HEADER OXIDOREDUCTASE 27-NOV-15 5FPA
TITLE CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3H,4H-
TITLE 2 PYRIDO-3,4-D-PYRIMIDIN-4-ONE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4D;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 11-341;
COMPND 5 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D,
COMPND 6 JU MONJI DOMAIN-CONTAINING PROTEIN 2D, HUMAN LYSINE-SPECIFIC
COMPND 7 DEMETHYL ASE 4D, JMJD2D;
COMPND 8 EC: 1.14.11.-;
COMPND 9 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, OXIDOREDUCATSE, INHIBITOR, LYSINE SPECIFIC HISTONE
KEYWDS 2 DEMETHYLASE, JMJD2D, KDM4D, JUMONJI
EXPDTA X-RAY DIFFRACTION
AUTHOR C.CHUNG
REVDAT 2 09-MAR-16 5FPA 1 JRNL
REVDAT 1 27-JAN-16 5FPA 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. 1.96 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.6.0117
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.59
REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.71
REMARK 3 NUMBER OF REFLECTIONS : 27580
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) : 0.17096
REMARK 3 R VALUE (WORKING SET) : 0.16928
REMARK 3 FREE R VALUE : 0.21060
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.1
REMARK 3 FREE R VALUE TEST SET COUNT : 1189
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) : 1.960
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.011
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1789
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.73
REMARK 3 BIN R VALUE (WORKING SET) : 0.203
REMARK 3 BIN FREE R VALUE SET COUNT : 72
REMARK 3 BIN FREE R VALUE : 0.271
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2732
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 55
REMARK 3 SOLVENT ATOMS : 563
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.873
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.36
REMARK 3 B22 (A**2) : 0.36
REMARK 3 B33 (A**2) : -0.73
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): 0.164
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.146
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.093
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.128
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2872 ; 0.006 ; 0.020
REMARK 3 BOND LENGTHS OTHERS (A): 1981 ; 0.003 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3906 ; 1.017 ; 1.948
REMARK 3 BOND ANGLES OTHERS (DEGREES): 4794 ; 0.786 ; 3.001
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 352 ; 5.450 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 144 ;34.155 ;23.611
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 475 ;11.636 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;19.054 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 396 ; 0.062 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3203 ; 0.004 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 634 ; 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): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
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 -10 A 9999
REMARK 3 ORIGIN FOR THE GROUP (A): 7.1655 3.4074 18.7255
REMARK 3 T TENSOR
REMARK 3 T11: 0.0171 T22: 0.0104
REMARK 3 T33: 0.0177 T12: -0.0050
REMARK 3 T13: -0.0019 T23: 0.0125
REMARK 3 L TENSOR
REMARK 3 L11: 0.6390 L22: 0.4155
REMARK 3 L33: 0.6699 L12: -0.0640
REMARK 3 L13: 0.1390 L23: 0.0358
REMARK 3 S TENSOR
REMARK 3 S11: 0.0359 S12: -0.0032 S13: -0.0111
REMARK 3 S21: 0.0114 S22: -0.0310 S23: -0.0237
REMARK 3 S31: 0.0570 S32: -0.0052 S33: -0.0050
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 5FPA 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-65664.
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 FRE 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 (SATURN A200)
REMARK 200 DETECTOR MANUFACTURER : RIGAKU
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28865
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.96
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 (%) : 99.8
REMARK 200 DATA REDUNDANCY : 5.1
REMARK 200 R MERGE (I) : 0.10
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 2.00
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 5.2
REMARK 200 R MERGE FOR SHELL (I) : 0.10
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.20
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 (%): NULL
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL
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 75.18300
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.76250
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.76250
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 112.77450
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.76250
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.76250
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.59150
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.76250
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.76250
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 112.77450
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.76250
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.76250
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.59150
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 75.18300
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 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 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 HOH A2023 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 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 470 PHE A 319 CG CD1 CD2 CE1 CE2 CZ
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 S SO4 A 1347 O1 SO4 A 1347 8555 0.99
REMARK 500 S SO4 A 1347 O2 SO4 A 1347 8555 1.62
REMARK 500 S SO4 A 1347 S SO4 A 1347 8555 0.57
REMARK 500 S SO4 A 1347 O3 SO4 A 1347 8555 1.66
REMARK 500 S SO4 A 1347 O4 SO4 A 1347 8555 1.92
REMARK 500 O1 SO4 A 1347 O2 SO4 A 1347 8555 1.14
REMARK 500 O1 SO4 A 1347 O3 SO4 A 1347 8555 1.71
REMARK 500 O1 SO4 A 1347 O4 SO4 A 1347 8555 1.60
REMARK 500 O2 SO4 A 1347 O4 SO4 A 1347 8555 1.75
REMARK 500 O3 SO4 A 1347 O3 SO4 A 1347 8555 1.20
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. = -24.4 DEGREES
REMARK 500 PHE A 319 N - CA - CB ANGL. DEV. = -34.3 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 -8.11 76.39
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 0.11 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS
REMARK 500 PHE A 319 53.9 L L OUTSIDE RANGE
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 87.7
REMARK 620 3 HOH A2399 O 85.9 97.7
REMARK 620 4 HIS A 192 NE2 103.0 86.3 170.4
REMARK 620 5 N5J A1342 N3 169.0 98.6 84.3 86.5
REMARK 620 6 HOH A2394 O 90.5 175.3 86.5 89.9 83.9
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 HIS A 244 NE2
REMARK 620 2 CYS A 238 SG 109.6
REMARK 620 3 CYS A 310 SG 107.6 120.6
REMARK 620 4 CYS A 312 SG 99.6 110.1 107.3
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 N5J A1342
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1343
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1344
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1345
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1346
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1347
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1348
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
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: 5FP9 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3-
REMARK 900 AMINOPYRIDINE-4-CARBOXYLIC ACID
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 5FPA A 11 341 UNP Q6B0I6 KDM4D_HUMAN 11 341
SEQADV 5FPA GLY A 8 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5FPA HIS A 9 UNP Q6B0I6 EXPRESSION TAG
SEQADV 5FPA 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
HET CSX A 168 7
HET ZN A 350 1
HET CO A 360 1
HET N5J A1342 11
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 N5J 3H-PYRIDO[3,4-D]PYRIMIDIN-4-ONE
HETNAM CO COBALT (II) ION
HETNAM SO4 SULFATE ION
HETNAM ZN ZINC ION
HETNAM CSX S-OXY CYSTEINE
FORMUL 2 N5J C7 H5 N3 O
FORMUL 3 CO CO 2+
FORMUL 4 SO4 7(O4 S 2-)
FORMUL 5 ZN ZN 2+
FORMUL 6 CSX C3 H7 N O3 S
FORMUL 7 HOH *563(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 SER A 107 1 10
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 THR A 297 ARG A 299 5 3
HELIX 15 15 TRP A 300 ALA A 307 1 8
HELIX 16 16 SER A 320 GLN A 329 1 10
HELIX 17 17 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 TYR A 279 ASN A 284 -1 O HIS A 280 N HIS A 192
SHEET 3 AC 4 LYS A 210 VAL A 215 -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 1.34
LINK ZN ZN A 350 NE2 HIS A 244 1555 1555 2.07
LINK ZN ZN A 350 SG CYS A 312 1555 1555 2.34
LINK ZN ZN A 350 SG CYS A 310 1555 1555 2.33
LINK ZN ZN A 350 SG CYS A 238 1555 1555 2.31
LINK CO CO A 360 O HOH A2394 1555 1555 2.17
LINK CO CO A 360 NE2 HIS A 192 1555 1555 2.25
LINK CO CO A 360 O HOH A2399 1555 1555 2.24
LINK CO CO A 360 NE2 HIS A 280 1555 1555 2.22
LINK CO CO A 360 OE2 GLU A 194 1555 1555 2.08
LINK CO CO A 360 N3 N5J A1342 1555 1555 2.18
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 N5J A1342
SITE 2 AC2 6 HOH A2394 HOH A2399
SITE 1 AC3 10 TYR A 136 TYR A 181 PHE A 189 HIS A 192
SITE 2 AC3 10 LYS A 210 TRP A 212 HIS A 280 CO A 360
SITE 3 AC3 10 HOH A2394 HOH A2399
SITE 1 AC4 6 PRO A 113 LYS A 124 ASN A 128 TRP A 185
SITE 2 AC4 6 LYS A 186 HOH A2331
SITE 1 AC5 8 ARG A 60 GLU A 61 THR A 62 ASN A 65
SITE 2 AC5 8 HOH A2177 HOH A2179 HOH A2192 HOH A2374
SITE 1 AC6 4 ARG A 123 LYS A 124 LYS A 127 ASN A 128
SITE 1 AC7 8 ARG A 102 HIS A 103 ASN A 106 HOH A2259
SITE 2 AC7 8 HOH A2268 HOH A2273 HOH A2558 HOH A2559
SITE 1 AC8 2 GLN A 116 ASN A 117
SITE 1 AC9 2 TYR A 303 MET A 306
SITE 1 BC1 6 TYR A 179 TYR A 181 GLU A 194 ALA A 292
SITE 2 BC1 6 ILE A 293 ASN A 294
CRYST1 71.525 71.525 150.366 90.00 90.00 90.00 P 43 21 2 1
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 0.013981 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013981 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006650 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
