HEADER TRANSCRIPTION 30-SEP-21 7VKH TITLE CRYSTAL STRUCTURE OF AF9 YEATS DOMAIN IN COMPLEX WITH HIT 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN AF-9; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ALL1-FUSED GENE FROM CHROMOSOME 9 PROTEIN,MYELOID/LYMPHOID COMPND 5 OR MIXED-LINEAGE LEUKEMIA TRANSLOCATED TO CHROMOSOME 3 PROTEIN,YEATS COMPND 6 DOMAIN-CONTAINING PROTEIN 3; COMPND 7 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: MLLT3, AF9, YEATS3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COMPLEX, INHIBITOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,K.RUAN REVDAT 3 29-NOV-23 7VKH 1 REMARK REVDAT 2 25-OCT-23 7VKH 1 JRNL REVDAT 1 05-OCT-22 7VKH 0 JRNL AUTH Y.LIU,R.JIN,H.LU,K.BIAN,R.WANG,L.WANG,R.GAO,J.ZHANG,J.WU, JRNL AUTH 2 X.YAO,X.LIU,D.LIU,X.WANG,Z.ZHANG,K.RUAN JRNL TITL FRAGMENT-BASED DISCOVERY OF AF9 YEATS DOMAIN INHIBITORS. JRNL REF INT J MOL SCI V. 23 2022 JRNL REFN ESSN 1422-0067 JRNL PMID 35409252 JRNL DOI 10.3390/IJMS23073893 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 13767 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 703 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 31.6500 - 3.8400 0.99 2656 140 0.1821 0.1977 REMARK 3 2 3.8400 - 3.0500 0.98 2631 153 0.2051 0.2467 REMARK 3 3 3.0500 - 2.6600 0.98 2646 137 0.2244 0.2805 REMARK 3 4 2.6600 - 2.4200 0.97 2600 145 0.2399 0.2997 REMARK 3 5 2.4200 - 2.2500 0.94 2531 128 0.2284 0.2888 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.21 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7VKH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1300024841. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-DEC-17 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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9774 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13767 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.38100 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: PHASER REMARK 200 STARTING MODEL: 4TMP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M TRIMETHYLAMINE N-OXIDE REMARK 280 DEHYDRATE, 0.1 M TRIS, 20% W/V PEGMME 2000, PH 8.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 ALA A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 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 VAL A 25 CG1 CG2 REMARK 470 GLU A 40 CG CD OE1 OE2 REMARK 470 LYS A 92 CG CD CE NZ REMARK 470 GLN B 18 CG CD OE1 NE2 REMARK 470 LYS B 21 CG CD CE NZ REMARK 470 LYS B 22 CG CD CE NZ REMARK 470 ARG B 61 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 109 CG CD OE1 OE2 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 92 51.80 -142.94 REMARK 500 GLU B 40 -133.97 52.57 REMARK 500 REMARK 500 REMARK: NULL DBREF 7VKH A 1 138 UNP P42568 AF9_HUMAN 1 138 DBREF 7VKH B 1 138 UNP P42568 AF9_HUMAN 1 138 SEQRES 1 A 138 MET ALA SER SER CYS ALA VAL GLN VAL LYS LEU GLU LEU SEQRES 2 A 138 GLY HIS ARG ALA GLN VAL ARG LYS LYS PRO THR VAL GLU SEQRES 3 A 138 GLY PHE THR HIS ASP TRP MET VAL PHE VAL ARG GLY PRO SEQRES 4 A 138 GLU HIS SER ASN ILE GLN HIS PHE VAL GLU LYS VAL VAL SEQRES 5 A 138 PHE HIS LEU HIS GLU SER PHE PRO ARG PRO LYS ARG VAL SEQRES 6 A 138 CYS LYS ASP PRO PRO TYR LYS VAL GLU GLU SER GLY TYR SEQRES 7 A 138 ALA GLY PHE ILE LEU PRO ILE GLU VAL TYR PHE LYS ASN SEQRES 8 A 138 LYS GLU GLU PRO ARG LYS VAL ARG PHE ASP TYR ASP LEU SEQRES 9 A 138 PHE LEU HIS LEU GLU GLY HIS PRO PRO VAL ASN HIS LEU SEQRES 10 A 138 ARG CYS GLU LYS LEU THR PHE ASN ASN PRO THR GLU ASP SEQRES 11 A 138 PHE ARG ARG LYS LEU LEU LYS ALA SEQRES 1 B 138 MET ALA SER SER CYS ALA VAL GLN VAL LYS LEU GLU LEU SEQRES 2 B 138 GLY HIS ARG ALA GLN VAL ARG LYS LYS PRO THR VAL GLU SEQRES 3 B 138 GLY PHE THR HIS ASP TRP MET VAL PHE VAL ARG GLY PRO SEQRES 4 B 138 GLU HIS SER ASN ILE GLN HIS PHE VAL GLU LYS VAL VAL SEQRES 5 B 138 PHE HIS LEU HIS GLU SER PHE PRO ARG PRO LYS ARG VAL SEQRES 6 B 138 CYS LYS ASP PRO PRO TYR LYS VAL GLU GLU SER GLY TYR SEQRES 7 B 138 ALA GLY PHE ILE LEU PRO ILE GLU VAL TYR PHE LYS ASN SEQRES 8 B 138 LYS GLU GLU PRO ARG LYS VAL ARG PHE ASP TYR ASP LEU SEQRES 9 B 138 PHE LEU HIS LEU GLU GLY HIS PRO PRO VAL ASN HIS LEU SEQRES 10 B 138 ARG CYS GLU LYS LEU THR PHE ASN ASN PRO THR GLU ASP SEQRES 11 B 138 PHE ARG ARG LYS LEU LEU LYS ALA HET 7IY A 201 14 HET GOL A 202 6 HET 7IY B 201 14 HET GOL B 202 6 HET GOL B 203 6 HETNAM 7IY ~{N}-(3-AZANYL-4-CHLORANYL-PHENYL)-2-METHOXY-ETHANAMIDE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 7IY 2(C9 H11 CL N2 O2) FORMUL 4 GOL 3(C3 H8 O3) FORMUL 8 HOH *35(H2 O) HELIX 1 AA1 ASN A 43 HIS A 46 5 4 HELIX 2 AA2 THR A 128 ALA A 138 1 11 HELIX 3 AA3 ASN B 43 HIS B 46 5 4 HELIX 4 AA4 THR B 128 ALA B 138 1 11 SHEET 1 AA1 7 TYR A 71 GLY A 77 0 SHEET 2 AA1 7 HIS A 30 ARG A 37 -1 N TRP A 32 O GLU A 75 SHEET 3 AA1 7 VAL A 7 VAL A 19 -1 N GLU A 12 O ARG A 37 SHEET 4 AA1 7 VAL A 114 PHE A 124 -1 O ARG A 118 N LEU A 13 SHEET 5 AA1 7 ALA B 6 VAL B 19 1 O ALA B 6 N LEU A 117 SHEET 6 AA1 7 HIS B 30 ARG B 37 -1 O ARG B 37 N GLU B 12 SHEET 7 AA1 7 TYR B 71 GLY B 77 -1 O TYR B 71 N VAL B 36 SHEET 1 AA2 6 TYR A 71 GLY A 77 0 SHEET 2 AA2 6 HIS A 30 ARG A 37 -1 N TRP A 32 O GLU A 75 SHEET 3 AA2 6 VAL A 7 VAL A 19 -1 N GLU A 12 O ARG A 37 SHEET 4 AA2 6 VAL A 114 PHE A 124 -1 O ARG A 118 N LEU A 13 SHEET 5 AA2 6 ALA B 6 VAL B 19 1 O ALA B 6 N LEU A 117 SHEET 6 AA2 6 VAL B 114 ASN B 125 -1 O GLU B 120 N LEU B 11 SHEET 1 AA3 4 LYS A 63 CYS A 66 0 SHEET 2 AA3 4 VAL A 48 HIS A 54 -1 N PHE A 53 O ARG A 64 SHEET 3 AA3 4 PHE A 81 PHE A 89 -1 O TYR A 88 N LYS A 50 SHEET 4 AA3 4 LYS A 97 LEU A 104 -1 O TYR A 102 N LEU A 83 SHEET 1 AA4 4 LYS B 63 CYS B 66 0 SHEET 2 AA4 4 VAL B 48 HIS B 54 -1 N PHE B 53 O ARG B 64 SHEET 3 AA4 4 PHE B 81 PHE B 89 -1 O TYR B 88 N LYS B 50 SHEET 4 AA4 4 LYS B 97 LEU B 104 -1 O TYR B 102 N LEU B 83 CISPEP 1 PRO A 69 PRO A 70 0 -3.19 CISPEP 2 GLU A 94 PRO A 95 0 0.14 CISPEP 3 PRO B 69 PRO B 70 0 0.46 CISPEP 4 GLU B 94 PRO B 95 0 0.65 CRYST1 31.652 41.426 59.725 102.00 90.87 90.36 P 1 2 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 0.031594 0.000197 0.000532 0.00000 SCALE2 0.000000 0.024140 0.005132 0.00000 SCALE3 0.000000 0.000000 0.017120 0.00000