HEADER RNA BINDING PROTEIN 14-APR-20 6YNN TITLE CRYSTAL STRUCTURE OF YTHDC1 WITH COMPOUND DHU_DC1_135 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 4 24-JAN-24 6YNN 1 REMARK REVDAT 3 31-MAR-21 6YNN 1 JRNL REVDAT 2 13-JAN-21 6YNN 1 JRNL REVDAT 1 15-JUL-20 6YNN 0 JRNL AUTH Y.LI,R.K.BEDI,L.WIEDMER,X.SUN,D.HUANG,A.CAFLISCH JRNL TITL ATOMISTIC AND THERMODYNAMIC ANALYSIS OF N6-METHYLADENOSINE JRNL TITL 2 (M 6 A) RECOGNITION BY THE READER DOMAIN OF YTHDC1. JRNL REF J CHEM THEORY COMPUT V. 17 1240 2021 JRNL REFN ISSN 1549-9626 JRNL PMID 33472367 JRNL DOI 10.1021/ACS.JCTC.0C01136 REMARK 2 REMARK 2 RESOLUTION. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 101607 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5081 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 40.7300 - 3.7300 0.99 3293 173 0.1576 0.1871 REMARK 3 2 3.7300 - 2.9600 0.99 3237 171 0.1551 0.1858 REMARK 3 3 2.9600 - 2.5900 1.00 3274 173 0.1777 0.1986 REMARK 3 4 2.5900 - 2.3500 1.00 3220 168 0.1830 0.2115 REMARK 3 5 2.3500 - 2.1800 1.00 3253 171 0.1856 0.2099 REMARK 3 6 2.1800 - 2.0500 0.99 3243 171 0.1778 0.2023 REMARK 3 7 2.0500 - 1.9500 1.00 3236 170 0.1824 0.1889 REMARK 3 8 1.9500 - 1.8700 1.00 3241 171 0.1878 0.2196 REMARK 3 9 1.8700 - 1.7900 1.00 3221 170 0.2001 0.1951 REMARK 3 10 1.7900 - 1.7300 1.00 3220 169 0.1977 0.1998 REMARK 3 11 1.7300 - 1.6800 1.00 3233 170 0.1956 0.2181 REMARK 3 12 1.6800 - 1.6300 1.00 3247 171 0.1889 0.2240 REMARK 3 13 1.6300 - 1.5900 0.99 3224 170 0.1956 0.1875 REMARK 3 14 1.5900 - 1.5500 1.00 3243 171 0.1983 0.2280 REMARK 3 15 1.5500 - 1.5100 0.99 3215 169 0.2047 0.2231 REMARK 3 16 1.5100 - 1.4800 0.99 3214 169 0.2141 0.2363 REMARK 3 17 1.4800 - 1.4500 0.99 3236 171 0.2307 0.2456 REMARK 3 18 1.4500 - 1.4200 1.00 3225 170 0.2345 0.2458 REMARK 3 19 1.4200 - 1.4000 0.99 3229 169 0.2367 0.2408 REMARK 3 20 1.4000 - 1.3800 0.99 3210 169 0.2351 0.2471 REMARK 3 21 1.3800 - 1.3500 0.99 3199 169 0.2491 0.2565 REMARK 3 22 1.3500 - 1.3300 0.99 3234 170 0.2585 0.2986 REMARK 3 23 1.3300 - 1.3100 0.99 3212 169 0.2718 0.3003 REMARK 3 24 1.3100 - 1.2900 0.99 3216 170 0.2773 0.2831 REMARK 3 25 1.2900 - 1.2800 0.99 3188 167 0.2808 0.3552 REMARK 3 26 1.2800 - 1.2600 0.99 3264 172 0.2876 0.2795 REMARK 3 27 1.2600 - 1.2400 0.99 3152 166 0.2969 0.3006 REMARK 3 28 1.2400 - 1.2300 0.99 3264 172 0.3149 0.3303 REMARK 3 29 1.2300 - 1.2200 0.99 3176 167 0.3109 0.3220 REMARK 3 30 1.2200 - 1.2000 0.90 2907 153 0.3235 0.3252 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) : 0.139 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.669 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.21 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 : 0.005 2778 REMARK 3 ANGLE : 0.777 3786 REMARK 3 CHIRALITY : 0.078 406 REMARK 3 PLANARITY : 0.005 471 REMARK 3 DIHEDRAL : 19.227 381 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 6YNN 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_1292107971. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-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-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 101872 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.330 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 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 (%): 38.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 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 51.90500 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 GLN A 353 CD OE1 NE2 REMARK 470 GLU A 366 OE1 REMARK 470 LYS A 374 CD CE NZ REMARK 470 ARG A 395 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 405 OE1 OE2 REMARK 470 GLU A 418 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 CE NZ REMARK 470 ARG A 475 CD NE CZ NH1 NH2 REMARK 470 GLU A 483 CG CD OE1 OE2 REMARK 470 GLN A 487 CD OE1 NE2 REMARK 470 LYS B 374 NZ REMARK 470 LYS B 386 CD CE NZ REMARK 470 ARG B 395 CG CD NE CZ NH1 NH2 REMARK 470 SER B 424 OG REMARK 470 LYS B 437 CB CG CD CE NZ REMARK 470 LYS B 444 CE NZ REMARK 470 GLN B 502 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 481 O HOH A 701 1.85 REMARK 500 O3 SO4 A 602 O HOH A 702 1.89 REMARK 500 O HOH B 894 O HOH B 984 1.90 REMARK 500 O HOH B 741 O HOH B 801 1.90 REMARK 500 O HOH B 704 O HOH B 812 1.90 REMARK 500 O HOH A 701 O HOH A 881 1.97 REMARK 500 NE2 GLN B 478 O HOH B 701 1.97 REMARK 500 OD1 ASP A 446 O HOH A 703 1.98 REMARK 500 O HOH A 951 O HOH B 895 1.99 REMARK 500 OE2 GLU A 452 O HOH A 704 2.01 REMARK 500 O HOH A 738 O HOH A 920 2.01 REMARK 500 O HOH B 709 O HOH B 840 2.02 REMARK 500 O4 SO4 B 606 O HOH B 702 2.02 REMARK 500 O HOH B 858 O HOH B 894 2.03 REMARK 500 O HOH B 838 O HOH B 851 2.04 REMARK 500 O HOH B 707 O HOH B 876 2.05 REMARK 500 O HOH A 761 O HOH A 900 2.05 REMARK 500 O HOH B 856 O HOH B 896 2.05 REMARK 500 O HOH A 745 O HOH A 865 2.05 REMARK 500 O HOH A 873 O HOH A 889 2.06 REMARK 500 O HOH A 824 O HOH A 906 2.06 REMARK 500 O HOH B 773 O HOH B 873 2.06 REMARK 500 O HOH A 871 O HOH A 906 2.06 REMARK 500 O HOH A 815 O HOH A 845 2.07 REMARK 500 O HOH A 779 O HOH A 850 2.07 REMARK 500 O HOH A 892 O HOH A 942 2.08 REMARK 500 O HOH B 710 O HOH B 882 2.08 REMARK 500 O HOH A 748 O HOH A 886 2.08 REMARK 500 O3 SO4 B 606 O HOH B 703 2.08 REMARK 500 O HOH A 788 O HOH A 935 2.09 REMARK 500 O HOH A 903 O HOH A 920 2.10 REMARK 500 O HOH A 779 O HOH A 897 2.10 REMARK 500 O HOH A 723 O HOH A 788 2.10 REMARK 500 OE1 GLN B 478 O HOH B 704 2.10 REMARK 500 O HOH B 916 O HOH B 926 2.11 REMARK 500 O1 SO4 A 602 O HOH A 705 2.11 REMARK 500 O HOH B 734 O HOH B 990 2.12 REMARK 500 O HOH B 851 O HOH B 897 2.13 REMARK 500 O HOH B 716 O HOH B 940 2.14 REMARK 500 O HOH A 811 O HOH A 872 2.14 REMARK 500 O2 SO4 A 602 O HOH A 702 2.14 REMARK 500 O HOH A 712 O HOH A 726 2.15 REMARK 500 O HOH A 938 O HOH A 951 2.15 REMARK 500 O HOH B 893 O HOH B 896 2.15 REMARK 500 NE ARG A 450 O HOH A 706 2.15 REMARK 500 OE1 GLU B 418 O HOH B 705 2.16 REMARK 500 O HOH B 873 O HOH B 921 2.16 REMARK 500 O HOH B 812 O HOH B 849 2.16 REMARK 500 O HOH B 735 O HOH B 913 2.16 REMARK 500 O3 SO4 A 602 O HOH A 705 2.17 REMARK 500 REMARK 500 THIS ENTRY HAS 59 CLOSE CONTACTS 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 725 O HOH B 901 2545 1.76 REMARK 500 O HOH A 710 O HOH B 826 2645 1.95 REMARK 500 O HOH A 722 O HOH B 881 1556 2.02 REMARK 500 O HOH B 702 O HOH B 857 1455 2.03 REMARK 500 O HOH A 940 O HOH B 737 2645 2.03 REMARK 500 O HOH A 708 O HOH A 940 1455 2.12 REMARK 500 O HOH A 727 O HOH B 721 1556 2.15 REMARK 500 O HOH A 750 O HOH B 735 2645 2.15 REMARK 500 O HOH A 912 O HOH B 982 2545 2.16 REMARK 500 O HOH A 722 O HOH B 916 1556 2.18 REMARK 500 O HOH A 756 O HOH B 816 1556 2.19 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 A1009 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A1010 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH B1012 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH B1013 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH B1014 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH B1015 DISTANCE = 7.15 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue P0B 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 P0B B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 606 DBREF 6YNN A 345 509 UNP Q96MU7 YTDC1_HUMAN 345 509 DBREF 6YNN B 345 509 UNP Q96MU7 YTDC1_HUMAN 345 509 SEQADV 6YNN MET A 327 UNP Q96MU7 INITIATING METHIONINE SEQADV 6YNN HIS A 328 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN HIS A 329 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN HIS A 330 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN HIS A 331 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN HIS A 332 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN HIS A 333 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN SER A 334 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN SER A 335 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN GLY A 336 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN ARG A 337 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN GLU A 338 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN ASN A 339 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN LEU A 340 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN TYR A 341 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN PHE A 342 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN GLN A 343 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN GLY A 344 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN MET B 327 UNP Q96MU7 INITIATING METHIONINE SEQADV 6YNN HIS B 328 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN HIS B 329 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN HIS B 330 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN HIS B 331 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN HIS B 332 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN HIS B 333 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN SER B 334 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN SER B 335 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN GLY B 336 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN ARG B 337 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN GLU B 338 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN ASN B 339 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN LEU B 340 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN TYR B 341 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN PHE B 342 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN GLN B 343 UNP Q96MU7 EXPRESSION TAG SEQADV 6YNN 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 P0B A 601 20 HET SO4 A 602 10 HET SO4 A 603 10 HET P0B B 601 20 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 HETNAM P0B 6-[[(2-CHLORANYL-6-FLUORANYL-PHENYL)METHYL-METHYL- HETNAM 2 P0B AMINO]METHYL]-1~{H}-PYRIMIDINE-2,4-DIONE HETNAM SO4 SULFATE ION FORMUL 3 P0B 2(C13 H13 CL F N3 O2) FORMUL 4 SO4 7(O4 S 2-) FORMUL 12 HOH *625(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 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 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 SER B 378 0 SHEET 2 AA3 6 VAL B 442 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 15 LYS A 361 ASN A 363 ASN A 367 TRP A 377 SITE 2 AC1 15 SER A 378 THR A 379 LEU A 380 ARG A 404 SITE 3 AC1 15 TRP A 428 VAL A 429 PRO A 431 MET A 434 SITE 4 AC1 15 LEU A 439 ASP A 476 HOH A 730 SITE 1 AC2 11 GLY A 344 THR A 345 SER A 346 LYS A 347 SITE 2 AC2 11 HOH A 702 HOH A 705 HOH A 724 HOH A 725 SITE 3 AC2 11 HOH A 733 HOH A 734 HOH A 797 SITE 1 AC3 5 LYS A 361 ARG A 404 ARG A 475 ASP A 476 SITE 2 AC3 5 HOH A 749 SITE 1 AC4 14 LYS B 361 ASN B 363 ASN B 367 TRP B 377 SITE 2 AC4 14 SER B 378 THR B 379 ARG B 404 TRP B 428 SITE 3 AC4 14 LEU B 430 PRO B 431 MET B 434 LEU B 439 SITE 4 AC4 14 ASP B 476 HOH B 754 SITE 1 AC5 8 ARG B 451 GLU B 452 HOH B 730 HOH B 757 SITE 2 AC5 8 HOH B 767 HOH B 777 HOH B 800 HOH B 811 SITE 1 AC6 9 LYS A 386 GLN A 478 GLU A 479 LYS B 347 SITE 2 AC6 9 HOH B 721 HOH B 761 HOH B 827 HOH B 853 SITE 3 AC6 9 HOH B 860 SITE 1 AC7 5 SER B 419 HIS B 420 HIS B 421 ARG B 451 SITE 2 AC7 5 HOH B 708 SITE 1 AC8 6 LYS B 361 ARG B 404 ARG B 475 ASP B 476 SITE 2 AC8 6 HOH B 706 HOH B 847 SITE 1 AC9 7 LYS B 385 ASN B 388 ARG B 392 LYS B 457 SITE 2 AC9 7 HOH B 702 HOH B 703 HOH B 705 CRYST1 39.800 103.810 42.060 90.00 104.47 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 0.025126 0.000000 0.006484 0.00000 SCALE2 0.000000 0.009633 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024554 0.00000