PDB Short entry for 4LXL HEADER OXIDOREDUCTASE/PEPTIDE 30-JUL-13 4LXL TITLE CRYSTAL STRUCTURE OF JMJD2B COMPLEXED WITH PYRIDINE-2,4-DICARBOXYLIC TITLE 2 ACID AND H3K9ME3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, UNP RESIDUES 1-348; COMPND 5 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3B, COMPND 6 JUMONJI DOMAIN-CONTAINING PROTEIN 2B; COMPND 7 EC: 1.14.11.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: H3 PEPTIDE; COMPND 11 CHAIN: D; COMPND 12 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: KDM4B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HUMAN; SOURCE 11 ORGANISM_COMMON: HOMO SAPIENS; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS. KEYWDS JMJC DOMAIN, DEMETHYLATION, HISTONE, METHYLATION, NUCLEUS, KEYWDS 2 OXIDOREDUCTASE-PEPTIDE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR W.-C.WANG,C.-H.CHU,C.-C.CHEN REVDAT 2 08-NOV-23 4LXL 1 REMARK SEQADV LINK REVDAT 1 30-JUL-14 4LXL 0 JRNL AUTH W.-C.WANG,C.-H.CHU,C.-C.CHEN JRNL TITL CRYSTAL STRUCTURE OF JMJD2B COMPLEXED WITH JRNL TITL 2 PYRIDINE-2,4-DICARBOXYLIC ACID AND H3K9ME3 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : 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) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 28644 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1529 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) : 1.87 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.92 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2044 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.31 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 114 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2749 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 262 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.52000 REMARK 3 B22 (A**2) : -1.47000 REMARK 3 B33 (A**2) : 0.95000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.144 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.138 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.905 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2839 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3841 ; 1.375 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 335 ; 7.220 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 136 ;37.029 ;23.382 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 478 ;18.352 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;18.093 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 394 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2187 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1346 ; 3.603 ; 3.171 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1679 ; 4.723 ; 5.309 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1493 ; 5.120 ; 3.608 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 USED IF PRESENT IN REMARK 3 THE INPUT U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 4LXL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000081212. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL12B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30173 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.20 REMARK 200 R MERGE FOR SHELL (I) : 0.36800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: 2YBS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG8000, 0.2M MAGNESIUM ACETATE, REMARK 280 0.1M MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 27.18200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.94650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.23750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.94650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.18200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.23750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 1810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 SER A 3 REMARK 465 GLU A 4 REMARK 465 ASP A 5 REMARK 465 HIS A 6 REMARK 465 GLY A 7 REMARK 465 ALA A 8 REMARK 465 ASP A 338 REMARK 465 LEU A 339 REMARK 465 THR A 340 REMARK 465 VAL A 341 REMARK 465 LEU A 342 REMARK 465 ASP A 343 REMARK 465 HIS A 344 REMARK 465 THR A 345 REMARK 465 ARG A 346 REMARK 465 PRO A 347 REMARK 465 THR A 348 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 ALA A 70 62.43 -151.19 REMARK 500 PHE A 128 -96.61 -83.04 REMARK 500 SER A 153 70.77 -156.52 REMARK 500 ARG A 155 68.08 61.68 REMARK 500 LYS A 183 -6.04 82.81 REMARK 500 ALA A 237 44.90 -141.88 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 NI A 402 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 189 NE2 REMARK 620 2 GLU A 191 OE2 98.4 REMARK 620 3 HIS A 277 NE2 86.4 87.7 REMARK 620 4 PD2 A 401 N1 97.9 162.0 100.9 REMARK 620 5 PD2 A 401 O22 82.4 96.8 168.5 77.8 REMARK 620 6 HOH A 752 O 176.5 85.0 93.0 78.8 97.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 235 SG REMARK 620 2 HIS A 241 NE2 110.3 REMARK 620 3 CYS A 307 SG 114.6 111.0 REMARK 620 4 CYS A 309 SG 116.6 92.2 110.0 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 PD2 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 ZN A 403 DBREF 4LXL A 1 348 UNP O94953 KDM4B_HUMAN 1 348 DBREF 4LXL D 7 14 PDB 4LXL 4LXL 7 14 SEQADV 4LXL MET A -19 UNP O94953 EXPRESSION TAG SEQADV 4LXL GLY A -18 UNP O94953 EXPRESSION TAG SEQADV 4LXL SER A -17 UNP O94953 EXPRESSION TAG SEQADV 4LXL SER A -16 UNP O94953 EXPRESSION TAG SEQADV 4LXL HIS A -15 UNP O94953 EXPRESSION TAG SEQADV 4LXL HIS A -14 UNP O94953 EXPRESSION TAG SEQADV 4LXL HIS A -13 UNP O94953 EXPRESSION TAG SEQADV 4LXL HIS A -12 UNP O94953 EXPRESSION TAG SEQADV 4LXL HIS A -11 UNP O94953 EXPRESSION TAG SEQADV 4LXL HIS A -10 UNP O94953 EXPRESSION TAG SEQADV 4LXL SER A -9 UNP O94953 EXPRESSION TAG SEQADV 4LXL SER A -8 UNP O94953 EXPRESSION TAG SEQADV 4LXL GLY A -7 UNP O94953 EXPRESSION TAG SEQADV 4LXL LEU A -6 UNP O94953 EXPRESSION TAG SEQADV 4LXL VAL A -5 UNP O94953 EXPRESSION TAG SEQADV 4LXL PRO A -4 UNP O94953 EXPRESSION TAG SEQADV 4LXL ARG A -3 UNP O94953 EXPRESSION TAG SEQADV 4LXL GLY A -2 UNP O94953 EXPRESSION TAG SEQADV 4LXL SER A -1 UNP O94953 EXPRESSION TAG SEQADV 4LXL HIS A 0 UNP O94953 EXPRESSION TAG SEQRES 1 A 368 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 368 LEU VAL PRO ARG GLY SER HIS MET GLY SER GLU ASP HIS SEQRES 3 A 368 GLY ALA GLN ASN PRO SER CYS LYS ILE MET THR PHE ARG SEQRES 4 A 368 PRO THR MET GLU GLU PHE LYS ASP PHE ASN LYS TYR VAL SEQRES 5 A 368 ALA TYR ILE GLU SER GLN GLY ALA HIS ARG ALA GLY LEU SEQRES 6 A 368 ALA LYS ILE ILE PRO PRO LYS GLU TRP LYS PRO ARG GLN SEQRES 7 A 368 THR TYR ASP ASP ILE ASP ASP VAL VAL ILE PRO ALA PRO SEQRES 8 A 368 ILE GLN GLN VAL VAL THR GLY GLN SER GLY LEU PHE THR SEQRES 9 A 368 GLN TYR ASN ILE GLN LYS LYS ALA MET THR VAL GLY GLU SEQRES 10 A 368 TYR ARG ARG LEU ALA ASN SER GLU LYS TYR CYS THR PRO SEQRES 11 A 368 ARG HIS GLN ASP PHE ASP ASP LEU GLU ARG LYS TYR TRP SEQRES 12 A 368 LYS ASN LEU THR PHE VAL SER PRO ILE TYR GLY ALA ASP SEQRES 13 A 368 ILE SER GLY SER LEU TYR ASP ASP ASP VAL ALA GLN TRP SEQRES 14 A 368 ASN ILE GLY SER LEU ARG THR ILE LEU ASP MET VAL GLU SEQRES 15 A 368 ARG GLU CYS GLY THR ILE ILE GLU GLY VAL ASN THR PRO SEQRES 16 A 368 TYR LEU TYR PHE GLY MET TRP LYS THR THR PHE ALA TRP SEQRES 17 A 368 HIS THR GLU ASP MET ASP LEU TYR SER ILE ASN TYR LEU SEQRES 18 A 368 HIS PHE GLY GLU PRO LYS SER TRP TYR ALA ILE PRO PRO SEQRES 19 A 368 GLU HIS GLY LYS ARG LEU GLU ARG LEU ALA ILE GLY PHE SEQRES 20 A 368 PHE PRO GLY SER SER GLN GLY CYS ASP ALA PHE LEU ARG SEQRES 21 A 368 HIS LYS MET THR LEU ILE SER PRO ILE ILE LEU LYS LYS SEQRES 22 A 368 TYR GLY ILE PRO PHE SER ARG ILE THR GLN GLU ALA GLY SEQRES 23 A 368 GLU PHE MET ILE THR PHE PRO TYR GLY TYR HIS ALA GLY SEQRES 24 A 368 PHE ASN HIS GLY PHE ASN CYS ALA GLU SER THR ASN PHE SEQRES 25 A 368 ALA THR LEU ARG TRP ILE ASP TYR GLY LYS VAL ALA THR SEQRES 26 A 368 GLN CYS THR CYS ARG LYS ASP MET VAL LYS ILE SER MET SEQRES 27 A 368 ASP VAL PHE VAL ARG ILE LEU GLN PRO GLU ARG TYR GLU SEQRES 28 A 368 LEU TRP LYS GLN GLY LYS ASP LEU THR VAL LEU ASP HIS SEQRES 29 A 368 THR ARG PRO THR SEQRES 1 D 8 ALA ARG M3L SER THR GLY GLY LYS MODRES 4LXL M3L D 9 LYS N-TRIMETHYLLYSINE HET M3L D 9 12 HET PD2 A 401 12 HET NI A 402 1 HET ZN A 403 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM PD2 PYRIDINE-2,4-DICARBOXYLIC ACID HETNAM NI NICKEL (II) ION HETNAM ZN ZINC ION FORMUL 2 M3L C9 H21 N2 O2 1+ FORMUL 3 PD2 C7 H5 N O4 FORMUL 4 NI NI 2+ FORMUL 5 ZN ZN 2+ FORMUL 6 HOH *262(H2 O) HELIX 1 1 THR A 21 LYS A 26 1 6 HELIX 2 2 ASP A 27 GLN A 38 1 12 HELIX 3 3 GLY A 39 ALA A 43 5 5 HELIX 4 4 ASP A 62 ASP A 65 5 4 HELIX 5 5 VAL A 95 SER A 104 1 10 HELIX 6 6 ASP A 114 LEU A 126 1 13 HELIX 7 7 THR A 156 LEU A 158 5 3 HELIX 8 8 ASP A 159 GLY A 166 1 8 HELIX 9 9 GLU A 191 LEU A 195 5 5 HELIX 10 10 PRO A 213 GLU A 215 5 3 HELIX 11 11 HIS A 216 PHE A 228 1 13 HELIX 12 12 PHE A 228 CYS A 235 1 8 HELIX 13 13 ALA A 237 LYS A 242 5 6 HELIX 14 14 SER A 247 TYR A 254 1 8 HELIX 15 15 THR A 294 ARG A 296 5 3 HELIX 16 16 TRP A 297 ALA A 304 1 8 HELIX 17 17 MET A 318 GLN A 326 1 9 HELIX 18 18 GLN A 326 GLN A 335 1 10 SHEET 1 A10 THR A 17 PHE A 18 0 SHEET 2 A10 LEU A 45 ILE A 48 1 O LYS A 47 N PHE A 18 SHEET 3 A10 PHE A 268 THR A 271 -1 O ILE A 270 N ALA A 46 SHEET 4 A10 TYR A 196 GLY A 204 -1 N ASN A 199 O MET A 269 SHEET 5 A10 ASN A 285 PHE A 292 -1 O GLU A 288 N TYR A 200 SHEET 6 A10 TYR A 176 GLY A 180 -1 N TYR A 178 O ALA A 287 SHEET 7 A10 ILE A 132 SER A 138 -1 N GLY A 134 O PHE A 179 SHEET 8 A10 ILE A 72 GLN A 79 -1 N ILE A 72 O TYR A 133 SHEET 9 A10 LEU A 82 GLN A 89 -1 O TYR A 86 N VAL A 75 SHEET 10 A10 THR A 244 ILE A 246 -1 O LEU A 245 N PHE A 83 SHEET 1 B 2 VAL A 67 ILE A 68 0 SHEET 2 B 2 MET A 93 THR A 94 -1 O MET A 93 N ILE A 68 SHEET 1 C 4 THR A 185 HIS A 189 0 SHEET 2 C 4 TYR A 276 ASN A 281 -1 O GLY A 279 N PHE A 186 SHEET 3 C 4 LYS A 207 ILE A 212 -1 N TYR A 210 O ALA A 278 SHEET 4 C 4 SER A 259 GLN A 263 -1 O GLN A 263 N LYS A 207 LINK C ARG D 8 N M3L D 9 1555 1555 1.33 LINK C M3L D 9 N SER D 10 1555 1555 1.33 LINK NE2 HIS A 189 NI NI A 402 1555 1555 2.15 LINK OE2 GLU A 191 NI NI A 402 1555 1555 2.08 LINK SG CYS A 235 ZN ZN A 403 1555 1555 2.23 LINK NE2 HIS A 241 ZN ZN A 403 1555 1555 2.15 LINK NE2 HIS A 277 NI NI A 402 1555 1555 2.15 LINK SG CYS A 307 ZN ZN A 403 1555 1555 2.26 LINK SG CYS A 309 ZN ZN A 403 1555 1555 2.40 LINK N1 PD2 A 401 NI NI A 402 1555 1555 2.12 LINK O22 PD2 A 401 NI NI A 402 1555 1555 2.13 LINK NI NI A 402 O HOH A 752 1555 1555 2.18 SITE 1 AC1 16 TYR A 133 TYR A 178 PHE A 186 HIS A 189 SITE 2 AC1 16 GLU A 191 LYS A 207 TRP A 209 LYS A 242 SITE 3 AC1 16 HIS A 277 NI A 402 HOH A 510 HOH A 511 SITE 4 AC1 16 HOH A 514 HOH A 752 M3L D 9 HOH D 101 SITE 1 AC2 5 HIS A 189 GLU A 191 HIS A 277 PD2 A 401 SITE 2 AC2 5 HOH A 752 SITE 1 AC3 4 CYS A 235 HIS A 241 CYS A 307 CYS A 309 CRYST1 54.364 78.475 83.893 90.00 90.00 90.00 P 21 21 21 4 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 0.018395 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012743 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011920 0.00000