HEADER OXIDOREDUCTASE/TRANSCRIPTION/INHIBITOR 10-OCT-17 5YJB
TITLE LSD1-COREST IN COMPLEX WITH 4-[5-(PIPERIDIN-4-YLMETHOXY)-2-(P-TOLYL)
TITLE 2 PYRIDIN-3-YL]BENZONITRILE
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 311-443;
COMPND 13 SYNONYM: PROTEIN COREST;
COMPND 14 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 KRX;
SOURCE 17 EXPRESSION_SYSTEM_TAXID: 1452720;
SOURCE 18 EXPRESSION_SYSTEM_STRAIN: KRX
KEYWDS DEMETHYLASE, AMINE OXIDASE, CHROMATIN, HISTONE, FAD, COREPRESSOR,
KEYWDS 2 OXIDOREDUCTASE-TRANSCRIPTION-INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR H.NIWA,S.SATO,T.HASHIMOTO,K.MATSUNO,T.UMEHARA
REVDAT 3 22-NOV-23 5YJB 1 REMARK
REVDAT 2 01-AUG-18 5YJB 1 JRNL
REVDAT 1 04-JUL-18 5YJB 0
JRNL AUTH H.NIWA,S.SATO,T.HASHIMOTO,K.MATSUNO,T.UMEHARA
JRNL TITL CRYSTAL STRUCTURE OF LSD1 IN COMPLEX WITH
JRNL TITL 2 4-[5-(PIPERIDIN-4-YLMETHOXY)-2-(P-TOLYL)
JRNL TITL 3 PYRIDIN-3-YL]BENZONITRILE.
JRNL REF MOLECULES V. 23 2018
JRNL REFN ESSN 1420-3049
JRNL PMID 29949906
JRNL DOI 10.3390/MOLECULES23071538
REMARK 2
REMARK 2 RESOLUTION. 2.96 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (1.12_2829: ???)
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 : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.96
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.82
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.220
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 53614
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.189
REMARK 3 R VALUE (WORKING SET) : 0.189
REMARK 3 FREE R VALUE : 0.219
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.970
REMARK 3 FREE R VALUE TEST SET COUNT : 1053
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 48.8283 - 7.2924 1.00 6756 124 0.1649 0.1820
REMARK 3 2 7.2924 - 5.7912 1.00 6746 142 0.1870 0.2195
REMARK 3 3 5.7912 - 5.0600 1.00 6787 125 0.1594 0.1983
REMARK 3 4 5.0600 - 4.5978 1.00 6742 124 0.1309 0.1802
REMARK 3 5 4.5978 - 4.2684 1.00 6750 111 0.1236 0.1579
REMARK 3 6 4.2684 - 4.0169 1.00 6714 134 0.1399 0.1448
REMARK 3 7 4.0169 - 3.8158 1.00 6774 127 0.1686 0.1787
REMARK 3 8 3.8158 - 3.6498 1.00 6718 145 0.2020 0.2321
REMARK 3 9 3.6498 - 3.5093 1.00 6705 177 0.2197 0.2284
REMARK 3 10 3.5093 - 3.3882 1.00 6710 129 0.2385 0.2555
REMARK 3 11 3.3882 - 3.2823 1.00 6764 142 0.2381 0.2932
REMARK 3 12 3.2823 - 3.1885 1.00 6701 147 0.2838 0.3179
REMARK 3 13 3.1885 - 3.1046 1.00 6804 111 0.3224 0.3866
REMARK 3 14 3.1046 - 3.0289 1.00 6715 159 0.3584 0.4082
REMARK 3 15 3.0289 - 2.9600 1.00 6660 135 0.3977 0.3832
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) : 0.410
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.230
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
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 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 : 0.008 6446
REMARK 3 ANGLE : 0.945 8746
REMARK 3 CHIRALITY : 0.048 976
REMARK 3 PLANARITY : 0.006 1150
REMARK 3 DIHEDRAL : 13.803 3892
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 7
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 172 THROUGH 371 )
REMARK 3 ORIGIN FOR THE GROUP (A): 15.2127 -56.5947 -17.0409
REMARK 3 T TENSOR
REMARK 3 T11: 0.6174 T22: 0.4661
REMARK 3 T33: 0.6009 T12: -0.1225
REMARK 3 T13: -0.1916 T23: 0.1194
REMARK 3 L TENSOR
REMARK 3 L11: 1.8195 L22: 1.8655
REMARK 3 L33: 3.6041 L12: -0.2100
REMARK 3 L13: -0.9109 L23: -0.4834
REMARK 3 S TENSOR
REMARK 3 S11: -0.0950 S12: -0.2390 S13: 0.3385
REMARK 3 S21: 0.0446 S22: -0.0402 S23: -0.5134
REMARK 3 S31: -0.4017 S32: 0.6014 S33: 0.1575
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 372 THROUGH 513 )
REMARK 3 ORIGIN FOR THE GROUP (A): -25.8694 -14.8152 -56.9416
REMARK 3 T TENSOR
REMARK 3 T11: 1.1812 T22: 0.7729
REMARK 3 T33: 1.0864 T12: 0.0296
REMARK 3 T13: -0.3705 T23: 0.3033
REMARK 3 L TENSOR
REMARK 3 L11: 2.9016 L22: 8.3048
REMARK 3 L33: 2.6027 L12: -6.1237
REMARK 3 L13: 3.4278 L23: -4.8317
REMARK 3 S TENSOR
REMARK 3 S11: -0.1648 S12: 0.1765 S13: 0.3799
REMARK 3 S21: 0.4356 S22: -0.0735 S23: -0.4680
REMARK 3 S31: -0.4190 S32: -0.0131 S33: 0.2049
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 514 THROUGH 832 )
REMARK 3 ORIGIN FOR THE GROUP (A): 2.6730 -62.9560 -33.7827
REMARK 3 T TENSOR
REMARK 3 T11: 0.8322 T22: 0.3984
REMARK 3 T33: 0.4246 T12: 0.0127
REMARK 3 T13: -0.0233 T23: 0.0874
REMARK 3 L TENSOR
REMARK 3 L11: 1.7976 L22: 3.2785
REMARK 3 L33: 1.7875 L12: -0.1138
REMARK 3 L13: -0.0337 L23: -0.1288
REMARK 3 S TENSOR
REMARK 3 S11: -0.0720 S12: 0.3738 S13: 0.0944
REMARK 3 S21: -0.6112 S22: -0.2293 S23: -0.1933
REMARK 3 S31: 0.0667 S32: 0.1065 S33: 0.2781
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: CHAIN 'B' AND (RESID 309 THROUGH 370 )
REMARK 3 ORIGIN FOR THE GROUP (A): -26.4831 -26.6262 -56.2624
REMARK 3 T TENSOR
REMARK 3 T11: 0.7668 T22: 0.6225
REMARK 3 T33: 0.7601 T12: 0.0112
REMARK 3 T13: -0.1830 T23: 0.1777
REMARK 3 L TENSOR
REMARK 3 L11: 3.2026 L22: 5.5562
REMARK 3 L33: 6.5251 L12: -3.2550
REMARK 3 L13: 3.5823 L23: -4.6319
REMARK 3 S TENSOR
REMARK 3 S11: 0.2755 S12: 0.2420 S13: -0.1745
REMARK 3 S21: -0.0577 S22: -0.0817 S23: 0.2845
REMARK 3 S31: 0.1349 S32: -0.3797 S33: -0.1934
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: CHAIN 'B' AND (RESID 371 THROUGH 384 )
REMARK 3 ORIGIN FOR THE GROUP (A): -33.5982 26.2815 -66.3882
REMARK 3 T TENSOR
REMARK 3 T11: 1.3505 T22: 1.1135
REMARK 3 T33: 1.6335 T12: -0.1726
REMARK 3 T13: -0.2629 T23: 0.0053
REMARK 3 L TENSOR
REMARK 3 L11: 4.7028 L22: 0.5890
REMARK 3 L33: 2.7017 L12: 1.5054
REMARK 3 L13: -0.6911 L23: -0.7494
REMARK 3 S TENSOR
REMARK 3 S11: 0.3717 S12: -1.2301 S13: 0.3206
REMARK 3 S21: 0.6382 S22: -0.0266 S23: -0.8279
REMARK 3 S31: -0.6356 S32: 0.7918 S33: -0.3337
REMARK 3 TLS GROUP : 6
REMARK 3 SELECTION: CHAIN 'B' AND (RESID 385 THROUGH 413 )
REMARK 3 ORIGIN FOR THE GROUP (A): -44.0182 23.3215 -61.8190
REMARK 3 T TENSOR
REMARK 3 T11: 1.7315 T22: 1.0555
REMARK 3 T33: 0.8831 T12: 0.0259
REMARK 3 T13: -0.5469 T23: 0.1954
REMARK 3 L TENSOR
REMARK 3 L11: 7.1637 L22: 1.9274
REMARK 3 L33: 4.7672 L12: -2.2213
REMARK 3 L13: -4.1113 L23: -0.0404
REMARK 3 S TENSOR
REMARK 3 S11: -0.3980 S12: -2.2212 S13: -0.6664
REMARK 3 S21: 0.7164 S22: 0.3075 S23: -0.9129
REMARK 3 S31: 0.2517 S32: 0.3421 S33: 0.0537
REMARK 3 TLS GROUP : 7
REMARK 3 SELECTION: CHAIN 'B' AND (RESID 414 THROUGH 439 )
REMARK 3 ORIGIN FOR THE GROUP (A): -50.4168 25.6474 -54.7992
REMARK 3 T TENSOR
REMARK 3 T11: 1.8403 T22: 1.2486
REMARK 3 T33: 0.7590 T12: 0.1702
REMARK 3 T13: -0.2606 T23: -0.0382
REMARK 3 L TENSOR
REMARK 3 L11: 6.8039 L22: 4.0737
REMARK 3 L33: 9.7084 L12: 1.0258
REMARK 3 L13: 5.3872 L23: 0.2817
REMARK 3 S TENSOR
REMARK 3 S11: 0.2042 S12: -1.4690 S13: -0.0329
REMARK 3 S21: 2.4537 S22: -0.2242 S23: -0.3171
REMARK 3 S31: -0.1502 S32: -0.0613 S33: 0.0414
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 5YJB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-OCT-17.
REMARK 100 THE DEPOSITION ID IS D_1300005391.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 21-APR-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 : 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 : NULL
REMARK 200 DATA SCALING SOFTWARE : AIMLESS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53652
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.960
REMARK 200 RESOLUTION RANGE LOW (A) : 49.160
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 7.500
REMARK 200 R MERGE (I) : 0.11400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.96
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.05
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 7.60
REMARK 200 R MERGE FOR SHELL (I) : 1.42000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> 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: PHASER
REMARK 200 STARTING MODEL: 5H6Q
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 82.64
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 7.09
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M N-(2-ACETAMIDO)IMINODIACETIC ACID
REMARK 280 (PH 5.5), 1.23M 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 60.57200
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 89.81200
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 117.47650
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 60.57200
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 89.81200
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 117.47650
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 60.57200
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 89.81200
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 117.47650
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 60.57200
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 89.81200
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 117.47650
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 7210 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 37050 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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 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 GLU A 239 CG CD OE1 OE2
REMARK 470 LYS A 276 CG CD CE NZ
REMARK 470 LYS A 359 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 ASN A 224 83.10 -167.54
REMARK 500 MET A 332 -17.56 -146.60
REMARK 500 LEU A 697 -7.36 -158.89
REMARK 500 PRO A 701 96.88 -65.35
REMARK 500 ASN A 717 31.62 -84.50
REMARK 500 ALA A 757 -55.38 -138.40
REMARK 500 SER A 760 -70.57 -100.01
REMARK 500 SER A 785 -70.38 -58.54
REMARK 500 PRO A 790 152.60 -49.56
REMARK 500 TYR A 807 49.28 -145.84
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 8WC 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
DBREF 5YJB A 172 833 UNP O60341 KDM1A_HUMAN 172 833
DBREF 5YJB B 308 440 UNP Q9UKL0 RCOR1_HUMAN 311 443
SEQADV 5YJB GLY A 165 UNP O60341 EXPRESSION TAG
SEQADV 5YJB PRO A 166 UNP O60341 EXPRESSION TAG
SEQADV 5YJB LEU A 167 UNP O60341 EXPRESSION TAG
SEQADV 5YJB GLY A 168 UNP O60341 EXPRESSION TAG
SEQADV 5YJB SER A 169 UNP O60341 EXPRESSION TAG
SEQADV 5YJB HIS A 170 UNP O60341 EXPRESSION TAG
SEQADV 5YJB MET A 171 UNP O60341 EXPRESSION TAG
SEQADV 5YJB GLY B 301 UNP Q9UKL0 EXPRESSION TAG
SEQADV 5YJB SER B 302 UNP Q9UKL0 EXPRESSION TAG
SEQADV 5YJB SER B 303 UNP Q9UKL0 EXPRESSION TAG
SEQADV 5YJB GLY B 304 UNP Q9UKL0 EXPRESSION TAG
SEQADV 5YJB SER B 305 UNP Q9UKL0 EXPRESSION TAG
SEQADV 5YJB ALA B 306 UNP Q9UKL0 EXPRESSION TAG
SEQADV 5YJB 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
HET FAD A 901 53
HET 8WC A 902 29
HET GOL A 903 6
HET GOL A 904 6
HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE
HETNAM 8WC 4-[2-(4-METHYLPHENYL)-5-(PIPERIDIN-4-YLMETHOXY)PYRIDIN-
HETNAM 2 8WC 3-YL]BENZENECARBONITRILE
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 3 FAD C27 H33 N9 O15 P2
FORMUL 4 8WC C25 H25 N3 O
FORMUL 5 GOL 2(C3 H8 O3)
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 SER A 201 1 6
HELIX 4 AA4 PRO A 203 ASP A 223 1 21
HELIX 5 AA5 THR A 230 LEU A 238 1 9
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 ASN A 350 1 11
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 ALA A 541 1 20
HELIX 13 AB4 PRO A 543 LEU A 547 5 5
HELIX 14 AB5 ASP A 553 GLU A 559 5 7
HELIX 15 AB6 SER A 572 GLU A 580 1 9
HELIX 16 AB7 PRO A 626 GLN A 632 1 7
HELIX 17 AB8 PRO A 644 MET A 654 1 11
HELIX 18 AB9 THR A 685 GLU A 690 5 6
HELIX 19 AC1 ALA A 708 ASN A 717 1 10
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 LEU A 830 1 21
HELIX 25 AC7 SER B 317 ALA B 326 1 10
HELIX 26 AC8 THR B 329 LEU B 363 1 35
HELIX 27 AC9 ILE B 367 ARG B 371 5 5
HELIX 28 AD1 THR B 384 GLY B 399 1 16
HELIX 29 AD2 ASP B 401 GLY B 410 1 10
HELIX 30 AD3 SER B 413 TYR B 424 1 12
HELIX 31 AD4 ASN B 429 GLU B 438 1 10
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 VAL A 281 O ASP A 303
SHEET 4 AA1 5 ALA A 620 CYS A 623 1 O LEU A 622 N ILE A 282
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 LEU A 693 ASN A 696 -1 O PHE A 694 N PHE A 678
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 ASN A 660 O VAL A 707
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 THR A 613 CYS A 618 0
SHEET 2 AA6 4 GLY A 599 ASN A 606 -1 N ALA A 604 O PHE A 614
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
CISPEP 1 ALA A 240 PRO A 241 0 -1.27
CISPEP 2 PRO A 470 PRO A 471 0 5.46
CISPEP 3 GLN A 633 PRO A 634 0 -3.80
CISPEP 4 VAL A 640 PRO A 641 0 3.75
SITE 1 AC1 33 GLY A 285 GLY A 287 VAL A 288 SER A 289
SITE 2 AC1 33 LEU A 307 GLU A 308 ALA A 309 ARG A 310
SITE 3 AC1 33 GLY A 314 GLY A 315 ARG A 316 VAL A 317
SITE 4 AC1 33 GLY A 330 ALA A 331 MET A 332 VAL A 333
SITE 5 AC1 33 THR A 588 ALA A 589 VAL A 590 THR A 624
SITE 6 AC1 33 LEU A 625 PRO A 626 VAL A 637 LEU A 659
SITE 7 AC1 33 TRP A 751 TRP A 756 SER A 760 TYR A 761
SITE 8 AC1 33 GLY A 800 GLU A 801 THR A 810 VAL A 811
SITE 9 AC1 33 8WC A 902
SITE 1 AC2 11 MET A 332 PHE A 538 ALA A 539 ASN A 540
SITE 2 AC2 11 ASP A 555 LEU A 659 LYS A 661 TRP A 695
SITE 3 AC2 11 TYR A 761 ALA A 809 FAD A 901
SITE 1 AC3 2 ARG A 526 ARG A 688
SITE 1 AC4 6 ARG A 310 ARG A 312 SER A 749 ARG A 750
SITE 2 AC4 6 TRP A 751 ASP A 754
CRYST1 121.144 179.624 234.953 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 0.008255 0.000000 0.000000 0.00000
SCALE2 0.000000 0.005567 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004256 0.00000
(ATOM LINES ARE NOT SHOWN.)
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