HEADER OXIDOREDUCTASE 22-JAN-21 7DYQ TITLE CRYSTAL STRUCTURE OF HISTONE LYSINE DEMETHYLASE 4D (KDM4D) IN COMPLEX TITLE 2 WITH THE INHIBITOR 5-HYDROXY-2-METHYLPYRAZOLO[1,5-A]PYRIDO[3,2- TITLE 3 E]PYRIMIDINE-3-CARBONITRILE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4D; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D, COMPND 5 JUMONJI DOMAIN-CONTAINING PROTEIN 2D,[HISTONE H3]-TRIMETHYL-L- COMPND 6 LYSINE(9) DEMETHYLASE 4D,HISTONE LYSINE DEMETHYLASE 4D; COMPND 7 EC: 1.14.11.66; 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KDM4D, INHIBITOR, COMPLEX, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.WANG,L.YANG REVDAT 3 09-OCT-24 7DYQ 1 REMARK REVDAT 2 29-NOV-23 7DYQ 1 REMARK REVDAT 1 26-JAN-22 7DYQ 0 JRNL AUTH T.WANG,L.YANG JRNL TITL CRYSTAL STRUCTURE OF HISTONE LYSINE DEMETHYLASE 4D (KDM4D) JRNL TITL 2 IN COMPLEX WITH THE INHIBITOR JRNL TITL 3 5-HYDROXY-2-METHYLPYRAZOLO[1,5-A]PYRIDO[3, JRNL TITL 4 2-E]PYRIMIDINE-3-CARBONITRILE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.02 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 26813 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1343 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 26.0230 - 4.2991 0.94 2664 145 0.1777 0.1839 REMARK 3 2 4.2991 - 3.4147 0.99 2598 159 0.1484 0.1636 REMARK 3 3 3.4147 - 2.9838 0.99 2592 140 0.1594 0.1903 REMARK 3 4 2.9838 - 2.7113 0.98 2581 111 0.1611 0.1942 REMARK 3 5 2.7113 - 2.5171 0.98 2544 131 0.1603 0.1778 REMARK 3 6 2.5171 - 2.3688 0.97 2499 132 0.1594 0.1891 REMARK 3 7 2.3688 - 2.2503 0.98 2501 136 0.1609 0.2067 REMARK 3 8 2.2503 - 2.1524 0.98 2526 119 0.1604 0.2029 REMARK 3 9 2.1524 - 2.0695 0.97 2490 129 0.1566 0.2030 REMARK 3 10 2.0695 - 1.9982 0.97 2475 141 0.1509 0.1901 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) : 16.690 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.85 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 : 0.014 2767 REMARK 3 ANGLE : 1.376 3751 REMARK 3 CHIRALITY : 0.066 378 REMARK 3 PLANARITY : 0.008 484 REMARK 3 DIHEDRAL : 12.275 1612 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 7DYQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1300020463. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JAN-20 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 : NFPSS REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97930 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 X CDTE 1M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27628 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.998 REMARK 200 RESOLUTION RANGE LOW (A) : 26.023 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 25.60 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 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 (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.30500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 4D6Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M POTASSIUM CITRATE TRIBASIC REMARK 280 MONOHYDRATE PH 8.3, 20% W/V PEG 3350, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291.15K 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 75.74300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.81750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.81750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 113.61450 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.81750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.81750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.87150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.81750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.81750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 113.61450 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.81750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.81750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.87150 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 75.74300 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 TOTAL BURIED SURFACE AREA: 140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 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 A 528 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 58 CD CE NZ REMARK 470 GLU A 61 CD OE1 OE2 REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 GLU A 119 CD OE1 OE2 REMARK 470 ARG A 225 NE CZ NH1 NH2 REMARK 470 ARG A 316 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 340 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HG1 THR A 211 HE2 HIS A 285 1.14 REMARK 500 HG CYS A 238 HG CYS A 310 1.20 REMARK 500 SG CYS A 238 HG CYS A 310 1.22 REMARK 500 SG CYS A 310 HG CYS A 312 1.35 REMARK 500 HE2 HIS A 244 SG CYS A 312 1.36 REMARK 500 HD21 ASN A 128 O HOH A 501 1.59 REMARK 500 HH12 ARG A 82 O HOH A 506 1.59 REMARK 500 O HOH A 734 O HOH A 760 1.82 REMARK 500 O HOH A 556 O HOH A 762 1.89 REMARK 500 O HOH A 541 O HOH A 731 1.92 REMARK 500 O HOH A 653 O HOH A 789 1.92 REMARK 500 O HOH A 506 O HOH A 621 1.93 REMARK 500 NE2 GLN A 77 OH TYR A 136 1.99 REMARK 500 O HOH A 701 O HOH A 739 2.03 REMARK 500 O HOH A 658 O HOH A 705 2.07 REMARK 500 ND2 ASN A 128 O HOH A 501 2.11 REMARK 500 O HOH A 794 O HOH A 797 2.15 REMARK 500 OE1 GLU A 167 O HOH A 502 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 732 O HOH A 746 8555 1.82 REMARK 500 O HOH A 611 O HOH A 761 6445 1.93 REMARK 500 N ASN A 132 OE2 GLU A 331 6545 2.08 REMARK 500 O HOH A 654 O HOH A 781 7555 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 TYR A 136 CG TYR A 136 CD2 -0.100 REMARK 500 TYR A 136 CE1 TYR A 136 CZ -0.091 REMARK 500 TYR A 136 CE2 TYR A 136 CD2 -0.176 REMARK 500 CYS A 312 CB CYS A 312 SG 0.257 REMARK 500 GLU A 331 CG GLU A 331 CD -0.093 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 TYR A 136 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 TYR A 136 CB - CG - CD1 ANGL. DEV. = 3.9 DEGREES REMARK 500 LEU A 248 CA - CB - CG ANGL. DEV. = -17.0 DEGREES REMARK 500 CYS A 310 CA - CB - SG ANGL. DEV. = -18.5 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 ASN A 117 -177.14 -170.83 REMARK 500 LYS A 186 -4.35 77.93 REMARK 500 ALA A 240 53.04 -144.43 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 FE A 402 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 192 NE2 REMARK 620 2 GLU A 194 OE2 104.7 REMARK 620 3 HIS A 280 NE2 88.9 100.7 REMARK 620 4 HR0 A 401 N6 106.2 123.4 125.8 REMARK 620 N 1 2 3 DBREF 7DYQ A 11 340 UNP Q6B0I6 KDM4D_HUMAN 11 340 SEQRES 1 A 330 ALA GLN ASN PRO ASN CYS ASN ILE MET ILE PHE HIS PRO SEQRES 2 A 330 THR LYS GLU GLU PHE ASN ASP PHE ASP LYS TYR ILE ALA SEQRES 3 A 330 TYR MET GLU SER GLN GLY ALA HIS ARG ALA GLY LEU ALA SEQRES 4 A 330 LYS ILE ILE PRO PRO LYS GLU TRP LYS ALA ARG GLU THR SEQRES 5 A 330 TYR ASP ASN ILE SER GLU ILE LEU ILE ALA THR PRO LEU SEQRES 6 A 330 GLN GLN VAL ALA SER GLY ARG ALA GLY VAL PHE THR GLN SEQRES 7 A 330 TYR HIS LYS LYS LYS LYS ALA MET THR VAL GLY GLU TYR SEQRES 8 A 330 ARG HIS LEU ALA ASN SER LYS LYS TYR GLN THR PRO PRO SEQRES 9 A 330 HIS GLN ASN PHE GLU ASP LEU GLU ARG LYS TYR TRP LYS SEQRES 10 A 330 ASN ARG ILE TYR ASN SER PRO ILE TYR GLY ALA ASP ILE SEQRES 11 A 330 SER GLY SER LEU PHE ASP GLU ASN THR LYS GLN TRP ASN SEQRES 12 A 330 LEU GLY HIS LEU GLY THR ILE GLN ASP LEU LEU GLU LYS SEQRES 13 A 330 GLU CYS GLY VAL VAL ILE GLU GLY VAL ASN THR PRO TYR SEQRES 14 A 330 LEU TYR PHE GLY MET TRP LYS THR THR PHE ALA TRP HIS SEQRES 15 A 330 THR GLU ASP MET ASP LEU TYR SER ILE ASN TYR LEU HIS SEQRES 16 A 330 LEU GLY GLU PRO LYS THR TRP TYR VAL VAL PRO PRO GLU SEQRES 17 A 330 HIS GLY GLN ARG LEU GLU ARG LEU ALA ARG GLU LEU PHE SEQRES 18 A 330 PRO GLY SER SER ARG GLY CYS GLY ALA PHE LEU ARG HIS SEQRES 19 A 330 LYS VAL ALA LEU ILE SER PRO THR VAL LEU LYS GLU ASN SEQRES 20 A 330 GLY ILE PRO PHE ASN ARG ILE THR GLN GLU ALA GLY GLU SEQRES 21 A 330 PHE MET VAL THR PHE PRO TYR GLY TYR HIS ALA GLY PHE SEQRES 22 A 330 ASN HIS GLY PHE ASN CYS ALA GLU ALA ILE ASN PHE ALA SEQRES 23 A 330 THR PRO ARG TRP ILE ASP TYR GLY LYS MET ALA SER GLN SEQRES 24 A 330 CYS SER CYS GLY GLU ALA ARG VAL THR PHE SER MET ASP SEQRES 25 A 330 ALA PHE VAL ARG ILE LEU GLN PRO GLU ARG TYR ASP LEU SEQRES 26 A 330 TRP LYS ARG GLY GLN HET HR0 A 401 24 HET FE A 402 1 HETNAM HR0 5-HYDROXY-2-METHYLPYRAZOLO[1,5-A]PYRIDO[3,2- HETNAM 2 HR0 E]PYRIMIDINE-3-CARBONITRILE HETNAM FE FE (III) ION FORMUL 2 HR0 C11 H7 N5 O FORMUL 3 FE FE 3+ FORMUL 4 HOH *302(H2 O) HELIX 1 AA1 GLU A 26 ASN A 29 5 4 HELIX 2 AA2 ASP A 30 GLN A 41 1 12 HELIX 3 AA3 GLY A 42 ALA A 46 5 5 HELIX 4 AA4 VAL A 98 ASN A 106 1 9 HELIX 5 AA5 ASN A 117 ARG A 129 1 13 HELIX 6 AA6 ILE A 130 ASN A 132 5 3 HELIX 7 AA7 THR A 159 GLY A 169 1 11 HELIX 8 AA8 GLU A 194 LEU A 198 5 5 HELIX 9 AA9 PRO A 216 GLU A 218 5 3 HELIX 10 AB1 HIS A 219 PHE A 231 1 13 HELIX 11 AB2 PHE A 231 CYS A 238 1 8 HELIX 12 AB3 ALA A 240 LYS A 245 5 6 HELIX 13 AB4 SER A 250 ASN A 257 1 8 HELIX 14 AB5 ARG A 299 ALA A 307 1 9 HELIX 15 AB6 PHE A 319 GLN A 329 1 11 HELIX 16 AB7 GLN A 329 GLY A 339 1 11 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 ILE A 140 O LEU A 180 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 GLN A 266 N LYS A 210 SSBOND 1 CYS A 238 CYS A 310 1555 1555 2.19 SSBOND 2 CYS A 238 CYS A 312 1555 1555 2.04 SSBOND 3 CYS A 310 CYS A 312 1555 1555 1.89 LINK NE2 HIS A 192 FE FE A 402 1555 1555 2.31 LINK OE2 GLU A 194 FE FE A 402 1555 1555 2.16 LINK NE2 HIS A 280 FE FE A 402 1555 1555 1.99 LINK N6 HR0 A 401 FE FE A 402 1555 1555 2.20 CRYST1 71.635 71.635 151.486 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 0.013960 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013960 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006601 0.00000