SHEET 1 AA7 2 GLY A 655 PHE A 656 0 SHEET 2 AA7 2 SER A 762 TYR A 763 -1 O TYR A 763 N GLY A 655 LINK C12 7UQ A 906 N5 FAD A 907 1555 1555 1.48 CISPEP 1 ALA A 240 PRO A 241 0 3.86 CISPEP 2 GLN A 633 PRO A 634 0 -5.98 CISPEP 3 VAL A 640 PRO A 641 0 -1.83 CRYST1 186.245 186.245 106.553 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 0.005369 0.003100 0.000000 0.00000 SCALE2 0.000000 0.006200 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009385 0.00000