HEADER RNA BINDING PROTEIN 13-APR-20 6YNI TITLE CRYSTAL STRUCTURE OF YTHDC1 WITH COMPOUND DHU_DC1_036 CAVEAT 6YNI P0Q B 608 HAS WRONG CHIRALITY AT ATOM CAN P0Q B 608 HAS CAVEAT 2 6YNI WRONG CHIRALITY AT ATOM CAO COMPND MOL_ID: 1; COMPND 2 MOLECULE: YTHDC1; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS YTHDC1, M6A, COMPLEX, INHIBITOR, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.K.BEDI,D.HUANG,L.WIEDMER,A.CAFLISCH REVDAT 3 24-JAN-24 6YNI 1 REMARK REVDAT 2 15-JUN-22 6YNI 1 JRNL REVDAT 1 15-JUL-20 6YNI 0 JRNL AUTH Y.LI,R.K.BEDI,F.NAI,V.VON ROTEN,A.DOLBOIS,F.ZALESAK, JRNL AUTH 2 R.NACHAWATI,D.HUANG,A.CAFLISCH JRNL TITL STRUCTURE-BASED DESIGN OF LIGANDS OF THE M6A-RNA READER JRNL TITL 2 YTHDC1 JRNL REF EUR J MED CHEM REP V. 5 00057 2022 JRNL REFN ESSN 2772-4174 JRNL DOI 10.1016/J.EJMCR.2022.100057 REMARK 2 REMARK 2 RESOLUTION. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 67737 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3387 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 40.3000 - 3.9300 1.00 2733 143 0.1599 0.1899 REMARK 3 2 3.9300 - 3.1200 0.99 2718 143 0.1553 0.1768 REMARK 3 3 3.1200 - 2.7200 1.00 2698 142 0.1845 0.2327 REMARK 3 4 2.7200 - 2.4800 0.99 2658 140 0.1988 0.2440 REMARK 3 5 2.4800 - 2.3000 0.99 2705 143 0.1838 0.1960 REMARK 3 6 2.3000 - 2.1600 0.99 2682 140 0.1798 0.2101 REMARK 3 7 2.1600 - 2.0500 1.00 2681 141 0.1766 0.1913 REMARK 3 8 2.0500 - 1.9600 1.00 2679 141 0.1787 0.2196 REMARK 3 9 1.9600 - 1.8900 1.00 2710 143 0.1870 0.2251 REMARK 3 10 1.8900 - 1.8200 1.00 2686 141 0.1978 0.2514 REMARK 3 11 1.8200 - 1.7700 1.00 2695 142 0.1978 0.2110 REMARK 3 12 1.7700 - 1.7200 0.99 2678 141 0.1984 0.2344 REMARK 3 13 1.7200 - 1.6700 1.00 2676 141 0.2015 0.2247 REMARK 3 14 1.6700 - 1.6300 1.00 2668 141 0.2084 0.2278 REMARK 3 15 1.6300 - 1.5900 1.00 2725 143 0.2137 0.2274 REMARK 3 16 1.5900 - 1.5600 0.99 2665 141 0.2374 0.2810 REMARK 3 17 1.5600 - 1.5300 0.99 2675 141 0.2469 0.2579 REMARK 3 18 1.5300 - 1.5000 1.00 2678 141 0.2679 0.2767 REMARK 3 19 1.5000 - 1.4700 0.99 2672 140 0.2843 0.3324 REMARK 3 20 1.4700 - 1.4500 0.99 2655 140 0.3112 0.3806 REMARK 3 21 1.4500 - 1.4200 0.99 2698 142 0.3155 0.3300 REMARK 3 22 1.4200 - 1.4000 0.99 2652 140 0.3327 0.3756 REMARK 3 23 1.4000 - 1.3800 0.99 2717 143 0.3504 0.3629 REMARK 3 24 1.3800 - 1.3600 0.96 2546 134 0.3580 0.4111 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) : 0.161 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.946 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.61 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.13 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 : 0.005 2737 REMARK 3 ANGLE : 0.798 3726 REMARK 3 CHIRALITY : 0.074 401 REMARK 3 PLANARITY : 0.005 461 REMARK 3 DIHEDRAL : 25.756 363 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 6YNI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292107959. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-18 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 : SLS REMARK 200 BEAMLINE : X06DA 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67741 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 40.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 2.970 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 4R3H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.2M AMMONIUM SULPHATE, REMARK 280 0.1M BIS-TRIS, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 51.52000 REMARK 290 SMTRY3 2 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 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 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 327 REMARK 465 HIS A 328 REMARK 465 HIS A 329 REMARK 465 HIS A 330 REMARK 465 HIS A 331 REMARK 465 HIS A 332 REMARK 465 HIS A 333 REMARK 465 SER A 334 REMARK 465 SER A 335 REMARK 465 GLY A 336 REMARK 465 ARG A 337 REMARK 465 GLU A 338 REMARK 465 ASN A 339 REMARK 465 LEU A 340 REMARK 465 TYR A 341 REMARK 465 PHE A 342 REMARK 465 GLN A 343 REMARK 465 ARG A 508 REMARK 465 HIS A 509 REMARK 465 MET B 327 REMARK 465 HIS B 328 REMARK 465 HIS B 329 REMARK 465 HIS B 330 REMARK 465 HIS B 331 REMARK 465 HIS B 332 REMARK 465 HIS B 333 REMARK 465 SER B 334 REMARK 465 SER B 335 REMARK 465 GLY B 336 REMARK 465 ARG B 337 REMARK 465 GLU B 338 REMARK 465 ASN B 339 REMARK 465 LEU B 340 REMARK 465 TYR B 341 REMARK 465 PHE B 342 REMARK 465 GLN B 343 REMARK 465 ARG B 508 REMARK 465 HIS B 509 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 GLY A 344 N REMARK 470 LYS A 374 CE NZ REMARK 470 LYS A 385 CE NZ REMARK 470 LYS A 386 NZ REMARK 470 ARG A 395 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 404 CD NE CZ NH1 NH2 REMARK 470 GLU A 405 CG CD OE1 OE2 REMARK 470 SER A 424 OG REMARK 470 LEU A 430 CD1 CD2 REMARK 470 LYS A 437 CG CD CE NZ REMARK 470 LYS A 444 CD CE NZ REMARK 470 LYS A 457 CD CE NZ REMARK 470 GLN A 487 OE1 NE2 REMARK 470 LYS B 374 CE NZ REMARK 470 LYS B 385 CG CD CE NZ REMARK 470 SER B 424 OG REMARK 470 LYS B 437 CG CD CE NZ REMARK 470 GLN B 502 CG CD OE1 NE2 REMARK 470 HIS B 505 CG ND1 CD2 CE1 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 OE1 GLU A 452 O HOH A 701 1.91 REMARK 500 O HOH B 745 O HOH B 802 1.97 REMARK 500 O HOH B 735 O HOH B 848 1.98 REMARK 500 O HOH A 747 O HOH A 837 1.99 REMARK 500 O HOH B 766 O HOH B 836 2.03 REMARK 500 O1 SO4 A 602 O HOH A 702 2.03 REMARK 500 O HOH B 750 O HOH B 897 2.04 REMARK 500 O HOH A 821 O HOH A 843 2.06 REMARK 500 O HOH A 701 O HOH A 848 2.07 REMARK 500 O HOH B 745 O HOH B 894 2.09 REMARK 500 O HOH A 754 O HOH A 790 2.10 REMARK 500 O HOH B 721 O HOH B 755 2.12 REMARK 500 O HOH A 865 O HOH A 877 2.12 REMARK 500 O HOH A 810 O HOH A 826 2.12 REMARK 500 O HOH A 747 O HOH A 834 2.15 REMARK 500 O HOH A 895 O HOH A 908 2.15 REMARK 500 O HOH A 706 O HOH A 869 2.15 REMARK 500 O HOH A 714 O HOH A 777 2.16 REMARK 500 O HOH A 836 O HOH A 895 2.16 REMARK 500 O HOH B 721 O HOH B 856 2.16 REMARK 500 O3 SO4 A 602 O HOH A 703 2.16 REMARK 500 O HOH B 859 O HOH B 937 2.16 REMARK 500 O HOH A 839 O HOH A 886 2.18 REMARK 500 O HOH A 858 O HOH A 877 2.18 REMARK 500 O HOH B 766 O HOH B 899 2.18 REMARK 500 O HOH A 703 O HOH A 798 2.19 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 B 806 O HOH B 897 1455 2.00 REMARK 500 O HOH B 820 O HOH B 897 1455 2.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue P0Q B 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue P0Q B 608 DBREF 6YNI A 345 509 UNP Q96MU7 YTDC1_HUMAN 345 509 DBREF 6YNI B 345 509 UNP Q96MU7 YTDC1_HUMAN 345 509 SEQADV 6YNI MET A 327 UNP Q96MU7 INITIATING METHIONINE SEQADV 6YNI HIS A 328 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI HIS A 329 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI HIS A 330 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI HIS A 331 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI HIS A 332 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI HIS A 333 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI SER A 334 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI SER A 335 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI GLY A 336 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI ARG A 337 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI GLU A 338 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI ASN A 339 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI LEU A 340 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI TYR A 341 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI PHE A 342 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI GLN A 343 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI GLY A 344 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI MET B 327 UNP Q96MU7 INITIATING METHIONINE SEQADV 6YNI HIS B 328 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI HIS B 329 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI HIS B 330 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI HIS B 331 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI HIS B 332 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI HIS B 333 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI SER B 334 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI SER B 335 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI GLY B 336 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI ARG B 337 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI GLU B 338 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI ASN B 339 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI LEU B 340 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI TYR B 341 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI PHE B 342 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI GLN B 343 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNI GLY B 344 UNP Q96MU7 EXPRESSION TAG SEQRES 1 A 183 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 A 183 LEU TYR PHE GLN GLY THR SER LYS LEU LYS TYR VAL LEU SEQRES 3 A 183 GLN ASP ALA ARG PHE PHE LEU ILE LYS SER ASN ASN HIS SEQRES 4 A 183 GLU ASN VAL SER LEU ALA LYS ALA LYS GLY VAL TRP SER SEQRES 5 A 183 THR LEU PRO VAL ASN GLU LYS LYS LEU ASN LEU ALA PHE SEQRES 6 A 183 ARG SER ALA ARG SER VAL ILE LEU ILE PHE SER VAL ARG SEQRES 7 A 183 GLU SER GLY LYS PHE GLN GLY PHE ALA ARG LEU SER SER SEQRES 8 A 183 GLU SER HIS HIS GLY GLY SER PRO ILE HIS TRP VAL LEU SEQRES 9 A 183 PRO ALA GLY MET SER ALA LYS MET LEU GLY GLY VAL PHE SEQRES 10 A 183 LYS ILE ASP TRP ILE CYS ARG ARG GLU LEU PRO PHE THR SEQRES 11 A 183 LYS SER ALA HIS LEU THR ASN PRO TRP ASN GLU HIS LYS SEQRES 12 A 183 PRO VAL LYS ILE GLY ARG ASP GLY GLN GLU ILE GLU LEU SEQRES 13 A 183 GLU CYS GLY THR GLN LEU CYS LEU LEU PHE PRO PRO ASP SEQRES 14 A 183 GLU SER ILE ASP LEU TYR GLN VAL ILE HIS LYS MET ARG SEQRES 15 A 183 HIS SEQRES 1 B 183 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 B 183 LEU TYR PHE GLN GLY THR SER LYS LEU LYS TYR VAL LEU SEQRES 3 B 183 GLN ASP ALA ARG PHE PHE LEU ILE LYS SER ASN ASN HIS SEQRES 4 B 183 GLU ASN VAL SER LEU ALA LYS ALA LYS GLY VAL TRP SER SEQRES 5 B 183 THR LEU PRO VAL ASN GLU LYS LYS LEU ASN LEU ALA PHE SEQRES 6 B 183 ARG SER ALA ARG SER VAL ILE LEU ILE PHE SER VAL ARG SEQRES 7 B 183 GLU SER GLY LYS PHE GLN GLY PHE ALA ARG LEU SER SER SEQRES 8 B 183 GLU SER HIS HIS GLY GLY SER PRO ILE HIS TRP VAL LEU SEQRES 9 B 183 PRO ALA GLY MET SER ALA LYS MET LEU GLY GLY VAL PHE SEQRES 10 B 183 LYS ILE ASP TRP ILE CYS ARG ARG GLU LEU PRO PHE THR SEQRES 11 B 183 LYS SER ALA HIS LEU THR ASN PRO TRP ASN GLU HIS LYS SEQRES 12 B 183 PRO VAL LYS ILE GLY ARG ASP GLY GLN GLU ILE GLU LEU SEQRES 13 B 183 GLU CYS GLY THR GLN LEU CYS LEU LEU PHE PRO PRO ASP SEQRES 14 B 183 GLU SER ILE ASP LEU TYR GLN VAL ILE HIS LYS MET ARG SEQRES 15 B 183 HIS HET SO4 A 601 5 HET SO4 A 602 5 HET SO4 A 603 5 HET SO4 A 604 5 HET SO4 B 601 5 HET SO4 B 602 5 HET SO4 B 603 5 HET SO4 B 604 5 HET SO4 B 605 5 HET SO4 B 606 5 HET P0Q B 607 32 HET P0Q B 608 16 HETNAM SO4 SULFATE ION HETNAM P0Q (2~{R},3~{R})-2-(3-CHLOROPHENYL)-3,5,5-TRIMETHYL- HETNAM 2 P0Q MORPHOLINE FORMUL 3 SO4 10(O4 S 2-) FORMUL 13 P0Q 2(C13 H18 CL N O) FORMUL 15 HOH *448(H2 O) HELIX 1 AA1 THR A 345 GLN A 353 1 9 HELIX 2 AA2 ASN A 364 GLY A 375 1 12 HELIX 3 AA3 LEU A 380 ALA A 394 1 15 HELIX 4 AA4 SER A 435 LEU A 439 5 5 HELIX 5 AA5 THR A 456 SER A 458 5 3 HELIX 6 AA6 ASN A 463 GLU A 467 5 5 HELIX 7 AA7 GLU A 481 PHE A 492 1 12 HELIX 8 AA8 LEU A 500 MET A 507 1 8 HELIX 9 AA9 THR B 345 GLN B 353 1 9 HELIX 10 AB1 ASN B 364 GLY B 375 1 12 HELIX 11 AB2 LEU B 380 ALA B 394 1 15 HELIX 12 AB3 SER B 435 LEU B 439 5 5 HELIX 13 AB4 THR B 456 SER B 458 5 3 HELIX 14 AB5 ASN B 463 GLU B 467 5 5 HELIX 15 AB6 GLU B 481 PHE B 492 1 12 HELIX 16 AB7 LEU B 500 MET B 507 1 8 SHEET 1 AA1 6 VAL A 376 TRP A 377 0 SHEET 2 AA1 6 PHE A 443 CYS A 449 -1 O PHE A 443 N TRP A 377 SHEET 3 AA1 6 GLY A 411 LEU A 415 -1 N ARG A 414 O ASP A 446 SHEET 4 AA1 6 VAL A 397 VAL A 403 -1 N LEU A 399 O ALA A 413 SHEET 5 AA1 6 ARG A 356 SER A 362 1 N ARG A 356 O ILE A 398 SHEET 6 AA1 6 GLU A 479 ILE A 480 -1 O ILE A 480 N PHE A 357 SHEET 1 AA2 2 LYS A 408 PHE A 409 0 SHEET 2 AA2 2 LEU A 453 PRO A 454 -1 O LEU A 453 N PHE A 409 SHEET 1 AA3 6 VAL B 376 TRP B 377 0 SHEET 2 AA3 6 PHE B 443 CYS B 449 -1 O PHE B 443 N TRP B 377 SHEET 3 AA3 6 GLY B 411 LEU B 415 -1 N ARG B 414 O ASP B 446 SHEET 4 AA3 6 SER B 396 VAL B 403 -1 N LEU B 399 O ALA B 413 SHEET 5 AA3 6 ALA B 355 SER B 362 1 N ARG B 356 O ILE B 398 SHEET 6 AA3 6 GLU B 479 ILE B 480 -1 O ILE B 480 N PHE B 357 SHEET 1 AA4 2 LYS B 408 PHE B 409 0 SHEET 2 AA4 2 LEU B 453 PRO B 454 -1 O LEU B 453 N PHE B 409 SITE 1 AC1 4 GLY A 344 SER A 346 LYS A 347 HOH A 704 SITE 1 AC2 7 TRP A 465 GLN A 478 GLU A 479 HOH A 702 SITE 2 AC2 7 HOH A 703 GLY B 344 LYS B 347 SITE 1 AC3 5 PHE A 391 SER A 417 GLU A 418 HIS A 420 SITE 2 AC3 5 HOH A 722 SITE 1 AC4 3 SER A 419 HIS A 420 HIS A 421 SITE 1 AC5 7 SER B 362 ASN B 363 ASN B 367 P0Q B 607 SITE 2 AC5 7 HOH B 721 HOH B 755 HOH B 773 SITE 1 AC6 7 ARG B 451 GLU B 452 HOH B 713 HOH B 731 SITE 2 AC6 7 HOH B 732 HOH B 742 HOH B 791 SITE 1 AC7 6 SER B 419 HIS B 420 HIS B 421 ARG B 451 SITE 2 AC7 6 PRO B 493 HOH B 730 SITE 1 AC8 4 ARG B 404 ARG B 475 ASP B 476 HOH B 734 SITE 1 AC9 7 LYS B 361 ARG B 404 GLU B 405 HOH B 706 SITE 2 AC9 7 HOH B 810 HOH B 849 HOH B 860 SITE 1 AD1 7 PHE B 391 SER B 417 GLU B 418 HIS B 420 SITE 2 AD1 7 HOH B 709 HOH B 724 HOH B 793 SITE 1 AD2 11 ASN B 367 TRP B 377 SER B 378 LEU B 380 SITE 2 AD2 11 TRP B 428 PRO B 431 SER B 435 MET B 438 SITE 3 AD2 11 LEU B 439 SO4 B 601 HOH B 771 SITE 1 AD3 5 TRP A 465 GLU A 481 TYR B 350 HIS B 427 SITE 2 AD3 5 TRP B 428 CRYST1 39.250 103.040 42.040 90.00 106.55 90.00 P 1 21 1 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 0.025478 0.000000 0.007569 0.00000 SCALE2 0.000000 0.009705 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024814 0.00000 CONECT 2577 2578 2579 2580 2581 CONECT 2578 2577 CONECT 2579 2577 CONECT 2580 2577 CONECT 2581 2577 CONECT 2582 2583 2584 2585 2586 CONECT 2583 2582 CONECT 2584 2582 CONECT 2585 2582 CONECT 2586 2582 CONECT 2587 2588 2589 2590 2591 CONECT 2588 2587 CONECT 2589 2587 CONECT 2590 2587 CONECT 2591 2587 CONECT 2592 2593 2594 2595 2596 CONECT 2593 2592 CONECT 2594 2592 CONECT 2595 2592 CONECT 2596 2592 CONECT 2597 2598 2599 2600 2601 CONECT 2598 2597 CONECT 2599 2597 CONECT 2600 2597 CONECT 2601 2597 CONECT 2602 2603 2604 2605 2606 CONECT 2603 2602 CONECT 2604 2602 CONECT 2605 2602 CONECT 2606 2602 CONECT 2607 2608 2609 2610 2611 CONECT 2608 2607 CONECT 2609 2607 CONECT 2610 2607 CONECT 2611 2607 CONECT 2612 2613 2614 2615 2616 CONECT 2613 2612 CONECT 2614 2612 CONECT 2615 2612 CONECT 2616 2612 CONECT 2617 2618 2619 2620 2621 CONECT 2618 2617 CONECT 2619 2617 CONECT 2620 2617 CONECT 2621 2617 CONECT 2622 2623 2624 2625 2626 CONECT 2623 2622 CONECT 2624 2622 CONECT 2625 2622 CONECT 2626 2622 CONECT 2627 2647 CONECT 2628 2648 CONECT 2629 2651 CONECT 2630 2652 CONECT 2631 2651 CONECT 2632 2652 CONECT 2633 2635 2637 CONECT 2634 2636 2638 CONECT 2635 2633 2643 CONECT 2636 2634 2644 CONECT 2637 2633 2645 CONECT 2638 2634 2646 CONECT 2639 2643 2645 CONECT 2640 2644 2646 CONECT 2641 2651 2655 CONECT 2642 2652 2656 CONECT 2643 2635 2639 2657 CONECT 2644 2636 2640 2658 CONECT 2645 2637 2639 2649 CONECT 2646 2638 2640 2650 CONECT 2647 2627 2649 2653 CONECT 2648 2628 2650 2654 CONECT 2649 2645 2647 2655 CONECT 2650 2646 2648 2656 CONECT 2651 2629 2631 2641 2653 CONECT 2652 2630 2632 2642 2654 CONECT 2653 2647 2651 CONECT 2654 2648 2652 CONECT 2655 2641 2649 CONECT 2656 2642 2650 CONECT 2657 2643 CONECT 2658 2644 CONECT 2659 2669 CONECT 2660 2671 CONECT 2661 2671 CONECT 2662 2663 2664 CONECT 2663 2662 2667 CONECT 2664 2662 2668 CONECT 2665 2667 2668 CONECT 2666 2671 2673 CONECT 2667 2663 2665 2674 CONECT 2668 2664 2665 2670 CONECT 2669 2659 2670 2672 CONECT 2670 2668 2669 2673 CONECT 2671 2660 2661 2666 2672 CONECT 2672 2669 2671 CONECT 2673 2666 2670 CONECT 2674 2667 MASTER 384 0 12 16 16 0 22 6 3082 2 98 30 END