HEADER HYDROLASE, LIGASE/INHIBITOR 27-OCT-17 6BG5 TITLE STRUCTURE OF 1-(BENZO[D][1,3]DIOXOL-5-YLMETHYL)-1-(1-PROPYLPIPERIDIN- TITLE 2 4-YL)-3-(3-(TRIFLUOROMETHYL)PHENYL)UREA BOUND TO DCN1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOLYSIN, DCN1-LIKE PROTEIN 1 CHIMERA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PONY; COMPND 5 SYNONYM: DCUN1 DOMAIN-CONTAINING PROTEIN 1,DEFECTIVE IN CULLIN COMPND 6 NEDDYLATION PROTEIN 1-LIKE PROTEIN 1,SQUAMOUS CELL CARCINOMA-RELATED COMPND 7 ONCOGENE,LYSIS PROTEIN,LYSOZYME,MURAMIDASE; COMPND 8 EC: 3.2.1.17; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4, HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 10665, 9606; SOURCE 5 GENE: E, DCUN1D1, DCUN1L1, RP42, SCCRO; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSF DUET KEYWDS E3 LIGASE, HYDROLASE, LIGASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.K.GUY,B.A.SCHULMAN,D.C.SCOTT,J.T.HAMMILL REVDAT 2 04-OCT-23 6BG5 1 REMARK REVDAT 1 26-SEP-18 6BG5 0 JRNL AUTH J.T.HAMMILL,D.C.SCOTT,J.MIN,M.C.CONNELLY,G.HOLBROOK,F.ZHU, JRNL AUTH 2 A.MATHENY,L.YANG,B.SINGH,B.A.SCHULMAN,R.K.GUY JRNL TITL PIPERIDINYL UREAS CHEMICALLY CONTROL DEFECTIVE IN CULLIN JRNL TITL 2 NEDDYLATION 1 (DCN1)-MEDIATED CULLIN NEDDYLATION. JRNL REF J. MED. CHEM. V. 61 2680 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 29547696 JRNL DOI 10.1021/ACS.JMEDCHEM.7B01277 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 141464 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 7054 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 49.2203 - 3.4449 0.97 4678 255 0.1526 0.1825 REMARK 3 2 3.4449 - 2.7344 0.99 4733 246 0.1485 0.1815 REMARK 3 3 2.7344 - 2.3888 0.97 4625 224 0.1503 0.1755 REMARK 3 4 2.3888 - 2.1704 0.98 4659 240 0.1419 0.1589 REMARK 3 5 2.1704 - 2.0148 0.98 4636 257 0.1373 0.1562 REMARK 3 6 2.0148 - 1.8960 0.98 4654 239 0.1457 0.1667 REMARK 3 7 1.8960 - 1.8010 0.98 4618 250 0.1467 0.1767 REMARK 3 8 1.8010 - 1.7226 0.96 4507 246 0.1463 0.1600 REMARK 3 9 1.7226 - 1.6563 0.96 4564 247 0.1447 0.1651 REMARK 3 10 1.6563 - 1.5992 0.96 4578 207 0.1364 0.1578 REMARK 3 11 1.5992 - 1.5492 0.96 4596 229 0.1338 0.1561 REMARK 3 12 1.5492 - 1.5049 0.96 4522 261 0.1356 0.1805 REMARK 3 13 1.5049 - 1.4653 0.96 4525 217 0.1372 0.1799 REMARK 3 14 1.4653 - 1.4295 0.95 4523 242 0.1413 0.1673 REMARK 3 15 1.4295 - 1.3970 0.95 4457 231 0.1432 0.1701 REMARK 3 16 1.3970 - 1.3673 0.95 4505 239 0.1394 0.1689 REMARK 3 17 1.3673 - 1.3399 0.95 4394 263 0.1378 0.1779 REMARK 3 18 1.3399 - 1.3146 0.95 4519 218 0.1373 0.1828 REMARK 3 19 1.3146 - 1.2912 0.94 4461 233 0.1369 0.1695 REMARK 3 20 1.2912 - 1.2693 0.94 4481 231 0.1369 0.1541 REMARK 3 21 1.2693 - 1.2488 0.94 4394 234 0.1381 0.1593 REMARK 3 22 1.2488 - 1.2296 0.94 4473 219 0.1408 0.1703 REMARK 3 23 1.2296 - 1.2115 0.93 4376 222 0.1411 0.1877 REMARK 3 24 1.2115 - 1.1944 0.93 4426 238 0.1401 0.1686 REMARK 3 25 1.1944 - 1.1783 0.93 4391 217 0.1395 0.1630 REMARK 3 26 1.1783 - 1.1630 0.93 4364 238 0.1474 0.1521 REMARK 3 27 1.1630 - 1.1484 0.92 4328 283 0.1531 0.1892 REMARK 3 28 1.1484 - 1.1346 0.92 4325 225 0.1625 0.2040 REMARK 3 29 1.1346 - 1.1214 0.90 4277 197 0.1765 0.1928 REMARK 3 30 1.1214 - 1.1088 0.81 3821 206 0.2043 0.2198 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.18 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 : 0.011 3134 REMARK 3 ANGLE : 1.372 4251 REMARK 3 CHIRALITY : 0.080 450 REMARK 3 PLANARITY : 0.008 552 REMARK 3 DIHEDRAL : 12.795 1216 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 6BG5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1000230756. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-14 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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 141508 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.29100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: 2LZM, 3TDU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6% PEG3350, 0.2M NH4BR, EVAPORATION, REMARK 280 TEMPERATURE 277K 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 48.38150 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 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 -21 REMARK 465 GLY A -20 REMARK 465 SER A -19 REMARK 465 SER A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 ILE A 1251 REMARK 465 ALA A 1252 REMARK 465 GLY A 1253 REMARK 465 THR A 1254 REMARK 465 LYS A 1255 REMARK 465 SER A 1256 REMARK 465 THR A 1257 REMARK 465 THR A 1258 REMARK 465 VAL A 1259 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 HIS A -12 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A1120 CG CD OE1 NE2 REMARK 470 HIS A1204 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A1205 CG CD CE NZ REMARK 470 ARG A1206 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 HH22 ARG A 1248 O HOH A 1401 1.22 REMARK 500 O HOH A 1431 O HOH A 1928 1.58 REMARK 500 O HOH A 1672 O HOH A 1864 1.84 REMARK 500 O HOH A 1752 O HOH A 1801 1.86 REMARK 500 O HOH A 1968 O HOH A 2064 1.86 REMARK 500 O HOH A 1637 O HOH A 1681 1.89 REMARK 500 O HOH A 1428 O HOH A 1877 1.91 REMARK 500 O HOH A 1907 O HOH A 2067 1.93 REMARK 500 O HOH A 1548 O HOH A 1680 1.94 REMARK 500 O HOH A 1743 O HOH A 1846 1.95 REMARK 500 NH2 ARG A 1248 O HOH A 1401 1.98 REMARK 500 O HOH A 1549 O HOH A 1829 1.98 REMARK 500 O HOH A 1410 O HOH A 1748 2.02 REMARK 500 OE1 GLU A 1066 O HOH A 1402 2.02 REMARK 500 O HOH A 1536 O HOH A 1954 2.03 REMARK 500 O HOH A 1651 O HOH A 1894 2.03 REMARK 500 O HOH A 1970 O HOH A 2045 2.04 REMARK 500 O HOH A 1821 O HOH A 1901 2.05 REMARK 500 OG SER A 1099 O HOH A 1403 2.05 REMARK 500 O HOH A 1822 O HOH A 1933 2.07 REMARK 500 O HOH A 1963 O HOH A 2014 2.08 REMARK 500 O HOH A 1795 O HOH A 1864 2.08 REMARK 500 O HOH A 1998 O HOH A 2060 2.09 REMARK 500 O HOH A 1714 O HOH A 1981 2.10 REMARK 500 O HOH A 2057 O HOH A 2087 2.10 REMARK 500 O HOH A 1837 O HOH A 1917 2.11 REMARK 500 OE1 GLU A 45 O HOH A 1404 2.13 REMARK 500 OD1 ASN A 1163 O HOH A 1405 2.13 REMARK 500 O HOH A 1607 O HOH A 1943 2.14 REMARK 500 O HOH A 1555 O HOH A 1896 2.14 REMARK 500 O HOH A 1907 O HOH A 2046 2.15 REMARK 500 O HOH A 1431 O HOH A 1781 2.15 REMARK 500 O HOH A 1635 O HOH A 1929 2.17 REMARK 500 O HOH A 1503 O HOH A 1867 2.18 REMARK 500 O HOH A 1459 O HOH A 1757 2.18 REMARK 500 NZ LYS A 147 O HOH A 1406 2.18 REMARK 500 O HOH A 1673 O HOH A 1750 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 1779 O HOH A 1881 2555 1.51 REMARK 500 O HOH A 1846 O HOH A 2033 1655 1.82 REMARK 500 O HOH A 1432 O HOH A 2071 1554 1.86 REMARK 500 O HOH A 2031 O HOH A 2069 2555 2.04 REMARK 500 O HOH A 2056 O HOH A 2092 1655 2.10 REMARK 500 O HOH A 1809 O HOH A 1843 1656 2.12 REMARK 500 O HOH A 1412 O HOH A 1692 1554 2.15 REMARK 500 NZ LYS A 1171 O HOH A 1507 1655 2.15 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 ARG A 76 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 PHE A1117 CB - CG - CD1 ANGL. DEV. = 4.2 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 PHE A 114 48.73 -83.99 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 A2087 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A2088 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A2089 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH A2090 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A2091 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH A2092 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 DQD A 1301 DBREF 6BG5 A 1 164 UNP P00720 ENLYS_BPT4 1 164 DBREF 6BG5 A 1062 1259 UNP Q96GG9 DCNL1_HUMAN 62 259 SEQADV 6BG5 MET A -21 UNP P00720 INITIATING METHIONINE SEQADV 6BG5 GLY A -20 UNP P00720 EXPRESSION TAG SEQADV 6BG5 SER A -19 UNP P00720 EXPRESSION TAG SEQADV 6BG5 SER A -18 UNP P00720 EXPRESSION TAG SEQADV 6BG5 HIS A -17 UNP P00720 EXPRESSION TAG SEQADV 6BG5 HIS A -16 UNP P00720 EXPRESSION TAG SEQADV 6BG5 HIS A -15 UNP P00720 EXPRESSION TAG SEQADV 6BG5 HIS A -14 UNP P00720 EXPRESSION TAG SEQADV 6BG5 HIS A -13 UNP P00720 EXPRESSION TAG SEQADV 6BG5 HIS A -12 UNP P00720 EXPRESSION TAG SEQADV 6BG5 SER A -11 UNP P00720 EXPRESSION TAG SEQADV 6BG5 GLN A -10 UNP P00720 EXPRESSION TAG SEQADV 6BG5 ASP A -9 UNP P00720 EXPRESSION TAG SEQADV 6BG5 LEU A -8 UNP P00720 EXPRESSION TAG SEQADV 6BG5 GLU A -7 UNP P00720 EXPRESSION TAG SEQADV 6BG5 ASN A -6 UNP P00720 EXPRESSION TAG SEQADV 6BG5 LEU A -5 UNP P00720 EXPRESSION TAG SEQADV 6BG5 TYR A -4 UNP P00720 EXPRESSION TAG SEQADV 6BG5 PHE A -3 UNP P00720 EXPRESSION TAG SEQADV 6BG5 GLN A -2 UNP P00720 EXPRESSION TAG SEQADV 6BG5 GLY A -1 UNP P00720 EXPRESSION TAG SEQADV 6BG5 SER A 0 UNP P00720 EXPRESSION TAG SEQADV 6BG5 GLY A 12 UNP P00720 ARG 12 CONFLICT SEQADV 6BG5 THR A 54 UNP P00720 CYS 54 CONFLICT SEQADV 6BG5 ALA A 97 UNP P00720 CYS 97 CONFLICT SEQADV 6BG5 ARG A 137 UNP P00720 ILE 137 CONFLICT SEQADV 6BG5 THR A 146 UNP P00720 ALA 146 CONFLICT SEQRES 1 A 384 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER GLN ASP SEQRES 2 A 384 LEU GLU ASN LEU TYR PHE GLN GLY SER MET ASN ILE PHE SEQRES 3 A 384 GLU MET LEU ARG ILE ASP GLU GLY LEU ARG LEU LYS ILE SEQRES 4 A 384 TYR LYS ASP THR GLU GLY TYR TYR THR ILE GLY ILE GLY SEQRES 5 A 384 HIS LEU LEU THR LYS SER PRO SER LEU ASN ALA ALA LYS SEQRES 6 A 384 SER GLU LEU ASP LYS ALA ILE GLY ARG ASN THR ASN GLY SEQRES 7 A 384 VAL ILE THR LYS ASP GLU ALA GLU LYS LEU PHE ASN GLN SEQRES 8 A 384 ASP VAL ASP ALA ALA VAL ARG GLY ILE LEU ARG ASN ALA SEQRES 9 A 384 LYS LEU LYS PRO VAL TYR ASP SER LEU ASP ALA VAL ARG SEQRES 10 A 384 ARG ALA ALA LEU ILE ASN MET VAL PHE GLN MET GLY GLU SEQRES 11 A 384 THR GLY VAL ALA GLY PHE THR ASN SER LEU ARG MET LEU SEQRES 12 A 384 GLN GLN LYS ARG TRP ASP GLU ALA ALA VAL ASN LEU ALA SEQRES 13 A 384 LYS SER ARG TRP TYR ASN GLN THR PRO ASN ARG THR LYS SEQRES 14 A 384 ARG VAL ILE THR THR PHE ARG THR GLY THR TRP ASP ALA SEQRES 15 A 384 TYR LYS ASN LEU ARG LYS LYS LEU GLU GLN LEU TYR ASN SEQRES 16 A 384 ARG TYR LYS ASP PRO GLN ASP GLU ASN LYS ILE GLY ILE SEQRES 17 A 384 ASP GLY ILE GLN GLN PHE CYS ASP ASP LEU ALA LEU ASP SEQRES 18 A 384 PRO ALA SER ILE SER VAL LEU ILE ILE ALA TRP LYS PHE SEQRES 19 A 384 ARG ALA ALA THR GLN CYS GLU PHE SER LYS GLN GLU PHE SEQRES 20 A 384 MET ASP GLY MET THR GLU LEU GLY CYS ASP SER ILE GLU SEQRES 21 A 384 LYS LEU LYS ALA GLN ILE PRO LYS MET GLU GLN GLU LEU SEQRES 22 A 384 LYS GLU PRO GLY ARG PHE LYS ASP PHE TYR GLN PHE THR SEQRES 23 A 384 PHE ASN PHE ALA LYS ASN PRO GLY GLN LYS GLY LEU ASP SEQRES 24 A 384 LEU GLU MET ALA ILE ALA TYR TRP ASN LEU VAL LEU ASN SEQRES 25 A 384 GLY ARG PHE LYS PHE LEU ASP LEU TRP ASN LYS PHE LEU SEQRES 26 A 384 LEU GLU HIS HIS LYS ARG SER ILE PRO LYS ASP THR TRP SEQRES 27 A 384 ASN LEU LEU LEU ASP PHE SER THR MET ILE ALA ASP ASP SEQRES 28 A 384 MET SER ASN TYR ASP GLU GLU GLY ALA TRP PRO VAL LEU SEQRES 29 A 384 ILE ASP ASP PHE VAL GLU PHE ALA ARG PRO GLN ILE ALA SEQRES 30 A 384 GLY THR LYS SER THR THR VAL HET DQD A1301 33 HETNAM DQD N-[(2H-1,3-BENZODIOXOL-5-YL)METHYL]-N-(1- HETNAM 2 DQD PROPYLPIPERIDIN-4-YL)-N'-[3-(TRIFLUOROMETHYL) HETNAM 3 DQD PHENYL]UREA FORMUL 2 DQD C24 H28 F3 N3 O3 FORMUL 3 HOH *692(H2 O) HELIX 1 AA1 ASP A -9 TYR A -4 5 6 HELIX 2 AA2 ASN A 2 GLU A 11 1 10 HELIX 3 AA3 SER A 38 GLY A 51 1 14 HELIX 4 AA4 THR A 59 ARG A 80 1 22 HELIX 5 AA5 LEU A 84 LEU A 91 1 8 HELIX 6 AA6 ASP A 92 GLY A 113 1 22 HELIX 7 AA7 PHE A 114 GLN A 123 1 10 HELIX 8 AA8 ARG A 125 LYS A 135 1 11 HELIX 9 AA9 SER A 136 THR A 142 1 7 HELIX 10 AB1 THR A 142 GLY A 156 1 15 HELIX 11 AB2 TRP A 158 TYR A 1072 1 18 HELIX 12 AB3 GLY A 1082 LEU A 1093 1 12 HELIX 13 AB4 SER A 1099 PHE A 1109 1 11 HELIX 14 AB5 LYS A 1119 LEU A 1129 1 11 HELIX 15 AB6 SER A 1133 LEU A 1148 1 16 HELIX 16 AB7 GLY A 1152 LYS A 1166 1 15 HELIX 17 AB8 LEU A 1175 LEU A 1186 1 12 HELIX 18 AB9 PHE A 1192 GLU A 1202 1 11 HELIX 19 AC1 PRO A 1209 ILE A 1223 1 15 HELIX 20 AC2 PRO A 1237 ARG A 1248 1 12 SHEET 1 AA1 3 ARG A 14 LYS A 19 0 SHEET 2 AA1 3 TYR A 25 GLY A 28 -1 O THR A 26 N TYR A 18 SHEET 3 AA1 3 HIS A 31 LEU A 32 -1 O HIS A 31 N ILE A 27 SHEET 1 AA2 3 LYS A1073 ASP A1074 0 SHEET 2 AA2 3 ASP A1077 ILE A1081 -1 O LYS A1080 N ASP A1074 SHEET 3 AA2 3 PHE A1117 SER A1118 -1 O PHE A1117 N ILE A1081 SHEET 1 AA3 2 LEU A1173 ASP A1174 0 SHEET 2 AA3 2 SER A1207 ILE A1208 -1 O ILE A1208 N LEU A1173 SITE 1 AC1 19 LYS A 83 ILE A1083 ILE A1086 GLN A1087 SITE 2 AC1 19 PHE A1089 PRO A1097 VAL A1102 ILE A1105 SITE 3 AC1 19 ALA A1106 THR A1113 GLN A1114 GLU A1116 SITE 4 AC1 19 PHE A1117 PHE A1164 ALA A1180 TYR A1181 SITE 5 AC1 19 HOH A1468 HOH A1665 HOH A1698 CRYST1 34.944 96.763 59.279 90.00 105.61 90.00 P 1 21 1 2 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 0.028617 0.000000 0.007994 0.00000 SCALE2 0.000000 0.010335 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017515 0.00000