HEADER OXIDOREDUCTASE/TRANSCRIPTION 19-JUN-20 7CDD TITLE CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH PRSFLVRR PEPTIDE 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; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: REST COREPRESSOR 1; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: PROTEIN COREST; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: PRO-ARG-SER-PHE-LEU-VAL-ARG-ARG; COMPND 15 CHAIN: C; COMPND 16 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 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: RCOR1, KIAA0071, RCOR; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 18 ORGANISM_TAXID: 9606 KEYWDS DEMETHYLASE, AMINE OXIDASE, CHROMATIN, HISTONE, FAD, COREPRESSOR, KEYWDS 2 OXIDOREDUCTASE-TRANSCRIPTION-INHIBITOR COMPLEX, OXIDOREDUCTASE, KEYWDS 3 OXIDOREDUCTASE-TRANSCRIPTION COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.KIKUCHI,H.KITAGAWA,S.SATO,N.UMEZAWA,T.HIGUCHI,T.UMEHARA REVDAT 3 29-NOV-23 7CDD 1 REMARK REVDAT 2 30-JUN-21 7CDD 1 JRNL REVDAT 1 23-JUN-21 7CDD 0 JRNL AUTH H.KITAGAWA,M.KIKUCHI,S.SATO,H.WATANABE,N.UMEZAWA,M.KATO, JRNL AUTH 2 Y.HISAMATSU,T.UMEHARA,T.HIGUCHI JRNL TITL STRUCTURE-BASED IDENTIFICATION OF POTENT LYSINE-SPECIFIC JRNL TITL 2 DEMETHYLASE 1 INHIBITOR PEPTIDES AND TEMPORARY CYCLIZATION JRNL TITL 3 TO ENHANCE PROTEOLYTIC STABILITY AND CELL GROWTH-INHIBITORY JRNL TITL 4 ACTIVITY. JRNL REF J.MED.CHEM. V. 64 3707 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 33754721 JRNL DOI 10.1021/ACS.JMEDCHEM.0C01371 REMARK 2 REMARK 2 RESOLUTION. 2.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 2.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 64986 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1324 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) : 2.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.83 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4736 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3770 REMARK 3 BIN FREE R VALUE SET COUNT : 106 REMARK 3 BIN FREE R VALUE : 0.3820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6245 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 87 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 84.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.80000 REMARK 3 B22 (A**2) : -4.70000 REMARK 3 B33 (A**2) : -2.10000 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): 0.229 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.198 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.192 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.815 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6441 ; 0.003 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 5974 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8747 ; 1.269 ; 1.642 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13857 ; 1.120 ; 1.573 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 798 ; 5.743 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 334 ;31.206 ;22.605 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1083 ;15.115 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;16.269 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 837 ; 0.043 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7201 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1314 ; 0.001 ; 0.020 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): 3201 ; 4.391 ; 8.989 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3200 ; 4.389 ; 8.988 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3996 ; 6.862 ;13.483 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3997 ; 6.861 ;13.485 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3240 ; 4.139 ; 9.375 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3241 ; 4.139 ; 9.377 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4752 ; 6.816 ;13.881 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6988 ; 9.862 ;04.968 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6989 ; 9.861 ;04.966 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 REMARK 4 REMARK 4 7CDD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1300017423. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-SEP-17 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 : SLS REMARK 200 BEAMLINE : X06DA 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66319 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.760 REMARK 200 RESOLUTION RANGE LOW (A) : 48.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.82 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5H6Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M N-(CARBAMOYLMETHYL)IMINODIACETIC REMARK 280 ACID, 1.23 M POTASSIUM SODIUM TARTRATE TETRAHYDRATE, VAPOR REMARK 280 DIFFUSION, 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 60.99350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 90.25750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 116.57700 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 60.99350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 90.25750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 116.57700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 60.99350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 90.25750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 116.57700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 60.99350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 90.25750 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 116.57700 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 MET A 833 REMARK 465 GLY B 301 REMARK 465 SER B 302 REMARK 465 SER B 303 REMARK 465 GLY B 304 REMARK 465 SER B 305 REMARK 465 ALA B 306 REMARK 465 SER B 307 REMARK 465 ARG B 308 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 LYS A 271 CG CD CE NZ REMARK 470 LEU A 273 CG CD1 CD2 REMARK 470 LYS A 276 CG CD CE NZ REMARK 470 GLU A 506 CG CD OE1 OE2 REMARK 470 GLN A 509 CG CD OE1 NE2 REMARK 470 LYS B 309 CG CD CE NZ REMARK 470 LYS B 312 CG CD CE NZ REMARK 470 SER B 325 OG REMARK 470 LYS B 360 CG CD CE NZ REMARK 470 LYS B 362 CG CD CE NZ REMARK 470 ARG B 371 CG CD NE CZ NH1 NH2 REMARK 470 VAL B 375 CG1 CG2 REMARK 470 ILE B 376 CG1 CG2 CD1 REMARK 470 GLN B 377 CG CD OE1 NE2 REMARK 470 LYS B 378 CG CD CE NZ REMARK 470 ARG B 382 CG CD NE CZ NH1 NH2 REMARK 470 VAL B 415 CG1 CG2 REMARK 470 LYS B 418 CG CD CE NZ 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 PHE A 196 49.50 -140.23 REMARK 500 ASN A 350 95.93 -67.05 REMARK 500 ASN A 402 35.94 73.44 REMARK 500 ASN A 514 68.59 -114.62 REMARK 500 LEU A 659 120.98 -172.56 REMARK 500 ALA A 757 -56.35 -145.95 REMARK 500 SER A 760 -62.22 -101.11 REMARK 500 GLN A 791 111.13 -36.40 REMARK 500 TYR A 807 43.33 -143.70 REMARK 500 LEU B 316 86.11 -151.40 REMARK 500 ASP B 401 76.59 -66.22 REMARK 500 ASN B 411 45.21 -151.87 REMARK 500 SER C 3 -37.90 -38.12 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 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 903 DBREF 7CDD A 172 833 UNP O60341 KDM1A_HUMAN 172 833 DBREF 7CDD B 308 440 UNP Q9UKL0 RCOR1_HUMAN 311 443 DBREF 7CDD C 1 8 PDB 7CDD 7CDD 1 8 SEQADV 7CDD GLY A 165 UNP O60341 EXPRESSION TAG SEQADV 7CDD PRO A 166 UNP O60341 EXPRESSION TAG SEQADV 7CDD LEU A 167 UNP O60341 EXPRESSION TAG SEQADV 7CDD GLY A 168 UNP O60341 EXPRESSION TAG SEQADV 7CDD SER A 169 UNP O60341 EXPRESSION TAG SEQADV 7CDD HIS A 170 UNP O60341 EXPRESSION TAG SEQADV 7CDD MET A 171 UNP O60341 EXPRESSION TAG SEQADV 7CDD GLY B 301 UNP Q9UKL0 EXPRESSION TAG SEQADV 7CDD SER B 302 UNP Q9UKL0 EXPRESSION TAG SEQADV 7CDD SER B 303 UNP Q9UKL0 EXPRESSION TAG SEQADV 7CDD GLY B 304 UNP Q9UKL0 EXPRESSION TAG SEQADV 7CDD SER B 305 UNP Q9UKL0 EXPRESSION TAG SEQADV 7CDD ALA B 306 UNP Q9UKL0 EXPRESSION TAG SEQADV 7CDD SER B 307 UNP Q9UKL0 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 SEQRES 1 B 140 GLY SER SER GLY SER ALA SER ARG LYS PRO PRO LYS GLY SEQRES 2 B 140 MET PHE LEU SER GLN GLU ASP VAL GLU ALA VAL SER ALA SEQRES 3 B 140 ASN ALA THR ALA ALA THR THR VAL LEU ARG GLN LEU ASP SEQRES 4 B 140 MET GLU LEU VAL SER VAL LYS ARG GLN ILE GLN ASN ILE SEQRES 5 B 140 LYS GLN THR ASN SER ALA LEU LYS GLU LYS LEU ASP GLY SEQRES 6 B 140 GLY ILE GLU PRO TYR ARG LEU PRO GLU VAL ILE GLN LYS SEQRES 7 B 140 CYS ASN ALA ARG TRP THR THR GLU GLU GLN LEU LEU ALA SEQRES 8 B 140 VAL GLN ALA ILE ARG LYS TYR GLY ARG ASP PHE GLN ALA SEQRES 9 B 140 ILE SER ASP VAL ILE GLY ASN LYS SER VAL VAL GLN VAL SEQRES 10 B 140 LYS ASN PHE PHE VAL ASN TYR ARG ARG ARG PHE ASN ILE SEQRES 11 B 140 ASP GLU VAL LEU GLN GLU TRP GLU ALA GLU SEQRES 1 C 8 PRO ARG SER PHE LEU VAL ARG ARG HET FAD A 901 53 HET GOL A 902 6 HET GOL A 903 6 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 FAD C27 H33 N9 O15 P2 FORMUL 5 GOL 2(C3 H8 O3) FORMUL 7 HOH *87(H2 O) HELIX 1 AA1 GLY A 173 SER A 181 1 9 HELIX 2 AA2 THR A 189 PHE A 196 1 8 HELIX 3 AA3 PHE A 196 SER A 201 1 6 HELIX 4 AA4 PRO A 203 ASN A 224 1 22 HELIX 5 AA5 THR A 230 GLN A 237 1 8 HELIX 6 AA6 ASP A 245 HIS A 259 1 15 HELIX 7 AA7 GLY A 287 PHE A 300 1 14 HELIX 8 AA8 PRO A 341 VAL A 349 1 9 HELIX 9 AA9 PRO A 371 GLN A 395 1 25 HELIX 10 AB1 SER A 407 GLU A 467 1 61 HELIX 11 AB2 ASP A 473 GLU A 512 1 40 HELIX 12 AB3 SER A 522 ASN A 540 1 19 HELIX 13 AB4 ASP A 555 GLU A 559 5 5 HELIX 14 AB5 SER A 572 ALA A 579 1 8 HELIX 15 AB6 PRO A 626 GLN A 632 1 7 HELIX 16 AB7 PRO A 644 MET A 654 1 11 HELIX 17 AB8 THR A 684 ARG A 688 5 5 HELIX 18 AB9 GLU A 710 GLU A 716 1 7 HELIX 19 AC1 SER A 719 GLY A 736 1 18 HELIX 20 AC2 SER A 769 GLN A 778 1 10 HELIX 21 AC3 GLY A 800 ILE A 804 5 5 HELIX 22 AC4 THR A 810 LEU A 830 1 21 HELIX 23 AC5 SER B 317 ALA B 326 1 10 HELIX 24 AC6 THR B 329 LEU B 363 1 35 HELIX 25 AC7 ILE B 367 ARG B 371 5 5 HELIX 26 AC8 THR B 384 TYR B 398 1 15 HELIX 27 AC9 ASP B 401 GLY B 410 1 10 HELIX 28 AD1 SER B 413 TYR B 424 1 12 HELIX 29 AD2 ASN B 429 GLU B 440 1 12 HELIX 30 AD3 PRO C 1 LEU C 5 5 5 SHEET 1 AA1 5 ILE A 584 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 VAL A 621 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 4 THR A 613 CYS A 618 0 SHEET 2 AA4 4 GLY A 599 ASN A 606 -1 N CYS A 600 O CYS A 618 SHEET 3 AA4 4 THR A 588 THR A 596 -1 N ARG A 594 O GLU A 601 SHEET 4 AA4 4 GLN A 638 VAL A 640 1 O VAL A 640 N VAL A 593 SHEET 1 AA5 2 GLY A 655 PHE A 656 0 SHEET 2 AA5 2 SER A 762 TYR A 763 -1 O TYR A 763 N GLY A 655 SHEET 1 AA6 5 LEU A 677 GLY A 679 0 SHEET 2 AA6 5 LEU A 693 TRP A 695 -1 O PHE A 694 N PHE A 678 SHEET 3 AA6 5 ILE A 702 VAL A 707 -1 O LEU A 704 N TRP A 695 SHEET 4 AA6 5 ASN A 660 CYS A 665 -1 N LEU A 664 O LEU A 703 SHEET 5 AA6 5 GLU A 745 VAL A 748 -1 O VAL A 747 N VAL A 663 CISPEP 1 ALA A 240 PRO A 241 0 3.49 CISPEP 2 PRO A 470 PRO A 471 0 3.33 CISPEP 3 GLN A 633 PRO A 634 0 5.97 CISPEP 4 VAL A 640 PRO A 641 0 1.89 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 LEU A 329 SITE 4 AC1 34 GLY A 330 ALA A 331 MET A 332 VAL A 333 SITE 5 AC1 34 THR A 588 VAL A 590 THR A 624 LEU A 625 SITE 6 AC1 34 PRO A 626 LEU A 659 TRP A 751 TRP A 756 SITE 7 AC1 34 SER A 760 TYR A 761 GLY A 800 GLU A 801 SITE 8 AC1 34 ALA A 809 THR A 810 VAL A 811 ALA A 814 SITE 9 AC1 34 HOH A1011 PHE C 4 SITE 1 AC2 3 GLU A 413 ARG A 526 ARG A 688 SITE 1 AC3 4 SER A 749 ARG A 750 TRP A 751 ASP A 754 CRYST1 121.987 180.515 233.154 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 0.008198 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005540 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004289 0.00000