HEADER OXIDOREDUCTASE/TRANSCRIPTION/INHIBITOR 14-NOV-16 5H6Q
TITLE CRYSTAL STRUCTURE OF LSD1-COREST IN COMPLEX WITH PEPTIDE 11
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 172-833;
COMPND 5 SYNONYM: BRAF35-HDAC COMPLEX PROTEIN BHC110,FLAVIN-CONTAINING AMINE
COMPND 6 OXIDASE DOMAIN-CONTAINING PROTEIN 2;
COMPND 7 EC: 1.-.-.-;
COMPND 8 ENGINEERED: YES;
COMPND 9 MOL_ID: 2;
COMPND 10 MOLECULE: REST COREPRESSOR 1;
COMPND 11 CHAIN: B;
COMPND 12 FRAGMENT: UNP RESIDUES 308-440;
COMPND 13 SYNONYM: PROTEIN COREST;
COMPND 14 ENGINEERED: YES;
COMPND 15 MOL_ID: 3;
COMPND 16 MOLECULE: PEPTIDE SRTMQTARKSTGGKAPRKQLK;
COMPND 17 CHAIN: C;
COMPND 18 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;
SOURCE 11 MOL_ID: 2;
SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 13 ORGANISM_COMMON: HUMAN;
SOURCE 14 ORGANISM_TAXID: 9606;
SOURCE 15 GENE: RCOR1, KIAA0071, RCOR;
SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 18 EXPRESSION_SYSTEM_STRAIN: KRX;
SOURCE 19 MOL_ID: 3;
SOURCE 20 SYNTHETIC: YES;
SOURCE 21 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 22 ORGANISM_TAXID: 9606
KEYWDS DEMETHYLASE, AMINE OXIDASE, CHROMATIN, HISTONE, FAD, COREPRESSOR,
KEYWDS 2 OXIDOREDUCTASE-TRANSCRIPTION-INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR M.KIKUCHI,Y.AMANO,S.SATO,S.YOKOYAMA,N.UMEZAWA,T.HIGUCHI,T.UMEHARA
REVDAT 3 08-NOV-23 5H6Q 1 REMARK
REVDAT 2 06-DEC-17 5H6Q 1 JRNL REMARK
REVDAT 1 12-APR-17 5H6Q 0
JRNL AUTH Y.AMANO,M.KIKUCHI,S.SATO,S.YOKOYAMA,T.UMEHARA,N.UMEZAWA,
JRNL AUTH 2 T.HIGUCHI
JRNL TITL DEVELOPMENT AND CRYSTALLOGRAPHIC EVALUATION OF HISTONE H3
JRNL TITL 2 PEPTIDE WITH N-TERMINAL SERINE SUBSTITUTION AS A POTENT
JRNL TITL 3 INHIBITOR OF LYSINE-SPECIFIC DEMETHYLASE 1.
JRNL REF BIOORG. MED. CHEM. V. 25 2617 2017
JRNL REFN ESSN 1464-3391
JRNL PMID 28336409
JRNL DOI 10.1016/J.BMC.2017.03.016
REMARK 2
REMARK 2 RESOLUTION. 2.53 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0135
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.53
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 83140
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) : 0.225
REMARK 3 R VALUE (WORKING SET) : 0.224
REMARK 3 FREE R VALUE : 0.247
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1686
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) : 2.53
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.60
REMARK 3 REFLECTION IN BIN (WORKING SET) : 5930
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.87
REMARK 3 BIN R VALUE (WORKING SET) : 0.3690
REMARK 3 BIN FREE R VALUE SET COUNT : 141
REMARK 3 BIN FREE R VALUE : 0.4060
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6266
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 77
REMARK 3 SOLVENT ATOMS : 42
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.32
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 6.12000
REMARK 3 B22 (A**2) : -5.62000
REMARK 3 B33 (A**2) : -0.50000
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): 0.191
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.175
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.158
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.519
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6489 ; 0.010 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 6209 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8807 ; 1.418 ; 1.970
REMARK 3 BOND ANGLES OTHERS (DEGREES): 14264 ; 0.937 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 808 ; 5.957 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 291 ;33.747 ;24.570
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1091 ;15.330 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;17.627 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 993 ; 0.075 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7356 ; 0.006 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 1471 ; 0.002 ; 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): 3235 ; 4.615 ; 6.990
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3234 ; 4.615 ; 6.989
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4042 ; 7.106 ;10.485
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4043 ; 7.105 ;10.486
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3254 ; 4.946 ; 7.388
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3255 ; 4.945 ; 7.387
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4766 ; 7.854 ;10.873
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7213 ;10.343 ;54.711
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7212 ;10.343 ;54.710
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 : NULL
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
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 5H6Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-NOV-16.
REMARK 100 THE DEPOSITION ID IS D_1300002119.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 16-OCT-15
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 : SI DOUBLE CRYSTAL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 84828
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.530
REMARK 200 RESOLUTION RANGE LOW (A) : 40.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 7.500
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.06300
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.53
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57
REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8
REMARK 200 DATA REDUNDANCY IN SHELL : 7.00
REMARK 200 R MERGE FOR SHELL (I) : 0.85700
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100
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: 2V1D
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-(2-ACETAMIDO) 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 60.41250
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 90.24400
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 116.68750
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 60.41250
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 90.24400
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 116.68750
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 60.41250
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 90.24400
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 116.68750
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 60.41250
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 90.24400
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 116.68750
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: 9650 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 36310 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 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 465 GLU B 440
REMARK 465 PRO C 16
REMARK 465 ARG C 17
REMARK 465 LYS C 18
REMARK 465 GLN C 19
REMARK 465 LEU C 20
REMARK 465 LYS C 21
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 470 ARG B 426 CG CD NE CZ NH1 NH2
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 ARG C 2 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES
REMARK 500 ARG C 2 NE - CZ - NH2 ANGL. DEV. = -3.9 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 ILE A 270 -71.38 -78.84
REMARK 500 LYS A 322 117.07 -162.67
REMARK 500 THR A 335 57.87 -90.72
REMARK 500 VAL A 468 97.14 -68.12
REMARK 500 ASN A 514 58.33 -116.96
REMARK 500 ASN A 717 33.16 -95.78
REMARK 500 ALA A 757 -55.28 -124.24
REMARK 500 GLN A 791 114.20 -31.31
REMARK 500 TYR A 807 43.80 -140.72
REMARK 500 LEU B 316 83.14 -156.92
REMARK 500 ALA B 326 -2.36 -58.63
REMARK 500 ASP B 401 78.82 -69.96
REMARK 500 ASN B 411 45.34 -151.19
REMARK 500 ASN B 429 51.40 30.31
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 GOL 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
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 904
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue FAD A 905
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 THE LAST LYS 21 OF CHAIN C IS ACTUALLY N-SERYL-LYSINE.
DBREF 5H6Q A 172 833 UNP O60341 KDM1A_HUMAN 172 833
DBREF 5H6Q B 308 440 UNP Q9UKL0 RCOR1_HUMAN 308 440
DBREF 5H6Q C 1 21 PDB 5H6Q 5H6Q 1 21
SEQADV 5H6Q GLY A 165 UNP O60341 EXPRESSION TAG
SEQADV 5H6Q PRO A 166 UNP O60341 EXPRESSION TAG
SEQADV 5H6Q LEU A 167 UNP O60341 EXPRESSION TAG
SEQADV 5H6Q GLY A 168 UNP O60341 EXPRESSION TAG
SEQADV 5H6Q SER A 169 UNP O60341 EXPRESSION TAG
SEQADV 5H6Q HIS A 170 UNP O60341 EXPRESSION TAG
SEQADV 5H6Q MET A 171 UNP O60341 EXPRESSION TAG
SEQADV 5H6Q GLY B 301 UNP Q9UKL0 EXPRESSION TAG
SEQADV 5H6Q SER B 302 UNP Q9UKL0 EXPRESSION TAG
SEQADV 5H6Q SER B 303 UNP Q9UKL0 EXPRESSION TAG
SEQADV 5H6Q GLY B 304 UNP Q9UKL0 EXPRESSION TAG
SEQADV 5H6Q SER B 305 UNP Q9UKL0 EXPRESSION TAG
SEQADV 5H6Q ALA B 306 UNP Q9UKL0 EXPRESSION TAG
SEQADV 5H6Q 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 21 SER ARG THR MET GLN THR ALA ARG LYS SER THR GLY GLY
SEQRES 2 C 21 LYS ALA PRO ARG LYS GLN LEU LYS
HET GOL A 901 6
HET GOL A 902 6
HET GOL A 903 6
HET GOL A 904 6
HET FAD A 905 53
HETNAM GOL GLYCEROL
HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 4 GOL 4(C3 H8 O3)
FORMUL 8 FAD C27 H33 N9 O15 P2
FORMUL 9 HOH *42(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 236 1 7
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 ASN A 340 VAL A 349 1 10
HELIX 9 AA9 PRO A 371 GLN A 395 1 25
HELIX 10 AB1 SER A 407 VAL A 468 1 62
HELIX 11 AB2 ASP A 473 ASN A 514 1 42
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 GLU A 580 1 9
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 GLY A 709 GLU A 716 1 8
HELIX 18 AB9 SER A 719 GLY A 736 1 18
HELIX 19 AC1 SER A 769 GLN A 778 1 10
HELIX 20 AC2 GLY A 800 ILE A 804 5 5
HELIX 21 AC3 THR A 810 LEU A 830 1 21
HELIX 22 AC4 SER B 317 ALA B 326 1 10
HELIX 23 AC5 THR B 329 LEU B 363 1 35
HELIX 24 AC6 THR B 384 TYR B 398 1 15
HELIX 25 AC7 ASP B 401 GLY B 410 1 10
HELIX 26 AC8 SER B 413 TYR B 424 1 12
HELIX 27 AC9 ASN B 429 ALA B 439 1 11
HELIX 28 AD1 SER C 1 GLN C 5 5 5
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 694 N PHE A 678
SHEET 4 AA4 6 ILE A 702 VAL A 707 -1 O LEU A 706 N LEU A 693
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 4 THR A 613 CYS A 618 0
SHEET 2 AA5 4 GLY A 599 ASN A 606 -1 N CYS A 600 O CYS A 618
SHEET 3 AA5 4 THR A 588 THR A 596 -1 N ARG A 591 O ILE A 603
SHEET 4 AA5 4 GLN A 638 VAL A 640 1 O VAL A 640 N VAL A 593
SHEET 1 AA6 2 GLY A 655 PHE A 656 0
SHEET 2 AA6 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 -0.29
CISPEP 2 PRO A 470 PRO A 471 0 -0.04
CISPEP 3 GLN A 633 PRO A 634 0 4.59
CISPEP 4 VAL A 640 PRO A 641 0 -3.93
SITE 1 AC1 4 GLY A 409 GLU A 413 ARG A 526 ARG A 688
SITE 1 AC2 2 LYS A 374 SER A 522
SITE 1 AC3 2 ARG A 182 ILE A 804
SITE 1 AC4 4 ARG A 312 SER A 749 ARG A 750 ASP A 754
SITE 1 AC5 32 GLY A 285 GLY A 287 VAL A 288 SER A 289
SITE 2 AC5 32 LEU A 307 GLU A 308 ALA A 309 ARG A 310
SITE 3 AC5 32 GLY A 314 GLY A 315 ARG A 316 LEU A 329
SITE 4 AC5 32 GLY A 330 ALA A 331 MET A 332 VAL A 333
SITE 5 AC5 32 THR A 588 VAL A 590 THR A 624 LEU A 625
SITE 6 AC5 32 PRO A 626 TRP A 751 TRP A 756 SER A 760
SITE 7 AC5 32 TYR A 761 GLY A 800 GLU A 801 THR A 810
SITE 8 AC5 32 VAL A 811 ALA A 814 HOH A1008 MET C 4
CRYST1 120.825 180.488 233.375 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 0.008276 0.000000 0.000000 0.00000
SCALE2 0.000000 0.005541 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004285 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
