HEADER TRANSFERASE 29-JUN-12 2LV9 TITLE SOLUTION NMR STRUCTURE OF THE PHD DOMAIN OF HUMAN MLL5, NORTHEAST TITLE 2 STRUCTURAL GENOMICS CONSORTIUM TARGET HR6512A COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE MLL5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHD-TYPE DOMAIN RESIDUES 109-188; COMPND 5 SYNONYM: LYSINE N-METHYLTRANSFERASE 2E, KMT2E, MYELOID/LYMPHOID OR COMPND 6 MIXED-LINEAGE LEUKEMIA PROTEIN 5; COMPND 7 EC: 2.1.1.43; 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: MLL5, KMT2E; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET28B KEYWDS ZINC FINGER, TRANSCRIPTION, PROTEIN BINDING, NESG, NORTHEAST KEYWDS 2 STRUCTURAL GENOMICS CONSORTIUM, SGC, STRUCTURAL GENOMICS CONSORTIUM, KEYWDS 3 PSI-BIOLOGY, TRANSFERASE, CHAPERONE-ENABLED STUDIES OF EPIGENETIC KEYWDS 4 REGULATION ENZYMES, CEBS EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.LEMAK,A.YEE,S.HOULISTON,M.GARCIA,H.WU,J.MIN,G.T.MONTELIONE, AUTHOR 2 C.ARROWSMITH,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (SGC),CHAPERONE-ENABLED STUDIES OF AUTHOR 4 EPIGENETIC REGULATION ENZYMES (CEBS) REVDAT 3 01-MAY-24 2LV9 1 REMARK SEQADV LINK REVDAT 2 28-NOV-12 2LV9 1 AUTHOR REVDAT 1 05-SEP-12 2LV9 0 JRNL AUTH A.LEMAK,A.YEE,S.HOULISTON,M.GARCIA,H.WU,J.MIN, JRNL AUTH 2 G.T.MONTELIONE,C.ARROWSMITH JRNL TITL NMR SOLUTION STRUCTURE OF THE HUMAN MLL5 PHD DOMAIN (CASP JRNL TITL 2 TARGET) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, CNS REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LV9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000102876. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 300 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-13C; U-15N] PROTEIN, REMARK 210 10 MM TRIS, 300 MM SODIUM REMARK 210 CHLORIDE, 10 UM ZNSO4, 1 MM DTT, REMARK 210 0.01 % NAN3, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCO; 3D HNCA; 3D CBCA(CO)NH; REMARK 210 3D HBHA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, FMC, TALOS, PSVS, CYANA REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 91 REMARK 465 HIS A 92 REMARK 465 HIS A 93 REMARK 465 HIS A 94 REMARK 465 HIS A 95 REMARK 465 HIS A 96 REMARK 465 HIS A 97 REMARK 465 SER A 98 REMARK 465 SER A 99 REMARK 465 GLY A 100 REMARK 465 ARG A 101 REMARK 465 GLU A 102 REMARK 465 ASN A 103 REMARK 465 LEU A 104 REMARK 465 TYR A 105 REMARK 465 PHE A 106 REMARK 465 GLN A 107 REMARK 465 GLY A 108 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 1 ASP A 111 -49.68 -154.11 REMARK 500 1 ARG A 120 79.78 -113.75 REMARK 500 1 LYS A 137 -70.84 -74.65 REMARK 500 1 ASP A 169 84.05 -67.01 REMARK 500 2 ASP A 169 100.67 -56.10 REMARK 500 3 ARG A 120 77.73 -118.89 REMARK 500 4 ASP A 128 -21.30 -144.11 REMARK 500 5 ARG A 120 74.14 -117.73 REMARK 500 6 ARG A 120 74.67 -109.27 REMARK 500 7 ASP A 111 47.13 -92.75 REMARK 500 7 ASP A 129 -60.73 -102.26 REMARK 500 7 SER A 139 -12.41 69.78 REMARK 500 8 ARG A 120 77.64 -109.96 REMARK 500 8 ASP A 128 -37.47 -143.25 REMARK 500 8 SER A 139 17.96 58.66 REMARK 500 8 SER A 185 76.92 -108.82 REMARK 500 9 ARG A 120 77.27 -114.19 REMARK 500 9 HIS A 127 114.19 -39.96 REMARK 500 9 SER A 185 46.89 -90.14 REMARK 500 10 GLU A 110 26.01 -77.73 REMARK 500 10 ARG A 120 72.48 -102.04 REMARK 500 10 ASP A 169 95.19 -65.54 REMARK 500 11 ARG A 120 73.97 -110.54 REMARK 500 11 THR A 157 73.15 -102.90 REMARK 500 13 ARG A 120 77.02 -114.37 REMARK 500 13 SER A 139 17.93 55.33 REMARK 500 14 SER A 113 89.45 -152.70 REMARK 500 14 ARG A 120 73.70 -109.47 REMARK 500 14 ASP A 186 89.36 -66.32 REMARK 500 15 ASP A 111 55.96 -116.53 REMARK 500 15 ASP A 129 -65.96 -121.94 REMARK 500 16 ARG A 120 74.90 -112.12 REMARK 500 16 THR A 157 75.14 -100.38 REMARK 500 17 ARG A 120 74.37 -115.71 REMARK 500 17 ASP A 129 -66.21 -103.20 REMARK 500 17 ASP A 169 88.37 -68.55 REMARK 500 18 ARG A 120 78.51 -119.25 REMARK 500 19 ARG A 120 74.80 -100.04 REMARK 500 20 GLU A 110 96.21 -165.74 REMARK 500 20 ARG A 120 75.54 -113.14 REMARK 500 20 HIS A 127 93.08 -63.44 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 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 121 SG REMARK 620 2 CYS A 123 SG 107.7 REMARK 620 3 HIS A 143 ND1 106.9 112.2 REMARK 620 4 CYS A 146 SG 112.1 111.1 106.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 135 SG REMARK 620 2 CYS A 138 SG 108.2 REMARK 620 3 CYS A 160 SG 110.0 109.9 REMARK 620 4 CYS A 163 SG 108.3 110.5 109.9 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18559 RELATED DB: BMRB REMARK 900 RELATED ID: NESG-HR6512A RELATED DB: TARGETTRACK DBREF 2LV9 A 109 188 UNP Q8IZD2 MLL5_HUMAN 109 188 SEQADV 2LV9 MET A 91 UNP Q8IZD2 EXPRESSION TAG SEQADV 2LV9 HIS A 92 UNP Q8IZD2 EXPRESSION TAG SEQADV 2LV9 HIS A 93 UNP Q8IZD2 EXPRESSION TAG SEQADV 2LV9 HIS A 94 UNP Q8IZD2 EXPRESSION TAG SEQADV 2LV9 HIS A 95 UNP Q8IZD2 EXPRESSION TAG SEQADV 2LV9 HIS A 96 UNP Q8IZD2 EXPRESSION TAG SEQADV 2LV9 HIS A 97 UNP Q8IZD2 EXPRESSION TAG SEQADV 2LV9 SER A 98 UNP Q8IZD2 EXPRESSION TAG SEQADV 2LV9 SER A 99 UNP Q8IZD2 EXPRESSION TAG SEQADV 2LV9 GLY A 100 UNP Q8IZD2 EXPRESSION TAG SEQADV 2LV9 ARG A 101 UNP Q8IZD2 EXPRESSION TAG SEQADV 2LV9 GLU A 102 UNP Q8IZD2 EXPRESSION TAG SEQADV 2LV9 ASN A 103 UNP Q8IZD2 EXPRESSION TAG SEQADV 2LV9 LEU A 104 UNP Q8IZD2 EXPRESSION TAG SEQADV 2LV9 TYR A 105 UNP Q8IZD2 EXPRESSION TAG SEQADV 2LV9 PHE A 106 UNP Q8IZD2 EXPRESSION TAG SEQADV 2LV9 GLN A 107 UNP Q8IZD2 EXPRESSION TAG SEQADV 2LV9 GLY A 108 UNP Q8IZD2 EXPRESSION TAG SEQRES 1 A 98 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 A 98 LEU TYR PHE GLN GLY SER GLU ASP GLY SER TYR GLY THR SEQRES 3 A 98 ASP VAL THR ARG CYS ILE CYS GLY PHE THR HIS ASP ASP SEQRES 4 A 98 GLY TYR MET ILE CYS CYS ASP LYS CYS SER VAL TRP GLN SEQRES 5 A 98 HIS ILE ASP CYS MET GLY ILE ASP ARG GLN HIS ILE PRO SEQRES 6 A 98 ASP THR TYR LEU CYS GLU ARG CYS GLN PRO ARG ASN LEU SEQRES 7 A 98 ASP LYS GLU ARG ALA VAL LEU LEU GLN ARG ARG LYS ARG SEQRES 8 A 98 GLU ASN MET SER ASP GLY ASP HET ZN A 201 1 HET ZN A 202 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 ASP A 169 MET A 184 1 16 SHEET 1 A 2 MET A 132 CYS A 134 0 SHEET 2 A 2 TRP A 141 HIS A 143 -1 O GLN A 142 N ILE A 133 LINK SG CYS A 121 ZN ZN A 201 1555 1555 2.31 LINK SG CYS A 123 ZN ZN A 201 1555 1555 2.35 LINK SG CYS A 135 ZN ZN A 202 1555 1555 2.34 LINK SG CYS A 138 ZN ZN A 202 1555 1555 2.35 LINK ND1 HIS A 143 ZN ZN A 201 1555 1555 2.09 LINK SG CYS A 146 ZN ZN A 201 1555 1555 2.35 LINK SG CYS A 160 ZN ZN A 202 1555 1555 2.36 LINK SG CYS A 163 ZN ZN A 202 1555 1555 2.35 SITE 1 AC1 5 CYS A 121 CYS A 123 HIS A 143 CYS A 146 SITE 2 AC1 5 GLN A 177 SITE 1 AC2 4 CYS A 135 CYS A 138 CYS A 160 CYS A 163 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1