HEADER RNA BINDING PROTEIN 02-OCT-19 6T01 TITLE CRYSTAL STRUCTURE OF YTHDC1 WITH FRAGMENT 13 (DHU_DC1_153) COMPND MOL_ID: 1; COMPND 2 MOLECULE: YTH DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SPLICING FACTOR YT521,YT521-B; COMPND 5 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: YTHDC1, KIAA1966, YT521; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FRAGMENT, COMPLEX, YTHDC1, EPITRANSCRIPTOMIC, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.K.BEDI,D.HUANG,P.SLEDZ,A.CAFLISCH REVDAT 3 24-JAN-24 6T01 1 REMARK REVDAT 2 01-APR-20 6T01 1 JRNL REVDAT 1 04-MAR-20 6T01 0 JRNL AUTH R.K.BEDI,D.HUANG,L.WIEDMER,Y.LI,A.DOLBOIS,J.A.WOJDYLA, JRNL AUTH 2 M.E.SHARPE,A.CAFLISCH,P.SLEDZ JRNL TITL SELECTIVELY DISRUPTING M6A-DEPENDENT PROTEIN-RNA JRNL TITL 2 INTERACTIONS WITH FRAGMENTS. JRNL REF ACS CHEM.BIOL. V. 15 618 2020 JRNL REFN ESSN 1554-8937 JRNL PMID 32101404 JRNL DOI 10.1021/ACSCHEMBIO.9B00894 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 51196 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 2551 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 40.6600 - 3.9400 0.99 2768 145 0.1612 0.1537 REMARK 3 2 3.9400 - 3.1300 0.99 2752 145 0.1583 0.1936 REMARK 3 3 3.1300 - 2.7300 1.00 2741 143 0.1848 0.2228 REMARK 3 4 2.7300 - 2.4800 1.00 2713 143 0.1951 0.2347 REMARK 3 5 2.4800 - 2.3000 1.00 2759 146 0.1944 0.2259 REMARK 3 6 2.3000 - 2.1700 0.91 2492 127 0.2865 0.3439 REMARK 3 7 2.1700 - 2.0600 0.99 2729 144 0.1881 0.2222 REMARK 3 8 2.0600 - 1.9700 1.00 2717 141 0.2056 0.2233 REMARK 3 9 1.9700 - 1.8900 0.95 2591 136 0.3467 0.4136 REMARK 3 10 1.8900 - 1.8300 0.97 2671 139 0.2460 0.3464 REMARK 3 11 1.8300 - 1.7700 1.00 2719 142 0.2272 0.2655 REMARK 3 12 1.7700 - 1.7200 1.00 2722 144 0.2467 0.3284 REMARK 3 13 1.7200 - 1.6800 1.00 2750 145 0.2521 0.3359 REMARK 3 14 1.6800 - 1.6300 1.00 2723 143 0.2462 0.2871 REMARK 3 15 1.6300 - 1.6000 1.00 2723 144 0.2504 0.2819 REMARK 3 16 1.6000 - 1.5600 1.00 2752 144 0.2656 0.2824 REMARK 3 17 1.5600 - 1.5300 1.00 2718 143 0.2760 0.3214 REMARK 3 18 1.5300 - 1.5000 0.95 2605 137 0.2857 0.3245 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) : 0.206 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.227 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.18 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 : 0.006 2685 REMARK 3 ANGLE : 0.991 3643 REMARK 3 CHIRALITY : 0.054 393 REMARK 3 PLANARITY : 0.007 458 REMARK 3 DIHEDRAL : 8.934 1863 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 6T01 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1292104630. 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 : 51239 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.360 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 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 (%): 38.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 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 51.66150 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 GLU A 366 CG CD OE1 OE2 REMARK 470 ARG A 395 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 405 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 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 483 CD OE1 OE2 REMARK 470 LYS B 361 CD CE NZ REMARK 470 LYS B 385 CG CD CE NZ REMARK 470 ARG B 395 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 420 CG ND1 CD2 CE1 NE2 REMARK 470 SER B 424 OG REMARK 470 LYS B 437 CG CD CE NZ REMARK 470 LYS B 444 CG CD CE NZ REMARK 470 ARG B 475 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 OE1 GLU B 496 O HOH B 701 1.89 REMARK 500 OE2 GLU B 496 O HOH B 702 1.91 REMARK 500 OG SER A 406 O HOH A 701 1.97 REMARK 500 O LYS A 408 O HOH A 701 2.02 REMARK 500 O HOH B 726 O HOH B 858 2.09 REMARK 500 O HOH A 714 O HOH A 733 2.09 REMARK 500 O HOH A 864 O HOH A 927 2.13 REMARK 500 O HOH B 922 O HOH B 964 2.13 REMARK 500 O HOH A 741 O HOH A 921 2.14 REMARK 500 O HOH B 704 O HOH B 744 2.15 REMARK 500 O HOH A 880 O HOH A 964 2.16 REMARK 500 O HOH B 863 O HOH B 951 2.17 REMARK 500 NH1 ARG A 404 O HOH A 702 2.17 REMARK 500 O HOH A 896 O HOH A 939 2.18 REMARK 500 O HOH B 937 O HOH B 975 2.19 REMARK 500 O HOH A 793 O HOH A 917 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 VAL A 382 O HOH B 702 1556 2.07 REMARK 500 O HOH A 917 O HOH B 841 2646 2.09 REMARK 500 O HOH A 945 O HOH B 875 1556 2.16 REMARK 500 O HOH A 778 O HOH B 964 2545 2.17 REMARK 500 O HOH A 778 O HOH B 922 2545 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 GLU A 405 -1.76 70.34 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 994 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A 995 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A 996 DISTANCE = 7.14 ANGSTROMS REMARK 525 HOH B 988 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH B 989 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH B 990 DISTANCE = 6.05 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue M4B 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 M4B 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 DBREF 6T01 A 345 509 UNP Q96MU7 YTDC1_HUMAN 345 509 DBREF 6T01 B 345 509 UNP Q96MU7 YTDC1_HUMAN 345 509 SEQADV 6T01 MET A 327 UNP Q96MU7 INITIATING METHIONINE SEQADV 6T01 HIS A 328 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 HIS A 329 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 HIS A 330 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 HIS A 331 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 HIS A 332 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 HIS A 333 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 SER A 334 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 SER A 335 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 GLY A 336 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 ARG A 337 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 GLU A 338 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 ASN A 339 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 LEU A 340 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 TYR A 341 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 PHE A 342 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 GLN A 343 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 GLY A 344 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 MET B 327 UNP Q96MU7 INITIATING METHIONINE SEQADV 6T01 HIS B 328 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 HIS B 329 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 HIS B 330 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 HIS B 331 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 HIS B 332 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 HIS B 333 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 SER B 334 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 SER B 335 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 GLY B 336 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 ARG B 337 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 GLU B 338 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 ASN B 339 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 LEU B 340 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 TYR B 341 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 PHE B 342 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 GLN B 343 UNP Q96MU7 EXPRESSION TAG SEQADV 6T01 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 M4B A 601 17 HET SO4 A 602 5 HET SO4 A 603 5 HET SO4 A 604 5 HET M4B B 601 17 HET SO4 B 602 5 HET SO4 B 603 5 HET SO4 B 604 5 HETNAM M4B 6-METHYL-5-NITRO-4-PHENYL-1~{H}-PYRIMIDIN-2-ONE HETNAM SO4 SULFATE ION FORMUL 3 M4B 2(C11 H9 N3 O3) FORMUL 4 SO4 6(O4 S 2-) FORMUL 11 HOH *586(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 ASP A 499 HIS A 505 1 7 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 LEU B 491 1 11 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 ILE A 360 O ILE A 400 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 ASN A 367 TRP A 377 SER A 378 THR A 379 SITE 2 AC1 15 LEU A 380 TRP A 428 VAL A 429 LEU A 430 SITE 3 AC1 15 PRO A 431 MET A 434 ASP A 476 HOH A 747 SITE 4 AC1 15 HOH A 790 HOH A 798 HOH A 830 SITE 1 AC2 9 GLN A 478 GLU A 479 HOH A 706 HOH A 711 SITE 2 AC2 9 HOH A 784 HOH A 805 GLY B 344 LYS B 347 SITE 3 AC2 9 HOH B 842 SITE 1 AC3 5 GLY A 344 SER A 346 LYS A 347 HOH A 705 SITE 2 AC3 5 HOH A 762 SITE 1 AC4 5 HIS A 420 HIS A 421 HOH A 774 HOH A 799 SITE 2 AC4 5 HOH A 854 SITE 1 AC5 14 ASN B 367 TRP B 377 SER B 378 THR B 379 SITE 2 AC5 14 LEU B 380 TRP B 428 VAL B 429 LEU B 430 SITE 3 AC5 14 PRO B 431 MET B 434 ASP B 476 HOH B 735 SITE 4 AC5 14 HOH B 760 HOH B 812 SITE 1 AC6 9 ARG B 451 GLU B 452 HOH B 712 HOH B 730 SITE 2 AC6 9 HOH B 755 HOH B 766 HOH B 767 HOH B 799 SITE 3 AC6 9 HOH B 803 SITE 1 AC7 6 HIS B 420 HIS B 421 ARG B 451 HOH B 726 SITE 2 AC7 6 HOH B 784 HOH B 864 SITE 1 AC8 6 ARG B 404 ARG B 475 ASP B 476 HOH B 709 SITE 2 AC8 6 HOH B 743 HOH B 804 CRYST1 39.678 103.323 42.246 90.00 105.77 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 0.025203 0.000000 0.007115 0.00000 SCALE2 0.000000 0.009678 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024596 0.00000