HEADER OXIDOREDUCTASE 27-NOV-15 5FP9 TITLE CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3- TITLE 2 AMINOPYRIDINE-4-CARBOXYLIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN LYSINE-SPECIFIC DEMETHYLASE 4D JMJC COMPND 3 DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D, JUMONJI COMPND 4 DOMAIN-CONTAINING PROTEIN 2D, JMJD2D; COMPND 5 CHAIN: A; COMPND 6 FRAGMENT: UNP RESIDUES 11-341; COMPND 7 EC: 1.14.11.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE, LYSINE SPECIFIC HISTONE DEMETHYLASE, JMJD2D, KDM4D, KEYWDS 2 JUMONJI EXPDTA X-RAY DIFFRACTION AUTHOR C.CHUNG REVDAT 2 09-MAR-16 5FP9 1 JRNL REVDAT 1 27-JAN-16 5FP9 0 JRNL AUTH S.M.WESTAWAY,A.G.S.PRESTON,M.D.BARKER,F.BROWN,J.A.BROWN, JRNL AUTH 2 M.CAMPBELL,C.CHUNG,H.DIALLO,C.DOUAULT,G.DREWES,R.EAGLE, JRNL AUTH 3 L.GORDON,C.HASLAM,T.G.HAYHOW,P.G.HUMPHREYS,G.JOBERTY, JRNL AUTH 4 R.KATSO,L.KRUIDENIER,M.LEVERIDGE,J.LIDDLE,J.MOSLEY, JRNL AUTH 5 M.MUELBAIER,R.RANDLE,I.RIOJA,A.RUEGER,G.A.SEAL,R.J.SHEPPARD, JRNL AUTH 6 O.SINGH,J.TAYLOR,P.THOMAS,D.THOMSON,D.M.WILSON,K.LEE, JRNL AUTH 7 R.K.PRINJHA JRNL TITL CELL PENETRANT INHIBITORS OF THE KDM4 AND KDM5 FAMILIES OF JRNL TITL 2 HISTONE LYSINE DEMETHYLASES. 1. 3-AMINO-4-PYRIDINE JRNL TITL 3 CARBOXYLATE DERIVATIVES. JRNL REF J.MED.CHEM. V. 59 1357 2016 JRNL REFN ISSN 0022-2623 JRNL PMID 26771107 JRNL DOI 10.1021/ACS.JMEDCHEM.5B01537 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU, REMARK 3 STEINER,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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 92.45 REMARK 3 NUMBER OF REFLECTIONS : 24068 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) : 0.15897 REMARK 3 R VALUE (WORKING SET) : 0.15673 REMARK 3 FREE R VALUE : 0.21141 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.1 REMARK 3 FREE R VALUE TEST SET COUNT : 1028 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) : 1.999 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.051 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1755 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.176 REMARK 3 BIN FREE R VALUE SET COUNT : 73 REMARK 3 BIN FREE R VALUE : 0.208 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2729 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 544 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.925 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.41 REMARK 3 B22 (A**2) : 0.41 REMARK 3 B33 (A**2) : -0.83 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.182 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.164 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.506 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2873 ; 0.005 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2635 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3907 ; 1.035 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6068 ; 0.717 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 351 ; 5.481 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 144 ;34.649 ;23.611 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 473 ;12.027 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;18.689 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 398 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3272 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 726 ; 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): 1341 ; 0.967 ; 2.188 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1340 ; 0.963 ; 2.183 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1683 ; 1.629 ; 4.894 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1532 ; 1.377 ; 2.497 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 11 A 360 REMARK 3 ORIGIN FOR THE GROUP (A): 7.2761 3.3479 18.6296 REMARK 3 T TENSOR REMARK 3 T11: 0.0171 T22: 0.0178 REMARK 3 T33: 0.0065 T12: -0.0038 REMARK 3 T13: -0.0016 T23: 0.0104 REMARK 3 L TENSOR REMARK 3 L11: 0.2881 L22: 0.1319 REMARK 3 L33: 0.3075 L12: -0.0394 REMARK 3 L13: 0.0916 L23: 0.0289 REMARK 3 S TENSOR REMARK 3 S11: 0.0229 S12: -0.0031 S13: 0.0059 REMARK 3 S21: 0.0070 S22: -0.0188 S23: -0.0080 REMARK 3 S31: 0.0325 S32: -0.0083 S33: -0.0042 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 5FP9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-NOV-15. REMARK 100 THE PDBE ID CODE IS EBI-65663. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SATURN A200 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25162 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.03 REMARK 200 RESOLUTION RANGE LOW (A) : 40.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 200 DATA REDUNDANCY : 6.0 REMARK 200 R MERGE (I) : 0.43 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.10 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.7 REMARK 200 R MERGE FOR SHELL (I) : 0.43 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.40 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, PH 7.4, 2.2M AMSO4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 75.14600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.70800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.70800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 112.71900 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.70800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.70800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.57300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.70800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.70800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 112.71900 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.70800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.70800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.57300 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 75.14600 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: 5410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -222.2 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 S SO4 A1347 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2022 LIES ON A SPECIAL POSITION. 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 8 REMARK 465 HIS A 9 REMARK 465 MET A 10 REMARK 465 VAL A 317 REMARK 465 THR A 318 REMARK 465 PHE A 319 REMARK 465 ASP A 341 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 ARG A 316 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2344 O HOH A 2344 7555 1.30 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 GLN A 221 CG - CD - OE1 ANGL. DEV. = -18.0 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 LYS A 186 -9.75 74.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLN A 221 0.13 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 360 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 194 OE2 REMARK 620 2 HIS A 280 NE2 85.8 REMARK 620 3 HOH A2384 O 87.3 95.7 REMARK 620 4 HIS A 192 NE2 98.1 84.4 174.6 REMARK 620 5 4SV A1342 N2 170.1 100.2 84.3 90.4 REMARK 620 6 HOH A2379 O 88.0 172.1 88.9 91.6 86.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 350 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 310 SG REMARK 620 2 CYS A 238 SG 118.5 REMARK 620 3 HIS A 244 NE2 110.3 108.3 REMARK 620 4 CYS A 312 SG 106.4 110.8 101.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 360 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 4SV A1342 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1344 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1345 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1346 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1347 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1348 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1349 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FP3 RELATED DB: PDB REMARK 900 CELL PENETRANT INHIBITORS OF THE JMJD2 (KDM4) AND REMARK 900 JARID1 (KDM5) FAMILIES OF HISTONE LYSINE DEMETHYLASES REMARK 900 RELATED ID: 5FP4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3-( REMARK 900 4-PHENYLBUTANAMIDO)PYRIDINE-4-CARBOXYLIC ACID REMARK 900 RELATED ID: 5FP7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3-4 REMARK 900 -METHYLTHIOPHEN-2-YL METHYLAMINOPYRIDINE-4-CARBOXYLIC REMARK 900 ACID REMARK 900 RELATED ID: 5FP8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3-4 REMARK 900 -METHYLTHIOPHEN-2-YLMETHYLAMINOPYRIDINE-4-CARBOXYLIC ACID REMARK 900 RELATED ID: 5FPA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3H, REMARK 900 4H-PYRIDO-3,4-D-PYRIMIDIN-4-ONE REMARK 900 RELATED ID: 5FPB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 2- REMARK 900 1H-PYRAZOL-4-YLOXY-3H,4H-PYRIDO-3,4-D-PYRIMIDIN- REMARK 900 4-ONE DBREF 5FP9 A 11 341 UNP Q6B0I6 KDM4D_HUMAN 11 341 SEQADV 5FP9 GLY A 8 UNP Q6B0I6 EXPRESSION TAG SEQADV 5FP9 HIS A 9 UNP Q6B0I6 EXPRESSION TAG SEQADV 5FP9 MET A 10 UNP Q6B0I6 EXPRESSION TAG SEQRES 1 A 334 GLY HIS MET ALA GLN ASN PRO ASN CYS ASN ILE MET ILE SEQRES 2 A 334 PHE HIS PRO THR LYS GLU GLU PHE ASN ASP PHE ASP LYS SEQRES 3 A 334 TYR ILE ALA TYR MET GLU SER GLN GLY ALA HIS ARG ALA SEQRES 4 A 334 GLY LEU ALA LYS ILE ILE PRO PRO LYS GLU TRP LYS ALA SEQRES 5 A 334 ARG GLU THR TYR ASP ASN ILE SER GLU ILE LEU ILE ALA SEQRES 6 A 334 THR PRO LEU GLN GLN VAL ALA SER GLY ARG ALA GLY VAL SEQRES 7 A 334 PHE THR GLN TYR HIS LYS LYS LYS LYS ALA MET THR VAL SEQRES 8 A 334 GLY GLU TYR ARG HIS LEU ALA ASN SER LYS LYS TYR GLN SEQRES 9 A 334 THR PRO PRO HIS GLN ASN PHE GLU ASP LEU GLU ARG LYS SEQRES 10 A 334 TYR TRP LYS ASN ARG ILE TYR ASN SER PRO ILE TYR GLY SEQRES 11 A 334 ALA ASP ILE SER GLY SER LEU PHE ASP GLU ASN THR LYS SEQRES 12 A 334 GLN TRP ASN LEU GLY HIS LEU GLY THR ILE GLN ASP LEU SEQRES 13 A 334 LEU GLU LYS GLU CSX GLY VAL VAL ILE GLU GLY VAL ASN SEQRES 14 A 334 THR PRO TYR LEU TYR PHE GLY MET TRP LYS THR THR PHE SEQRES 15 A 334 ALA TRP HIS THR GLU ASP MET ASP LEU TYR SER ILE ASN SEQRES 16 A 334 TYR LEU HIS LEU GLY GLU PRO LYS THR TRP TYR VAL VAL SEQRES 17 A 334 PRO PRO GLU HIS GLY GLN ARG LEU GLU ARG LEU ALA ARG SEQRES 18 A 334 GLU LEU PHE PRO GLY SER SER ARG GLY CYS GLY ALA PHE SEQRES 19 A 334 LEU ARG HIS LYS VAL ALA LEU ILE SER PRO THR VAL LEU SEQRES 20 A 334 LYS GLU ASN GLY ILE PRO PHE ASN ARG ILE THR GLN GLU SEQRES 21 A 334 ALA GLY GLU PHE MET VAL THR PHE PRO TYR GLY TYR HIS SEQRES 22 A 334 ALA GLY PHE ASN HIS GLY PHE ASN CYS ALA GLU ALA ILE SEQRES 23 A 334 ASN PHE ALA THR PRO ARG TRP ILE ASP TYR GLY LYS MET SEQRES 24 A 334 ALA SER GLN CYS SER CYS GLY GLU ALA ARG VAL THR PHE SEQRES 25 A 334 SER MET ASP ALA PHE VAL ARG ILE LEU GLN PRO GLU ARG SEQRES 26 A 334 TYR ASP LEU TRP LYS ARG GLY GLN ASP MODRES 5FP9 CSX A 168 CYS S-OXY CYSTEINE HET CSX A 168 7 HET ZN A 350 1 HET CO A 360 1 HET GOL A1341 6 HET 4SV A1342 10 HET SO4 A1343 5 HET SO4 A1344 5 HET SO4 A1345 5 HET SO4 A1346 5 HET SO4 A1347 5 HET SO4 A1348 5 HET SO4 A1349 5 HETNAM CO COBALT (II) ION HETNAM 4SV 3-AMINOPYRIDINE-4-CARBOXYLIC ACID HETNAM SO4 SULFATE ION HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETNAM CSX S-OXY CYSTEINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CO CO 2+ FORMUL 3 4SV C6 H6 N2 O2 FORMUL 4 SO4 7(O4 S 2-) FORMUL 5 ZN ZN 2+ FORMUL 6 GOL C3 H8 O3 FORMUL 7 CSX C3 H7 N O3 S FORMUL 8 HOH *544(H2 O) HELIX 1 1 GLU A 26 ASN A 29 5 4 HELIX 2 2 ASP A 30 GLN A 41 1 12 HELIX 3 3 GLY A 42 ALA A 46 5 5 HELIX 4 4 VAL A 98 ASN A 106 1 9 HELIX 5 5 ASN A 117 ARG A 129 1 13 HELIX 6 6 ILE A 130 ASN A 132 5 3 HELIX 7 7 THR A 159 GLY A 169 1 11 HELIX 8 8 GLU A 194 LEU A 198 5 5 HELIX 9 9 PRO A 216 GLU A 218 5 3 HELIX 10 10 HIS A 219 PHE A 231 1 13 HELIX 11 11 PHE A 231 CYS A 238 1 8 HELIX 12 12 ALA A 240 LYS A 245 5 6 HELIX 13 13 SER A 250 ASN A 257 1 8 HELIX 14 14 ARG A 299 ALA A 307 1 9 HELIX 15 15 SER A 320 GLN A 329 1 10 HELIX 16 16 GLN A 329 GLN A 340 1 12 SHEET 1 AA10 MET A 19 PHE A 21 0 SHEET 2 AA10 LEU A 48 ILE A 51 1 O LEU A 48 N MET A 19 SHEET 3 AA10 PHE A 271 THR A 274 -1 O PHE A 271 N ILE A 51 SHEET 4 AA10 TYR A 199 GLY A 207 -1 O SER A 200 N THR A 274 SHEET 5 AA10 ASN A 288 PHE A 295 -1 O CYS A 289 N HIS A 205 SHEET 6 AA10 TYR A 179 GLY A 183 -1 O TYR A 179 N ALA A 292 SHEET 7 AA10 ILE A 135 SER A 141 -1 O GLY A 137 N PHE A 182 SHEET 8 AA10 LEU A 75 ARG A 82 -1 O LEU A 75 N TYR A 136 SHEET 9 AA10 VAL A 85 LYS A 92 -1 O VAL A 85 N ARG A 82 SHEET 10 AA10 ALA A 247 ILE A 249 -1 O LEU A 248 N PHE A 86 SHEET 1 AB 2 LEU A 70 ILE A 71 0 SHEET 2 AB 2 MET A 96 THR A 97 -1 O MET A 96 N ILE A 71 SHEET 1 AC 4 THR A 188 HIS A 192 0 SHEET 2 AC 4 HIS A 280 ASN A 284 -1 O HIS A 280 N HIS A 192 SHEET 3 AC 4 LYS A 210 VAL A 214 -1 O THR A 211 N PHE A 283 SHEET 4 AC 4 ASN A 262 GLN A 266 -1 O ASN A 262 N VAL A 214 LINK C GLU A 167 N CSX A 168 1555 1555 1.33 LINK C CSX A 168 N GLY A 169 1555 1555 1.33 LINK ZN ZN A 350 SG CYS A 310 1555 1555 2.33 LINK ZN ZN A 350 SG CYS A 312 1555 1555 2.35 LINK ZN ZN A 350 NE2 HIS A 244 1555 1555 2.06 LINK ZN ZN A 350 SG CYS A 238 1555 1555 2.32 LINK CO CO A 360 O HOH A2379 1555 1555 2.19 LINK CO CO A 360 N2 4SV A1342 1555 1555 2.09 LINK CO CO A 360 NE2 HIS A 192 1555 1555 2.28 LINK CO CO A 360 O HOH A2384 1555 1555 2.16 LINK CO CO A 360 NE2 HIS A 280 1555 1555 2.22 LINK CO CO A 360 OE2 GLU A 194 1555 1555 2.09 SITE 1 AC1 4 CYS A 238 HIS A 244 CYS A 310 CYS A 312 SITE 1 AC2 6 HIS A 192 GLU A 194 HIS A 280 4SV A1342 SITE 2 AC2 6 HOH A2379 HOH A2384 SITE 1 AC3 8 PHE A 31 LYS A 150 GLN A 151 TRP A 152 SITE 2 AC3 8 ASN A 153 HIS A 156 HOH A2076 HOH A2078 SITE 1 AC4 9 TYR A 136 PHE A 189 HIS A 192 LYS A 210 SITE 2 AC4 9 TRP A 212 HIS A 280 CO A 360 HOH A2379 SITE 3 AC4 9 HOH A2384 SITE 1 AC5 7 PRO A 113 LYS A 124 ASN A 128 TRP A 185 SITE 2 AC5 7 LYS A 186 HOH A2310 HOH A2536 SITE 1 AC6 7 ARG A 60 GLU A 61 THR A 62 ASN A 65 SITE 2 AC6 7 HOH A2163 HOH A2165 HOH A2175 SITE 1 AC7 5 ARG A 123 LYS A 124 LYS A 127 ASN A 128 SITE 2 AC7 5 HOH A2310 SITE 1 AC8 7 ARG A 102 HIS A 103 ASN A 106 HOH A2247 SITE 2 AC8 7 HOH A2537 HOH A2538 HOH A2539 SITE 1 AC9 2 GLN A 116 ASN A 117 SITE 1 BC1 3 ASP A 302 TYR A 303 MET A 306 SITE 1 BC2 7 TYR A 179 TYR A 181 GLU A 194 ALA A 292 SITE 2 BC2 7 ILE A 293 ASN A 294 HOH A2535 CRYST1 71.416 71.416 150.292 90.00 90.00 90.00 P 43 21 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 0.014002 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014002 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006654 0.00000