HEADER RNA BINDING PROTEIN 22-MAY-19 6RT4 TITLE THE YTH DOMAIN OF YTHDC1 PROTEIN IN COMPLEX WITH M6ACU OLIGONUCLEOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*(6MZ)P*C)-3'); COMPND 3 CHAIN: C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: YTH DOMAIN-CONTAINING PROTEIN 1; COMPND 7 CHAIN: B, A; COMPND 8 SYNONYM: SPLICING FACTOR YT521,YT521-B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: YTHDC1, KIAA1966, YT521; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN-RNA INTERACTION, EPITRANSCRIPTOMICS, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.BEDI,P.SLEDZ,A.CAFLISCH REVDAT 3 24-JAN-24 6RT4 1 REMARK REVDAT 2 18-DEC-19 6RT4 1 JRNL REVDAT 1 27-NOV-19 6RT4 0 JRNL AUTH Y.LI,R.K.BEDI,L.WIEDMER,D.HUANG,P.SLEDZ,A.CAFLISCH JRNL TITL FLEXIBLE BINDING OF M6A READER PROTEIN YTHDC1 TO ITS JRNL TITL 2 PREFERRED RNA MOTIF. JRNL REF J CHEM THEORY COMPUT V. 15 7004 2019 JRNL REFN ISSN 1549-9626 JRNL PMID 31670957 JRNL DOI 10.1021/ACS.JCTC.9B00987 REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 53206 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.770 REMARK 3 FREE R VALUE TEST SET COUNT : 2006 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 38.8069 - 3.5794 0.98 3702 149 0.1643 0.2142 REMARK 3 2 3.5794 - 2.8414 0.99 3715 152 0.1936 0.1894 REMARK 3 3 2.8414 - 2.4823 0.97 3627 138 0.2126 0.2069 REMARK 3 4 2.4823 - 2.2554 0.99 3721 139 0.2107 0.2312 REMARK 3 5 2.2554 - 2.0937 0.99 3711 145 0.2190 0.2458 REMARK 3 6 2.0937 - 1.9703 0.99 3751 143 0.2262 0.2635 REMARK 3 7 1.9703 - 1.8716 0.99 3700 141 0.2322 0.2821 REMARK 3 8 1.8716 - 1.7901 0.97 3577 146 0.2449 0.3173 REMARK 3 9 1.7901 - 1.7212 0.98 3677 144 0.2406 0.2963 REMARK 3 10 1.7212 - 1.6618 0.99 3670 150 0.2538 0.2856 REMARK 3 11 1.6618 - 1.6099 0.99 3684 132 0.2610 0.2882 REMARK 3 12 1.6099 - 1.5638 1.00 3714 158 0.2892 0.3103 REMARK 3 13 1.5638 - 1.5227 0.99 3710 141 0.3159 0.3703 REMARK 3 14 1.5227 - 1.4855 0.87 3241 128 0.3534 0.3823 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 2717 REMARK 3 ANGLE : 0.785 3686 REMARK 3 CHIRALITY : 0.078 409 REMARK 3 PLANARITY : 0.005 448 REMARK 3 DIHEDRAL : 9.831 1553 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 6RT4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1292102459. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-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) : 1.000002 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53214 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 38.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 3.470 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.26 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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 (%): 42.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS AT PH 6.5, 0.2 M REMARK 280 AMMONIUM SULFATE AND 30% PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 51.75150 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 U C 102 REMARK 465 GLY B 422 REMARK 465 GLY B 423 REMARK 465 SER B 424 REMARK 465 PRO B 425 REMARK 465 ARG B 508 REMARK 465 HIS B 509 REMARK 465 ARG A 508 REMARK 465 HIS A 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 C C 101 C5' C4' O4' C3' O3' C2' O2' REMARK 470 C C 101 C1' N1 C2 O2 N3 C4 N4 REMARK 470 C C 101 C5 C6 REMARK 470 LYS B 374 CD CE NZ REMARK 470 ARG B 395 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 427 CG ND1 CD2 CE1 NE2 REMARK 470 SER B 435 OG REMARK 470 LYS B 437 CG CD CE NZ REMARK 470 LYS B 444 CE NZ REMARK 470 LYS B 457 CE NZ REMARK 470 GLU B 483 CD OE1 OE2 REMARK 470 HIS B 505 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 354 CG OD1 OD2 REMARK 470 LYS A 374 CE NZ REMARK 470 LYS A 385 CG CD CE NZ REMARK 470 ARG A 404 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 420 CG ND1 CD2 CE1 NE2 REMARK 470 SER A 424 OG REMARK 470 HIS A 427 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 437 CG CD CE NZ REMARK 470 ARG A 475 CA 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 C 201 O HOH C 202 1.81 REMARK 500 O HOH B 817 O HOH B 834 1.87 REMARK 500 O LEU B 439 O HOH B 701 1.88 REMARK 500 O HOH B 812 O HOH B 815 1.90 REMARK 500 O ALA A 432 O HOH A 701 2.01 REMARK 500 NH2 ARG A 392 O HOH A 702 2.01 REMARK 500 O HOH A 849 O HOH A 880 2.02 REMARK 500 O HOH B 703 O HOH B 708 2.03 REMARK 500 OG SER B 369 O HOH B 702 2.06 REMARK 500 O HOH A 822 O HOH A 871 2.09 REMARK 500 OG1 THR A 462 O HOH A 703 2.09 REMARK 500 O HOH B 747 O HOH B 786 2.12 REMARK 500 O HOH A 729 O HOH A 741 2.14 REMARK 500 O HOH A 826 O HOH A 844 2.18 REMARK 500 O HOH A 837 O HOH A 847 2.19 REMARK 500 O2 SO4 B 601 O HOH B 703 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 811 O HOH A 884 2646 2.10 REMARK 500 O HOH B 804 O HOH A 720 2545 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 C D 2 O3' - P - OP1 ANGL. DEV. = 10.6 DEGREES 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 HIS B 427 62.20 75.05 REMARK 500 ALA B 432 88.82 -60.50 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 884 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH A 885 DISTANCE = 7.21 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide 6MZ D 1 and C D 2 DBREF 6RT4 C 1 102 PDB 6RT4 6RT4 1 102 DBREF 6RT4 B 345 509 UNP Q96MU7 YTDC1_HUMAN 345 509 DBREF 6RT4 A 345 509 UNP Q96MU7 YTDC1_HUMAN 345 509 DBREF 6RT4 D 1 3 PDB 6RT4 6RT4 1 3 SEQADV 6RT4 GLY B 344 UNP Q96MU7 EXPRESSION TAG SEQADV 6RT4 GLY A 344 UNP Q96MU7 EXPRESSION TAG SEQRES 1 C 3 6MZ C U SEQRES 1 B 166 GLY THR SER LYS LEU LYS TYR VAL LEU GLN ASP ALA ARG SEQRES 2 B 166 PHE PHE LEU ILE LYS SER ASN ASN HIS GLU ASN VAL SER SEQRES 3 B 166 LEU ALA LYS ALA LYS GLY VAL TRP SER THR LEU PRO VAL SEQRES 4 B 166 ASN GLU LYS LYS LEU ASN LEU ALA PHE ARG SER ALA ARG SEQRES 5 B 166 SER VAL ILE LEU ILE PHE SER VAL ARG GLU SER GLY LYS SEQRES 6 B 166 PHE GLN GLY PHE ALA ARG LEU SER SER GLU SER HIS HIS SEQRES 7 B 166 GLY GLY SER PRO ILE HIS TRP VAL LEU PRO ALA GLY MET SEQRES 8 B 166 SER ALA LYS MET LEU GLY GLY VAL PHE LYS ILE ASP TRP SEQRES 9 B 166 ILE CYS ARG ARG GLU LEU PRO PHE THR LYS SER ALA HIS SEQRES 10 B 166 LEU THR ASN PRO TRP ASN GLU HIS LYS PRO VAL LYS ILE SEQRES 11 B 166 GLY ARG ASP GLY GLN GLU ILE GLU LEU GLU CYS GLY THR SEQRES 12 B 166 GLN LEU CYS LEU LEU PHE PRO PRO ASP GLU SER ILE ASP SEQRES 13 B 166 LEU TYR GLN VAL ILE HIS LYS MET ARG HIS SEQRES 1 A 166 GLY THR SER LYS LEU LYS TYR VAL LEU GLN ASP ALA ARG SEQRES 2 A 166 PHE PHE LEU ILE LYS SER ASN ASN HIS GLU ASN VAL SER SEQRES 3 A 166 LEU ALA LYS ALA LYS GLY VAL TRP SER THR LEU PRO VAL SEQRES 4 A 166 ASN GLU LYS LYS LEU ASN LEU ALA PHE ARG SER ALA ARG SEQRES 5 A 166 SER VAL ILE LEU ILE PHE SER VAL ARG GLU SER GLY LYS SEQRES 6 A 166 PHE GLN GLY PHE ALA ARG LEU SER SER GLU SER HIS HIS SEQRES 7 A 166 GLY GLY SER PRO ILE HIS TRP VAL LEU PRO ALA GLY MET SEQRES 8 A 166 SER ALA LYS MET LEU GLY GLY VAL PHE LYS ILE ASP TRP SEQRES 9 A 166 ILE CYS ARG ARG GLU LEU PRO PHE THR LYS SER ALA HIS SEQRES 10 A 166 LEU THR ASN PRO TRP ASN GLU HIS LYS PRO VAL LYS ILE SEQRES 11 A 166 GLY ARG ASP GLY GLN GLU ILE GLU LEU GLU CYS GLY THR SEQRES 12 A 166 GLN LEU CYS LEU LEU PHE PRO PRO ASP GLU SER ILE ASP SEQRES 13 A 166 LEU TYR GLN VAL ILE HIS LYS MET ARG HIS SEQRES 1 D 3 6MZ C U HET 6MZ C 1 20 HET 6MZ D 1 20 HET SO4 B 601 5 HET SO4 B 602 5 HET SO4 A 601 5 HET SO4 A 602 5 HET SO4 A 603 5 HET SO4 A 604 5 HETNAM 6MZ N6-METHYLADENOSINE-5'-MONOPHOSPHATE HETNAM SO4 SULFATE ION FORMUL 1 6MZ 2(C11 H16 N5 O7 P) FORMUL 5 SO4 6(O4 S 2-) FORMUL 11 HOH *328(H2 O) HELIX 1 AA1 THR B 345 GLN B 353 1 9 HELIX 2 AA2 ASN B 364 GLY B 375 1 12 HELIX 3 AA3 LEU B 380 ALA B 394 1 15 HELIX 4 AA4 LYS B 437 GLY B 441 5 5 HELIX 5 AA5 THR B 456 ALA B 459 5 4 HELIX 6 AA6 ASN B 463 GLU B 467 5 5 HELIX 7 AA7 GLU B 481 PHE B 492 1 12 HELIX 8 AA8 ASP B 499 HIS B 505 1 7 HELIX 9 AA9 THR A 345 GLN A 353 1 9 HELIX 10 AB1 ASN A 364 GLY A 375 1 12 HELIX 11 AB2 LEU A 380 ALA A 394 1 15 HELIX 12 AB3 THR A 456 ALA A 459 5 4 HELIX 13 AB4 ASN A 463 GLU A 467 5 5 HELIX 14 AB5 GLU A 481 PHE A 492 1 12 HELIX 15 AB6 LEU A 500 LYS A 506 1 7 SHEET 1 AA1 6 VAL B 376 TRP B 377 0 SHEET 2 AA1 6 PHE B 443 CYS B 449 -1 O PHE B 443 N TRP B 377 SHEET 3 AA1 6 GLY B 411 LEU B 415 -1 N ARG B 414 O ASP B 446 SHEET 4 AA1 6 VAL B 397 VAL B 403 -1 N LEU B 399 O ALA B 413 SHEET 5 AA1 6 ARG B 356 SER B 362 1 N ARG B 356 O ILE B 398 SHEET 6 AA1 6 GLU B 479 ILE B 480 -1 O ILE B 480 N PHE B 357 SHEET 1 AA2 2 LYS B 408 PHE B 409 0 SHEET 2 AA2 2 LEU B 453 PRO B 454 -1 O LEU B 453 N PHE B 409 SHEET 1 AA3 6 VAL A 376 TRP A 377 0 SHEET 2 AA3 6 PHE A 443 CYS A 449 -1 O PHE A 443 N TRP A 377 SHEET 3 AA3 6 GLY A 411 LEU A 415 -1 N PHE A 412 O ILE A 448 SHEET 4 AA3 6 SER A 396 VAL A 403 -1 N LEU A 399 O ALA A 413 SHEET 5 AA3 6 ALA A 355 SER A 362 1 N ARG A 356 O ILE A 398 SHEET 6 AA3 6 GLU A 479 ILE A 480 -1 O ILE A 480 N PHE A 357 SHEET 1 AA4 2 LYS A 408 PHE A 409 0 SHEET 2 AA4 2 LEU A 453 PRO A 454 -1 O LEU A 453 N PHE A 409 LINK O3' 6MZ C 1 P C C 101 1555 1555 1.61 LINK O3' 6MZ D 1 P C D 2 1555 1555 1.56 SITE 1 AC1 5 GLY B 344 SER B 346 LYS B 347 HOH B 703 SITE 2 AC1 5 HOH B 708 SITE 1 AC2 7 HIS A 505 ASN B 363 ARG B 404 PRO B 431 SITE 2 AC2 7 ALA B 432 HOH B 711 HOH B 745 SITE 1 AC3 7 ARG A 451 GLU A 452 HOH A 712 HOH A 727 SITE 2 AC3 7 HOH A 749 HOH A 765 HOH A 818 SITE 1 AC4 7 GLY A 344 LYS A 347 HOH A 708 HOH A 785 SITE 2 AC4 7 LYS B 386 GLN B 478 GLU B 479 SITE 1 AC5 4 HIS A 420 HIS A 421 ARG A 451 HOH A 780 SITE 1 AC6 3 ASN A 363 PRO A 431 ALA A 432 SITE 1 AC7 20 LYS B 361 SER B 362 ASN B 363 ASN B 367 SITE 2 AC7 20 TRP B 377 SER B 378 LEU B 380 ARG B 404 SITE 3 AC7 20 TRP B 428 MET B 434 ILE B 473 GLY B 474 SITE 4 AC7 20 ARG B 475 ASP B 476 HOH B 725 HOH B 736 SITE 5 AC7 20 U D 3 HOH D 102 HOH D 103 HOH D 104 CRYST1 40.105 103.503 41.955 90.00 104.69 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 0.024935 0.000000 0.006538 0.00000 SCALE2 0.000000 0.009662 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024641 0.00000 HETATM 1 C2 6MZ C 1 3.498 -0.647 6.359 1.00 26.88 C HETATM 2 C4 6MZ C 1 2.454 0.944 4.969 1.00 27.67 C HETATM 3 C5 6MZ C 1 1.840 -0.047 4.305 1.00 26.57 C HETATM 4 N9 6MZ C 1 2.082 2.113 4.385 1.00 25.46 N HETATM 5 N3 6MZ C 1 3.275 0.667 5.986 1.00 27.00 N HETATM 6 N1 6MZ C 1 2.875 -1.651 5.705 1.00 25.62 N HETATM 7 C6 6MZ C 1 2.066 -1.372 4.679 1.00 22.77 C HETATM 8 N6 6MZ C 1 1.344 -2.491 3.943 1.00 24.75 N HETATM 9 C9 6MZ C 1 1.543 -3.925 4.340 1.00 23.85 C HETATM 10 N7 6MZ C 1 1.089 0.501 3.333 1.00 26.69 N HETATM 11 C8 6MZ C 1 1.223 1.858 3.406 1.00 27.13 C HETATM 12 O5' 6MZ C 1 -0.050 5.260 7.777 1.00 54.54 O HETATM 13 C5' 6MZ C 1 0.058 5.566 6.396 1.00 43.64 C HETATM 14 C4' 6MZ C 1 1.420 5.206 5.856 1.00 38.37 C HETATM 15 O4' 6MZ C 1 1.603 3.778 5.898 1.00 35.30 O HETATM 16 C1' 6MZ C 1 2.550 3.394 4.937 1.00 25.72 C HETATM 17 C2' 6MZ C 1 2.646 4.515 3.891 1.00 24.12 C HETATM 18 O2' 6MZ C 1 3.962 5.034 3.921 1.00 33.72 O HETATM 19 C3' 6MZ C 1 1.658 5.577 4.402 1.00 39.42 C HETATM 20 O3' 6MZ C 1 2.159 6.898 4.280 1.00 54.12 O