HEADER TRANSFERASE 05-APR-23 8OOD TITLE CRYSTAL STRUCTURE OF HUMAN DCAF1 WD40 REPEATS (Q1250L) IN COMPLEX WITH TITLE 2 COMPOUND 15 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DDB1- AND CUL4-ASSOCIATED FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HIV-1 VPR-BINDING PROTEIN,VPRBP,SERINE/THREONINE-PROTEIN COMPND 5 KINASE VPRBP,VPR-INTERACTING PROTEIN; COMPND 6 EC: 2.7.11.1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DCAF1, KIAA0800, RIP, VPRBP; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS DCAF1, LIGASE, COMPOUND, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.SCHROEDER,M.RENATUS REVDAT 2 19-JUN-24 8OOD 1 REMARK REVDAT 1 24-MAY-23 8OOD 0 JRNL AUTH M.SCHRODER,M.RENATUS,C.R.THOMA JRNL TITL REINSTATING TARGETED PROTEIN DEGRADATION WITH DCAF1 PROTACS JRNL TITL 2 IN CRBN PROTAC RESISTANT SETTINGS JRNL REF BIORXIV 2023 JRNL REFN ISSN 2692-8205 JRNL DOI 10.1101/2023.04.09.536153 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN 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) : 52.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 74110 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.955 REMARK 3 FREE R VALUE TEST SET COUNT : 3672 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4964 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.3680 REMARK 3 BIN FREE R VALUE SET COUNT : 267 REMARK 3 BIN FREE R VALUE : 0.3810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2384 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 104 REMARK 3 SOLVENT ATOMS : 316 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.22400 REMARK 3 B22 (A**2) : 0.22400 REMARK 3 B33 (A**2) : -0.72800 REMARK 3 B12 (A**2) : 0.11200 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.059 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.059 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.041 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.230 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2788 ; 0.021 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2468 ; 0.001 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3804 ; 2.500 ; 1.700 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5685 ; 1.615 ; 1.578 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 342 ; 7.982 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 142 ;33.765 ;22.042 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 445 ;13.465 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;18.377 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 352 ; 0.365 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3200 ; 0.015 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 659 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 509 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 54 ; 0.172 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1242 ; 0.185 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 291 ; 0.207 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.068 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1313 ; 1.487 ; 1.298 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1310 ; 1.464 ; 1.296 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1672 ; 2.407 ; 1.936 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1673 ; 2.409 ; 1.937 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1475 ; 2.563 ; 1.744 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1357 ; 2.440 ; 1.627 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2132 ; 3.787 ; 2.476 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1967 ; 3.605 ; 2.307 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1080 A 1389 REMARK 3 ORIGIN FOR THE GROUP (A): -14.9699 -31.6907 11.4333 REMARK 3 T TENSOR REMARK 3 T11: 0.0342 T22: 0.0035 REMARK 3 T33: 0.0105 T12: -0.0087 REMARK 3 T13: 0.0024 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 1.4341 L22: 0.8527 REMARK 3 L33: 0.6450 L12: -0.5092 REMARK 3 L13: 0.1194 L23: 0.1530 REMARK 3 S TENSOR REMARK 3 S11: 0.0064 S12: 0.0382 S13: -0.1120 REMARK 3 S21: -0.0287 S22: -0.0013 S23: 0.0666 REMARK 3 S31: 0.0484 S32: -0.0152 S33: -0.0051 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8OOD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-APR-23. REMARK 100 THE DEPOSITION ID IS D_1292129716. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74179 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.497 REMARK 200 RESOLUTION RANGE LOW (A) : 52.259 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 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) : 1.52 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 1.72600 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.13M LISO4, 0.1M TRIS PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 77.57433 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 155.14867 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 116.36150 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 193.93583 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.78717 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 77.57433 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 155.14867 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 193.93583 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 116.36150 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 38.78717 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 C ACT A1502 LIES ON A SPECIAL POSITION. REMARK 375 CH3 ACT A1502 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1609 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1902 LIES ON A SPECIAL POSITION. 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 GLY A 1035 REMARK 465 GLY A 1036 REMARK 465 GLY A 1037 REMARK 465 ARG A 1038 REMARK 465 GLU A 1039 REMARK 465 PRO A 1040 REMARK 465 LYS A 1041 REMARK 465 GLN A 1042 REMARK 465 ARG A 1043 REMARK 465 ARG A 1044 REMARK 465 GLN A 1045 REMARK 465 ALA A 1046 REMARK 465 PRO A 1047 REMARK 465 ILE A 1048 REMARK 465 ASN A 1049 REMARK 465 PHE A 1050 REMARK 465 THR A 1051 REMARK 465 SER A 1052 REMARK 465 ARG A 1053 REMARK 465 LEU A 1054 REMARK 465 ASN A 1055 REMARK 465 ARG A 1056 REMARK 465 ARG A 1057 REMARK 465 ALA A 1058 REMARK 465 SER A 1059 REMARK 465 PHE A 1060 REMARK 465 PRO A 1061 REMARK 465 LYS A 1062 REMARK 465 TYR A 1063 REMARK 465 GLY A 1064 REMARK 465 GLY A 1065 REMARK 465 VAL A 1066 REMARK 465 ASP A 1067 REMARK 465 GLY A 1068 REMARK 465 GLY A 1069 REMARK 465 CYS A 1070 REMARK 465 PHE A 1071 REMARK 465 ASP A 1072 REMARK 465 ARG A 1073 REMARK 465 HIS A 1074 REMARK 465 LEU A 1075 REMARK 465 ILE A 1076 REMARK 465 PHE A 1077 REMARK 465 SER A 1078 REMARK 465 ARG A 1079 REMARK 465 ASP A 1316 REMARK 465 ASP A 1317 REMARK 465 GLU A 1318 REMARK 465 ASP A 1319 REMARK 465 ASP A 1320 REMARK 465 LEU A 1321 REMARK 465 MET A 1322 REMARK 465 GLU A 1323 REMARK 465 GLU A 1324 REMARK 465 ARG A 1325 REMARK 465 GLY A 1390 REMARK 465 ARG A 1391 REMARK 465 GLN A 1392 REMARK 465 ARG A 1393 REMARK 465 LEU A 1394 REMARK 465 ALA A 1395 REMARK 465 GLU A 1396 REMARK 465 ASP A 1397 REMARK 465 GLU A 1398 REMARK 465 ASP A 1399 REMARK 465 GLU A 1400 REMARK 465 GLU A 1401 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 HD1 HIS A 1267 H ASN A 1269 1.09 REMARK 500 HG SER A 1136 H TRP A 1156 1.26 REMARK 500 HO2 EDO A 1505 O HOH A 1604 1.43 REMARK 500 HE ARG A 1283 O HOH A 1601 1.52 REMARK 500 O HOH A 1649 O HOH A 1747 1.84 REMARK 500 O HOH A 1603 O HOH A 1821 2.07 REMARK 500 O HOH A 1608 O HOH A 1876 2.07 REMARK 500 NE ARG A 1283 O HOH A 1601 2.08 REMARK 500 O HOH A 1722 O HOH A 1728 2.08 REMARK 500 O MET A 1326 O HOH A 1602 2.14 REMARK 500 O1 EDO A 1506 O HOH A 1603 2.17 REMARK 500 O HOH A 1781 O HOH A 1892 2.18 REMARK 500 O HOH A 1853 O HOH A 1858 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 1900 O HOH A 1900 12545 0.94 REMARK 500 O HOH A 1665 O HOH A 1665 12545 0.96 REMARK 500 O HOH A 1822 O HOH A 1822 12555 1.02 REMARK 500 O HOH A 1786 O HOH A 1803 12555 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A1106 C ARG A1106 O 0.115 REMARK 500 GLU A1370 CD GLU A1370 OE2 0.085 REMARK 500 SER A1374 CB SER A1374 OG -0.079 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 A1191 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A1191 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP A1295 CB - CG - OD2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ARG A1298 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A1298 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 PRO A1329 N - CA - CB ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG A1352 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A1385 CG - CD - NE ANGL. DEV. = -15.1 DEGREES REMARK 500 ARG A1385 NE - CZ - NH2 ANGL. DEV. = -4.0 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 ASN A1090 24.70 81.10 REMARK 500 ARG A1106 -4.80 73.25 REMARK 500 TRP A1156 67.85 -157.91 REMARK 500 TRP A1156 67.85 -159.58 REMARK 500 SER A1168 -44.25 81.46 REMARK 500 ASN A1276 -118.51 58.23 REMARK 500 ASP A1381 73.97 -151.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLU A1178 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 VY3 A 1509 REMARK 610 VY3 A 1510 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A1114 O REMARK 620 2 ASN A1132 OD1 121.7 REMARK 620 3 HIS A1134 O 114.1 102.7 REMARK 620 4 HOH A1637 O 96.2 103.8 119.0 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8OO5 RELATED DB: PDB DBREF 8OOD A 1039 1401 UNP Q9Y4B6 DCAF1_HUMAN 1039 1401 SEQADV 8OOD GLY A 1035 UNP Q9Y4B6 EXPRESSION TAG SEQADV 8OOD GLY A 1036 UNP Q9Y4B6 EXPRESSION TAG SEQADV 8OOD GLY A 1037 UNP Q9Y4B6 EXPRESSION TAG SEQADV 8OOD ARG A 1038 UNP Q9Y4B6 EXPRESSION TAG SEQADV 8OOD LEU A 1250 UNP Q9Y4B6 GLN 1250 ENGINEERED MUTATION SEQRES 1 A 367 GLY GLY GLY ARG GLU PRO LYS GLN ARG ARG GLN ALA PRO SEQRES 2 A 367 ILE ASN PHE THR SER ARG LEU ASN ARG ARG ALA SER PHE SEQRES 3 A 367 PRO LYS TYR GLY GLY VAL ASP GLY GLY CYS PHE ASP ARG SEQRES 4 A 367 HIS LEU ILE PHE SER ARG PHE ARG PRO ILE SER VAL PHE SEQRES 5 A 367 ARG GLU ALA ASN GLU ASP GLU SER GLY PHE THR CYS CYS SEQRES 6 A 367 ALA PHE SER ALA ARG GLU ARG PHE LEU MET LEU GLY THR SEQRES 7 A 367 CYS THR GLY GLN LEU LYS LEU TYR ASN VAL PHE SER GLY SEQRES 8 A 367 GLN GLU GLU ALA SER TYR ASN CYS HIS ASN SER ALA ILE SEQRES 9 A 367 THR HIS LEU GLU PRO SER ARG ASP GLY SER LEU LEU LEU SEQRES 10 A 367 THR SER ALA THR TRP SER GLN PRO LEU SER ALA LEU TRP SEQRES 11 A 367 GLY MET LYS SER VAL PHE ASP MET LYS HIS SER PHE THR SEQRES 12 A 367 GLU ASP HIS TYR VAL GLU PHE SER LYS HIS SER GLN ASP SEQRES 13 A 367 ARG VAL ILE GLY THR LYS GLY ASP ILE ALA HIS ILE TYR SEQRES 14 A 367 ASP ILE GLN THR GLY ASN LYS LEU LEU THR LEU PHE ASN SEQRES 15 A 367 PRO ASP LEU ALA ASN ASN TYR LYS ARG ASN CYS ALA THR SEQRES 16 A 367 PHE ASN PRO THR ASP ASP LEU VAL LEU ASN ASP GLY VAL SEQRES 17 A 367 LEU TRP ASP VAL ARG SER ALA LEU ALA ILE HIS LYS PHE SEQRES 18 A 367 ASP LYS PHE ASN MET ASN ILE SER GLY VAL PHE HIS PRO SEQRES 19 A 367 ASN GLY LEU GLU VAL ILE ILE ASN THR GLU ILE TRP ASP SEQRES 20 A 367 LEU ARG THR PHE HIS LEU LEU HIS THR VAL PRO ALA LEU SEQRES 21 A 367 ASP GLN CYS ARG VAL VAL PHE ASN HIS THR GLY THR VAL SEQRES 22 A 367 MET TYR GLY ALA MET LEU GLN ALA ASP ASP GLU ASP ASP SEQRES 23 A 367 LEU MET GLU GLU ARG MET LYS SER PRO PHE GLY SER SER SEQRES 24 A 367 PHE ARG THR PHE ASN ALA THR ASP TYR LYS PRO ILE ALA SEQRES 25 A 367 THR ILE ASP VAL LYS ARG ASN ILE PHE ASP LEU CYS THR SEQRES 26 A 367 ASP THR LYS ASP CYS TYR LEU ALA VAL ILE GLU ASN GLN SEQRES 27 A 367 GLY SER MET ASP ALA LEU ASN MET ASP THR VAL CYS ARG SEQRES 28 A 367 LEU TYR GLU VAL GLY ARG GLN ARG LEU ALA GLU ASP GLU SEQRES 29 A 367 ASP GLU GLU HET MG A1501 1 HET ACT A1502 7 HET ACT A1503 7 HET EDO A1504 10 HET EDO A1505 10 HET EDO A1506 10 HET EDO A1507 10 HET EDO A1508 10 HET VY3 A1509 43 HET VY3 A1510 64 HETNAM MG MAGNESIUM ION HETNAM ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM VY3 ~{N}-[2-[2-[2-[2-[2-[2-[3-[4-[4-(2-AZANYLETHYLAMINO)-2- HETNAM 2 VY3 [1-(4-CHLOROPHENYL)CYCLOPENTYL]QUINAZOLIN-7- HETNAM 3 VY3 YL]PIPERAZIN-1-YL]-3-OXIDANYLIDENE- HETNAM 4 VY3 PROPOXY]ETHOXY]ETHOXY]ETHOXY]ETHOXY]ETHOXY]ETHYL]ETHAN HETNAM 5 VY3 AMIDE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MG MG 2+ FORMUL 3 ACT 2(C2 H3 O2 1-) FORMUL 5 EDO 5(C2 H6 O2) FORMUL 10 VY3 2(C42 H62 CL N7 O8) FORMUL 12 HOH *316(H2 O) HELIX 1 AA1 PRO A 1292 ASP A 1295 5 4 SHEET 1 AA1 4 ARG A1081 ARG A1087 0 SHEET 2 AA1 4 THR A1382 GLU A1388 -1 O LEU A1386 N ILE A1083 SHEET 3 AA1 4 TYR A1365 ASN A1371 -1 N LEU A1366 O TYR A1387 SHEET 4 AA1 4 ASN A1353 THR A1359 -1 N CYS A1358 O ALA A1367 SHEET 1 AA2 4 PHE A1096 PHE A1101 0 SHEET 2 AA2 4 PHE A1107 THR A1112 -1 O MET A1109 N ALA A1100 SHEET 3 AA2 4 GLN A1116 ASN A1121 -1 O TYR A1120 N LEU A1108 SHEET 4 AA2 4 GLU A1127 ASN A1132 -1 O GLU A1128 N LEU A1119 SHEET 1 AA3 4 ILE A1138 PRO A1143 0 SHEET 2 AA3 4 LEU A1149 ALA A1154 -1 O SER A1153 N THR A1139 SHEET 3 AA3 4 SER A1161 GLY A1165 -1 O TRP A1164 N LEU A1150 SHEET 4 AA3 4 ASP A1171 PHE A1176 -1 O LYS A1173 N LEU A1163 SHEET 1 AA4 4 TYR A1181 PHE A1184 0 SHEET 2 AA4 4 ARG A1191 LYS A1196 -1 O ILE A1193 N GLU A1183 SHEET 3 AA4 4 ILE A1199 ASP A1204 -1 O TYR A1203 N VAL A1192 SHEET 4 AA4 4 LYS A1210 LEU A1214 -1 O LEU A1214 N ALA A1200 SHEET 1 AA5 4 THR A1229 PHE A1230 0 SHEET 2 AA5 4 LEU A1236 ASN A1239 -1 O LEU A1238 N THR A1229 SHEET 3 AA5 4 VAL A1242 ASP A1245 -1 O TRP A1244 N VAL A1237 SHEET 4 AA5 4 LEU A1250 LYS A1254 -1 O ILE A1252 N LEU A1243 SHEET 1 AA6 4 VAL A1265 PHE A1266 0 SHEET 2 AA6 4 GLU A1272 ILE A1275 -1 O ILE A1274 N VAL A1265 SHEET 3 AA6 4 GLU A1278 ASP A1281 -1 O GLU A1278 N ILE A1275 SHEET 4 AA6 4 LEU A1287 THR A1290 -1 O LEU A1288 N ILE A1279 SHEET 1 AA7 4 CYS A1297 PHE A1301 0 SHEET 2 AA7 4 VAL A1307 LEU A1313 -1 O TYR A1309 N VAL A1300 SHEET 3 AA7 4 PHE A1330 ASN A1338 -1 O ARG A1335 N GLY A1310 SHEET 4 AA7 4 PRO A1344 ASP A1349 -1 O ILE A1348 N PHE A1334 LINK O THR A1114 MG MG A1501 1555 1555 1.93 LINK OD1 ASN A1132 MG MG A1501 1555 1555 2.00 LINK O HIS A1134 MG MG A1501 1555 1555 1.92 LINK MG MG A1501 O HOH A1637 1555 1555 2.04 CISPEP 1 GLN A 1158 PRO A 1159 0 2.83 CRYST1 81.496 81.496 232.723 90.00 90.00 120.00 P 61 2 2 12 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 0.012271 0.007084 0.000000 0.00000 SCALE2 0.000000 0.014169 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004297 0.00000