HEADER RNA BINDING PROTEIN 14-APR-20 6YOQ TITLE CRYSTAL STRUCTURE OF YTHDC1 WITH COMPOUND VVR_DC1_002 CAVEAT 6YOQ P5H A 601 HAS WRONG CHIRALITY AT ATOM C03 P5H B 601 HAS CAVEAT 2 6YOQ WRONG CHIRALITY AT ATOM C03 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 V.VON ROTEN,R.K.BEDI,A.CAFLISCH REVDAT 3 24-JAN-24 6YOQ 1 REMARK REVDAT 2 15-JUN-22 6YOQ 1 JRNL REVDAT 1 15-JUL-20 6YOQ 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. 1.30 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 78254 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3912 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 40.2000 - 3.9500 0.99 2696 141 0.1581 0.1607 REMARK 3 2 3.9500 - 3.1400 0.99 2690 142 0.1535 0.1564 REMARK 3 3 3.1400 - 2.7400 1.00 2680 141 0.1728 0.2174 REMARK 3 4 2.7400 - 2.4900 1.00 2649 139 0.1817 0.2013 REMARK 3 5 2.4900 - 2.3100 0.99 2642 140 0.1798 0.1815 REMARK 3 6 2.3100 - 2.1700 0.99 2671 140 0.1802 0.1938 REMARK 3 7 2.1700 - 2.0700 0.99 2657 140 0.1740 0.1995 REMARK 3 8 2.0700 - 1.9800 0.99 2646 139 0.1835 0.2018 REMARK 3 9 1.9800 - 1.9000 1.00 2681 142 0.1835 0.1965 REMARK 3 10 1.9000 - 1.8300 1.00 2666 140 0.1906 0.2187 REMARK 3 11 1.8300 - 1.7800 0.99 2636 139 0.1914 0.2130 REMARK 3 12 1.7800 - 1.7300 1.00 2669 140 0.1958 0.2389 REMARK 3 13 1.7300 - 1.6800 1.00 2670 141 0.2030 0.2126 REMARK 3 14 1.6800 - 1.6400 1.00 2656 140 0.1981 0.2378 REMARK 3 15 1.6400 - 1.6000 0.99 2653 139 0.2015 0.2438 REMARK 3 16 1.6000 - 1.5700 1.00 2637 139 0.2062 0.2291 REMARK 3 17 1.5700 - 1.5400 1.00 2697 142 0.2123 0.2643 REMARK 3 18 1.5400 - 1.5100 1.00 2627 138 0.2191 0.2222 REMARK 3 19 1.5100 - 1.4800 1.00 2663 140 0.2254 0.2950 REMARK 3 20 1.4800 - 1.4600 1.00 2652 138 0.2387 0.2523 REMARK 3 21 1.4600 - 1.4300 1.00 2659 140 0.2553 0.2821 REMARK 3 22 1.4300 - 1.4100 0.99 2646 140 0.2573 0.2904 REMARK 3 23 1.4100 - 1.3900 0.99 2636 138 0.2647 0.2862 REMARK 3 24 1.3900 - 1.3700 1.00 2676 141 0.2694 0.2608 REMARK 3 25 1.3700 - 1.3500 0.99 2591 137 0.2927 0.2791 REMARK 3 26 1.3500 - 1.3300 0.99 2707 142 0.2962 0.2962 REMARK 3 27 1.3300 - 1.3200 0.99 2618 138 0.3114 0.2939 REMARK 3 28 1.3200 - 1.3000 0.97 2571 136 0.3406 0.3686 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.152 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.584 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.88 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 2719 REMARK 3 ANGLE : 0.820 3703 REMARK 3 CHIRALITY : 0.078 398 REMARK 3 PLANARITY : 0.005 464 REMARK 3 DIHEDRAL : 15.078 368 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 6YOQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292108009. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-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 : 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-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78421 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 40.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.428 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 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 (%): 37.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 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 51.86000 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 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 LYS A 361 CE NZ REMARK 470 GLU A 366 CG CD OE1 OE2 REMARK 470 LYS A 374 CE NZ REMARK 470 VAL A 382 CG2 REMARK 470 ARG A 395 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 404 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 405 CG CD OE1 OE2 REMARK 470 SER A 424 OG REMARK 470 LYS A 437 CG CD CE NZ REMARK 470 LYS A 444 CE NZ REMARK 470 LYS A 457 CD CE NZ REMARK 470 ARG A 475 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 483 CD OE1 OE2 REMARK 470 ARG A 508 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 361 CE NZ REMARK 470 LYS B 385 CG CD CE NZ REMARK 470 ARG B 404 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 405 OE1 OE2 REMARK 470 SER B 424 OG REMARK 470 SER B 435 CB OG REMARK 470 ALA B 436 CB REMARK 470 LYS B 437 CG CD CE NZ REMARK 470 LYS B 444 CE NZ REMARK 470 ARG B 475 CG CD NE CZ NH1 NH2 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 O HOH A 727 O HOH A 852 1.95 REMARK 500 O1 SO4 B 603 O HOH B 701 1.99 REMARK 500 O HOH A 857 O HOH A 867 2.00 REMARK 500 O HOH A 705 O HOH A 849 2.00 REMARK 500 O HOH A 754 O HOH A 796 2.02 REMARK 500 O HOH B 727 O HOH B 913 2.02 REMARK 500 O HOH A 759 O HOH A 775 2.04 REMARK 500 O HOH A 705 O HOH A 788 2.04 REMARK 500 O HOH A 852 O HOH A 888 2.07 REMARK 500 O HOH A 727 O HOH A 824 2.07 REMARK 500 O HOH A 798 O HOH A 888 2.08 REMARK 500 O HOH B 807 O HOH B 917 2.08 REMARK 500 O HOH A 703 O HOH A 704 2.09 REMARK 500 O HOH B 713 O HOH B 824 2.09 REMARK 500 O HOH B 836 O HOH B 917 2.10 REMARK 500 O HOH A 757 O HOH A 967 2.10 REMARK 500 O HOH A 875 O HOH A 921 2.10 REMARK 500 O HOH B 841 O HOH B 900 2.13 REMARK 500 O GLY A 422 O HOH A 701 2.14 REMARK 500 O HOH A 702 O HOH A 829 2.14 REMARK 500 O HOH A 775 O HOH A 894 2.15 REMARK 500 OE2 GLU A 452 O HOH A 702 2.15 REMARK 500 O HOH A 724 O HOH A 917 2.17 REMARK 500 O HOH B 914 O HOH B 926 2.18 REMARK 500 O HOH B 955 O HOH B 957 2.19 REMARK 500 O HOH B 865 O HOH B 920 2.19 REMARK 500 O HOH A 839 O HOH A 971 2.19 REMARK 500 O HOH B 779 O HOH B 806 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 A 824 O HOH B 706 2554 2.01 REMARK 500 O HOH A 919 O HOH B 841 2555 2.11 REMARK 500 O HOH A 946 O HOH B 876 1455 2.14 REMARK 500 O HOH A 725 O HOH B 779 1455 2.14 REMARK 500 O HOH A 956 O HOH B 887 2555 2.15 REMARK 500 O HOH A 940 O HOH B 943 2555 2.19 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 SER B 435 -28.87 71.86 REMARK 500 ALA B 436 -24.09 100.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 979 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A 980 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH B 958 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH B 959 DISTANCE = 7.08 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue P5H 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 P5H 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 DBREF 6YOQ A 345 509 UNP Q96MU7 YTDC1_HUMAN 345 509 DBREF 6YOQ B 345 509 UNP Q96MU7 YTDC1_HUMAN 345 509 SEQADV 6YOQ MET A 327 UNP Q96MU7 INITIATING METHIONINE SEQADV 6YOQ HIS A 328 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ HIS A 329 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ HIS A 330 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ HIS A 331 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ HIS A 332 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ HIS A 333 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ SER A 334 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ SER A 335 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ GLY A 336 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ ARG A 337 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ GLU A 338 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ ASN A 339 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ LEU A 340 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ TYR A 341 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ PHE A 342 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ GLN A 343 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ GLY A 344 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ MET B 327 UNP Q96MU7 INITIATING METHIONINE SEQADV 6YOQ HIS B 328 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ HIS B 329 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ HIS B 330 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ HIS B 331 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ HIS B 332 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ HIS B 333 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ SER B 334 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ SER B 335 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ GLY B 336 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ ARG B 337 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ GLU B 338 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ ASN B 339 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ LEU B 340 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ TYR B 341 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ PHE B 342 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ GLN B 343 UNP Q96MU7 EXPRESSION TAG SEQADV 6YOQ 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 P5H A 601 18 HET SO4 A 602 10 HET SO4 A 603 5 HET SO4 A 604 5 HET P5H B 601 18 HET SO4 B 602 5 HET SO4 B 603 5 HET SO4 B 604 5 HET SO4 B 605 5 HETNAM P5H 6-METHYL-~{N}-[2-(METHYLSULFONYLAMINO)ETHYL]-2- HETNAM 2 P5H OXIDANYLIDENE-3~{H}-PYRIDINE-3-CARBOXAMIDE HETNAM SO4 SULFATE ION FORMUL 3 P5H 2(C10 H15 N3 O4 S) FORMUL 4 SO4 7(O4 S 2-) FORMUL 12 HOH *539(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 ALA A 459 5 4 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 ARG A 508 1 9 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 THR B 456 SER B 458 5 3 HELIX 13 AB4 ASN B 463 GLU B 467 5 5 HELIX 14 AB5 GLU B 481 PHE B 492 1 12 HELIX 15 AB6 LEU B 500 MET B 507 1 8 SHEET 1 AA1 6 VAL A 376 SER A 378 0 SHEET 2 AA1 6 VAL A 442 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 VAL B 397 VAL B 403 -1 N LEU B 399 O ALA B 413 SHEET 5 AA3 6 ARG B 356 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 15 LYS A 361 ASN A 363 ASN A 367 TRP A 377 SITE 2 AC1 15 SER A 378 LEU A 380 TRP A 428 PRO A 431 SITE 3 AC1 15 MET A 434 ASP A 476 SO4 A 604 HOH A 714 SITE 4 AC1 15 HOH A 731 HOH A 820 HOH A 862 SITE 1 AC2 10 GLY A 344 THR A 345 SER A 346 LYS A 347 SITE 2 AC2 10 HOH A 703 HOH A 704 HOH A 713 HOH A 772 SITE 3 AC2 10 LYS B 386 GLU B 479 SITE 1 AC3 5 HIS A 420 HIS A 421 HOH A 707 HOH A 822 SITE 2 AC3 5 HOH A 864 SITE 1 AC4 5 ARG A 475 ASP A 476 P5H A 601 HOH A 752 SITE 2 AC4 5 HOH A 820 SITE 1 AC5 12 LYS B 361 ASN B 363 ASN B 367 TRP B 377 SITE 2 AC5 12 SER B 378 LEU B 380 TRP B 428 LEU B 430 SITE 3 AC5 12 MET B 434 ASP B 476 SO4 B 605 HOH B 746 SITE 1 AC6 8 ARG B 451 GLU B 452 HOH B 714 HOH B 728 SITE 2 AC6 8 HOH B 747 HOH B 750 HOH B 770 HOH B 854 SITE 1 AC7 4 GLY B 344 LYS B 347 HOH B 701 HOH B 709 SITE 1 AC8 5 SER B 419 HIS B 420 HIS B 421 ARG B 451 SITE 2 AC8 5 HOH B 827 SITE 1 AC9 7 SER A 424 PRO A 425 ARG B 475 ASP B 476 SITE 2 AC9 7 P5H B 601 HOH B 759 HOH B 783 CRYST1 39.350 103.720 41.870 90.00 106.23 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 0.025413 0.000000 0.007396 0.00000 SCALE2 0.000000 0.009641 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024874 0.00000