HEADER OXIDOREDUCTASE 26-OCT-17 6ETE
TITLE CRYSTAL STRUCTURE OF KDM4D WITH TETRAZOLHYDRAZIDE COMPOUND 5
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4D;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: JMJD2D;
COMPND 5 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D,
COMPND 6 JUMONJI DOMAIN-CONTAINING PROTEIN 2D;
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 GENE: KDM4D, JHDM3D, JMJD2D;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID
KEYWDS KDM4D, LIGAND BINDING, TETRAZOLYLHYDRAZIDE, TETRAZOLE, INHIBITOR
KEYWDS 2 DESIGN, CANCER, EPIGENETICS, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR P.H.MALECKI,M.S.WEISS,U.HEINEMANN,A.LINK
REVDAT 1 20-FEB-19 6ETE 0
JRNL AUTH P.H.MALECKI,A.LINK,M.S.WEISS,U.HEINEMANN
JRNL TITL CRYSTAL STRUCTURE OF KDM4D WITH TETRAZOLYLHYDRAZIDE LIGAND
JRNL TITL 2 NR128
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.47 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX
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) : 1.47
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.73
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 127487
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.128
REMARK 3 R VALUE (WORKING SET) : 0.128
REMARK 3 FREE R VALUE : 0.153
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.630
REMARK 3 FREE R VALUE TEST SET COUNT : 2081
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 35.7426 - 3.6190 1.00 8366 132 0.1327 0.1706
REMARK 3 2 3.6190 - 2.8729 1.00 8364 142 0.1246 0.1251
REMARK 3 3 2.8729 - 2.5098 1.00 8370 134 0.1218 0.1350
REMARK 3 4 2.5098 - 2.2804 1.00 8361 138 0.1165 0.1386
REMARK 3 5 2.2804 - 2.1170 1.00 8382 139 0.1075 0.1598
REMARK 3 6 2.1170 - 1.9922 1.00 8375 141 0.1083 0.1177
REMARK 3 7 1.9922 - 1.8924 1.00 8365 143 0.1073 0.1619
REMARK 3 8 1.8924 - 1.8100 1.00 8409 141 0.1128 0.1347
REMARK 3 9 1.8100 - 1.7404 1.00 8283 139 0.1262 0.1670
REMARK 3 10 1.7404 - 1.6803 1.00 8400 143 0.1353 0.1718
REMARK 3 11 1.6803 - 1.6278 1.00 8332 136 0.1461 0.1669
REMARK 3 12 1.6278 - 1.5812 1.00 8409 139 0.1579 0.2104
REMARK 3 13 1.5812 - 1.5396 1.00 8358 141 0.1777 0.2146
REMARK 3 14 1.5396 - 1.5021 1.00 8425 136 0.1973 0.2113
REMARK 3 15 1.5021 - 1.4679 0.98 8207 137 0.2254 0.2668
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) : 0.130
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.980
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 18.05
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.33
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 : 0.031 3074
REMARK 3 ANGLE : 2.362 4205
REMARK 3 CHIRALITY : 0.166 421
REMARK 3 PLANARITY : 0.016 558
REMARK 3 DIHEDRAL : 15.719 1182
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
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 6ETE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-OCT-17.
REMARK 100 THE DEPOSITION ID IS D_1200007227.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 04-MAY-16
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : BESSY
REMARK 200 BEAMLINE : 14.1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.918
REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 127491
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470
REMARK 200 RESOLUTION RANGE LOW (A) : 47.923
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 4.607
REMARK 200 R MERGE (I) : 0.04400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.1600
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3
REMARK 200 DATA REDUNDANCY IN SHELL : 4.54
REMARK 200 R MERGE FOR SHELL (I) : 0.69400
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.020
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: REFMAC
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.42
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES, 180MM AMMONIUM SULPHATE,
REMARK 280 24% PEG 3350, PH 7, VAPOR DIFFUSION, TEMPERATURE 293K
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 75.53500
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.73200
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.73200
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 113.30250
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.73200
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.73200
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.76750
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.73200
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.73200
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 113.30250
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.73200
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.73200
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.76750
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 75.53500
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2100 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 14950 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 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 MET A 1
REMARK 465 GLU A 2
REMARK 465 THR A 3
REMARK 465 MET A 4
REMARK 465 LYS A 5
REMARK 465 SER A 6
REMARK 465 LYS A 7
REMARK 465 ALA A 8
REMARK 465 ASN A 9
REMARK 465 CYS A 10
REMARK 465 ASP A 341
REMARK 465 ARG A 342
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 ARG A 228 N ARG A 228 CA 0.135
REMARK 500 MET A 321 N MET A 321 CA 0.185
REMARK 500 GLU A 331 N GLU A 331 CA 0.121
REMARK 500 ASP A 334 CA ASP A 334 C 0.162
REMARK 500 ASP A 334 CA ASP A 334 C 0.162
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 ARG A 102 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES
REMARK 500 ARG A 102 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES
REMARK 500 ILE A 160 CB - CA - C ANGL. DEV. = -15.4 DEGREES
REMARK 500 MET A 196 CG - SD - CE ANGL. DEV. = 13.0 DEGREES
REMARK 500 MET A 321 CG - SD - CE ANGL. DEV. = 13.0 DEGREES
REMARK 500 ASP A 322 CB - CG - OD1 ANGL. DEV. = 7.5 DEGREES
REMARK 500 ASP A 322 CB - CG - OD2 ANGL. DEV. = -6.1 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 -7.75 75.61
REMARK 500 MET A 196 19.92 50.89
REMARK 500 MET A 196 21.15 49.80
REMARK 500 ASP A 334 -58.54 -29.89
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 850 DISTANCE = 5.87 ANGSTROMS
REMARK 525 HOH A 851 DISTANCE = 8.44 ANGSTROMS
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 NI A 403 NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 156 NE2
REMARK 620 2 HOH A 721 O 83.1
REMARK 620 N 1
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NI A 402 NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 192 NE2
REMARK 620 2 GLU A 194 OE2 98.9
REMARK 620 3 HIS A 280 NE2 85.9 86.7
REMARK 620 4 BWK A 413 O 89.5 171.5 92.8
REMARK 620 5 BWK A 413 N4 142.3 118.7 98.5 53.0
REMARK 620 6 BWK A 413 N5 168.3 92.2 98.4 79.5 26.5
REMARK 620 7 HOH A 569 O 87.9 91.2 173.1 90.3 88.2 88.2
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 401 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 238 SG
REMARK 620 2 HIS A 244 NE2 107.7
REMARK 620 3 CYS A 310 SG 116.1 109.7
REMARK 620 4 CYS A 312 SG 114.5 101.5 106.3
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 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 403
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 409
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 410
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 411
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 412
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue BWK A 413
DBREF 6ETE A 1 342 UNP Q6B0I6 KDM4D_HUMAN 1 342
SEQRES 1 A 342 MET GLU THR MET LYS SER LYS ALA ASN CYS ALA GLN ASN
SEQRES 2 A 342 PRO ASN CYS ASN ILE MET ILE PHE HIS PRO THR LYS GLU
SEQRES 3 A 342 GLU PHE ASN ASP PHE ASP LYS TYR ILE ALA TYR MET GLU
SEQRES 4 A 342 SER GLN GLY ALA HIS ARG ALA GLY LEU ALA LYS ILE ILE
SEQRES 5 A 342 PRO PRO LYS GLU TRP LYS ALA ARG GLU THR TYR ASP ASN
SEQRES 6 A 342 ILE SER GLU ILE LEU ILE ALA THR PRO LEU GLN GLN VAL
SEQRES 7 A 342 ALA SER GLY ARG ALA GLY VAL PHE THR GLN TYR HIS LYS
SEQRES 8 A 342 LYS LYS LYS ALA MET THR VAL GLY GLU TYR ARG HIS LEU
SEQRES 9 A 342 ALA ASN SER LYS LYS TYR GLN THR PRO PRO HIS GLN ASN
SEQRES 10 A 342 PHE GLU ASP LEU GLU ARG LYS TYR TRP LYS ASN ARG ILE
SEQRES 11 A 342 TYR ASN SER PRO ILE TYR GLY ALA ASP ILE SER GLY SER
SEQRES 12 A 342 LEU PHE ASP GLU ASN THR LYS GLN TRP ASN LEU GLY HIS
SEQRES 13 A 342 LEU GLY THR ILE GLN ASP LEU LEU GLU LYS GLU CYS GLY
SEQRES 14 A 342 VAL VAL ILE GLU GLY VAL ASN THR PRO TYR LEU TYR PHE
SEQRES 15 A 342 GLY MET TRP LYS THR THR PHE ALA TRP HIS THR GLU ASP
SEQRES 16 A 342 MET ASP LEU TYR SER ILE ASN TYR LEU HIS LEU GLY GLU
SEQRES 17 A 342 PRO LYS THR TRP TYR VAL VAL PRO PRO GLU HIS GLY GLN
SEQRES 18 A 342 ARG LEU GLU ARG LEU ALA ARG GLU LEU PHE PRO GLY SER
SEQRES 19 A 342 SER ARG GLY CYS GLY ALA PHE LEU ARG HIS LYS VAL ALA
SEQRES 20 A 342 LEU ILE SER PRO THR VAL LEU LYS GLU ASN GLY ILE PRO
SEQRES 21 A 342 PHE ASN ARG ILE THR GLN GLU ALA GLY GLU PHE MET VAL
SEQRES 22 A 342 THR PHE PRO TYR GLY TYR HIS ALA GLY PHE ASN HIS GLY
SEQRES 23 A 342 PHE ASN CYS ALA GLU ALA ILE ASN PHE ALA THR PRO ARG
SEQRES 24 A 342 TRP ILE ASP TYR GLY LYS MET ALA SER GLN CYS SER CYS
SEQRES 25 A 342 GLY GLU ALA ARG VAL THR PHE SER MET ASP ALA PHE VAL
SEQRES 26 A 342 ARG ILE LEU GLN PRO GLU ARG TYR ASP LEU TRP LYS ARG
SEQRES 27 A 342 GLY GLN ASP ARG
HET ZN A 401 1
HET NI A 402 1
HET NI A 403 1
HET EDO A 404 10
HET EDO A 405 10
HET EDO A 406 10
HET EDO A 407 10
HET EDO A 408 10
HET EDO A 409 10
HET EDO A 410 10
HET SO4 A 411 5
HET SO4 A 412 5
HET BWK A 413 21
HETNAM ZN ZINC ION
HETNAM NI NICKEL (II) ION
HETNAM EDO 1,2-ETHANEDIOL
HETNAM SO4 SULFATE ION
HETNAM BWK [2-(1-METHYL-1,2,3,4-TETRAZOL-4-IUM-5-YL)
HETNAM 2 BWK ETHANOYLAMINO]AZANIUM
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 ZN ZN 2+
FORMUL 3 NI 2(NI 2+)
FORMUL 5 EDO 7(C2 H6 O2)
FORMUL 12 SO4 2(O4 S 2-)
FORMUL 14 BWK C4 H10 N6 O 2+
FORMUL 15 HOH *351(H2 O)
HELIX 1 AA1 ASP A 30 GLN A 41 1 12
HELIX 2 AA2 GLY A 42 ALA A 46 5 5
HELIX 3 AA3 VAL A 98 ASN A 106 1 9
HELIX 4 AA4 ASN A 117 ARG A 129 1 13
HELIX 5 AA5 ILE A 130 ASN A 132 5 3
HELIX 6 AA6 THR A 159 GLY A 169 1 11
HELIX 7 AA7 GLU A 194 LEU A 198 5 5
HELIX 8 AA8 PRO A 216 GLU A 218 5 3
HELIX 9 AA9 HIS A 219 PHE A 231 1 13
HELIX 10 AB1 PHE A 231 CYS A 238 1 8
HELIX 11 AB2 ALA A 240 LYS A 245 5 6
HELIX 12 AB3 SER A 250 ASN A 257 1 8
HELIX 13 AB4 ARG A 299 ALA A 307 1 9
HELIX 14 AB5 THR A 318 GLN A 329 1 12
HELIX 15 AB6 GLN A 329 GLN A 340 1 12
SHEET 1 AA110 MET A 19 PHE A 21 0
SHEET 2 AA110 LEU A 48 ILE A 51 1 O LYS A 50 N PHE A 21
SHEET 3 AA110 PHE A 271 THR A 274 -1 O PHE A 271 N ILE A 51
SHEET 4 AA110 TYR A 199 GLY A 207 -1 N ASN A 202 O MET A 272
SHEET 5 AA110 ASN A 288 PHE A 295 -1 O GLU A 291 N TYR A 203
SHEET 6 AA110 TYR A 179 GLY A 183 -1 N TYR A 181 O ALA A 290
SHEET 7 AA110 ILE A 135 SER A 141 -1 N GLY A 137 O PHE A 182
SHEET 8 AA110 LEU A 75 ARG A 82 -1 N LEU A 75 O TYR A 136
SHEET 9 AA110 VAL A 85 LYS A 92 -1 O LYS A 91 N GLN A 76
SHEET 10 AA110 ALA A 247 ILE A 249 -1 O LEU A 248 N PHE A 86
SHEET 1 AA2 2 LEU A 70 ILE A 71 0
SHEET 2 AA2 2 MET A 96 THR A 97 -1 O MET A 96 N ILE A 71
SHEET 1 AA3 4 THR A 188 HIS A 192 0
SHEET 2 AA3 4 TYR A 279 ASN A 284 -1 O GLY A 282 N PHE A 189
SHEET 3 AA3 4 LYS A 210 VAL A 215 -1 N TYR A 213 O ALA A 281
SHEET 4 AA3 4 ASN A 262 GLN A 266 -1 O ILE A 264 N TRP A 212
LINK NE2 HIS A 156 NI NI A 403 1555 1555 2.18
LINK NE2 HIS A 192 NI NI A 402 1555 1555 2.12
LINK OE2 GLU A 194 NI NI A 402 1555 1555 2.04
LINK SG CYS A 238 ZN ZN A 401 1555 1555 2.30
LINK NE2 HIS A 244 ZN ZN A 401 1555 1555 2.10
LINK NE2 HIS A 280 NI NI A 402 1555 1555 2.11
LINK SG CYS A 310 ZN ZN A 401 1555 1555 2.29
LINK SG CYS A 312 ZN ZN A 401 1555 1555 2.31
LINK NI NI A 402 O BBWK A 413 1555 1555 2.08
LINK NI NI A 402 N4 BBWK A 413 1555 1555 2.63
LINK NI NI A 402 N5 BBWK A 413 1555 1555 1.76
LINK NI NI A 402 O HOH A 569 1555 1555 2.12
LINK NI NI A 403 O HOH A 721 1555 1555 2.33
SITE 1 AC1 4 CYS A 238 HIS A 244 CYS A 310 CYS A 312
SITE 1 AC2 5 HIS A 192 GLU A 194 HIS A 280 BWK A 413
SITE 2 AC2 5 HOH A 569
SITE 1 AC3 2 HIS A 156 HOH A 721
SITE 1 AC4 4 ARG A 123 LYS A 124 LYS A 127 ASN A 128
SITE 1 AC5 8 LYS A 150 GLN A 151 TRP A 152 ASN A 153
SITE 2 AC5 8 HIS A 156 LEU A 157 HOH A 550 HOH A 704
SITE 1 AC6 3 LYS A 255 ARG A 263 HOH A 539
SITE 1 AC7 5 PHE A 118 ARG A 263 ILE A 264 THR A 265
SITE 2 AC7 5 HOH A 542
SITE 1 AC8 7 LYS A 109 GLN A 111 ASN A 132 TRP A 185
SITE 2 AC8 7 LYS A 186 SO4 A 411 HOH A 511
SITE 1 AC9 4 HIS A 103 ASN A 106 HOH A 518 HOH A 624
SITE 1 AD1 8 TYR A 179 TYR A 181 GLU A 194 SER A 200
SITE 2 AD1 8 ALA A 292 ASN A 294 BWK A 413 HOH A 569
SITE 1 AD2 6 PRO A 113 LYS A 124 ASN A 128 TRP A 185
SITE 2 AD2 6 LYS A 186 EDO A 408
SITE 1 AD3 6 ARG A 60 GLU A 61 THR A 62 HOH A 503
SITE 2 AD3 6 HOH A 523 HOH A 851
SITE 1 AD4 13 TYR A 181 HIS A 192 GLU A 194 SER A 200
SITE 2 AD4 13 ASN A 202 LYS A 210 TRP A 212 HIS A 280
SITE 3 AD4 13 ALA A 292 NI A 402 EDO A 410 HOH A 569
SITE 4 AD4 13 HOH A 580
CRYST1 71.464 71.464 151.070 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 0.013993 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013993 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006619 0.00000
(ATOM LINES ARE NOT SHOWN.)
END