HEADER TRANSFERASE 25-MAR-15 4YZM TITLE HUMANIZED ROCO4 BOUND TO LRRK2-IN1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE SERINE/THREONINE-PROTEIN KINASE ROCO4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1019-1292; COMPND 5 SYNONYM: RAS OF COMPLEX PROTEINS AND C-TERMINAL OF ROC 4; COMPND 6 EC: 2.7.11.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DICTYOSTELIUM DISCOIDEUM; SOURCE 3 ORGANISM_COMMON: SLIME MOLD; SOURCE 4 ORGANISM_TAXID: 44689; SOURCE 5 GENE: ROCO4, DDB_G0288251; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX4T1 NTEV KEYWDS ROCO-PROTEIN, KINASE, LRRK2, INHIBITOR, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR B.K.GILSBACH,A.C.MESSIAS,G.ITO,M.SATTLER,D.R.ALESSI,A.WITTINGHOFER, AUTHOR 2 A.KORTHOLT REVDAT 3 10-JAN-24 4YZM 1 REMARK REVDAT 2 27-MAY-15 4YZM 1 JRNL REVDAT 1 06-MAY-15 4YZM 0 JRNL AUTH B.K.GILSBACH,A.C.MESSIAS,G.ITO,M.SATTLER,D.R.ALESSI, JRNL AUTH 2 A.WITTINGHOFER,A.KORTHOLT JRNL TITL STRUCTURAL CHARACTERIZATION OF LRRK2 INHIBITORS. JRNL REF J.MED.CHEM. V. 58 3751 2015 JRNL REFN ISSN 0022-2623 JRNL PMID 25897865 JRNL DOI 10.1021/JM5018779 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 13688 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 719 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 886 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.68 REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.4070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4203 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : 0.00000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.491 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.345 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 38.046 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.843 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4512 ; 0.014 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6108 ; 1.943 ; 2.003 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 534 ; 7.271 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 199 ;40.100 ;24.271 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 792 ;19.163 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;22.897 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 652 ; 0.142 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3397 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 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 -10 A 9999 REMARK 3 ORIGIN FOR THE GROUP (A): -20.8366 0.0293 -31.7111 REMARK 3 T TENSOR REMARK 3 T11: 0.0675 T22: 0.0923 REMARK 3 T33: 0.0828 T12: 0.0043 REMARK 3 T13: -0.0056 T23: -0.0219 REMARK 3 L TENSOR REMARK 3 L11: 1.4287 L22: 1.6092 REMARK 3 L33: 1.5744 L12: 0.7800 REMARK 3 L13: -0.6515 L23: -0.2203 REMARK 3 S TENSOR REMARK 3 S11: 0.1326 S12: -0.1586 S13: 0.0192 REMARK 3 S21: 0.2589 S22: -0.1101 S23: -0.0303 REMARK 3 S31: 0.0853 S32: 0.0370 S33: -0.0226 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B -10 B 9999 REMARK 3 ORIGIN FOR THE GROUP (A): -1.0339 41.8263 -15.1241 REMARK 3 T TENSOR REMARK 3 T11: 0.0610 T22: 0.0567 REMARK 3 T33: 0.0645 T12: 0.0015 REMARK 3 T13: 0.0103 T23: 0.0061 REMARK 3 L TENSOR REMARK 3 L11: 1.4413 L22: 1.5453 REMARK 3 L33: 2.0793 L12: 0.2828 REMARK 3 L13: 0.3038 L23: 0.3571 REMARK 3 S TENSOR REMARK 3 S11: 0.1503 S12: -0.0382 S13: -0.1019 REMARK 3 S21: 0.2039 S22: -0.0977 S23: -0.0238 REMARK 3 S31: -0.1111 S32: -0.0663 S33: -0.0526 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4YZM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000208002. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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) : 0.97889 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13688 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 44.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.36600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.360 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: 4F0F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM 1,3-BIS(TRIS REMARK 280 (HYDROXYMETHYL)METHYLAMINO)PROPANE (PH 8.5), 200 MM NA/K REMARK 280 TARTRATE, 11% (M/V) PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 21.51500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 88.85500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.53500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 88.85500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.51500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.53500 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLY A 1006 REMARK 465 ALA A 1007 REMARK 465 MET A 1008 REMARK 465 GLY A 1009 REMARK 465 GLY A 1010 REMARK 465 SER A 1011 REMARK 465 GLU A 1012 REMARK 465 PHE A 1013 REMARK 465 PRO A 1014 REMARK 465 LYS A 1015 REMARK 465 SER A 1016 REMARK 465 GLY A 1060 REMARK 465 ASP A 1061 REMARK 465 SER A 1062 REMARK 465 GLU A 1063 REMARK 465 GLY A 1064 REMARK 465 GLU A 1065 REMARK 465 SER A 1184 REMARK 465 VAL A 1185 REMARK 465 HIS A 1186 REMARK 465 SER A 1187 REMARK 465 VAL A 1188 REMARK 465 SER A 1189 REMARK 465 GLY A 1190 REMARK 465 LEU A 1191 REMARK 465 GLU A 1208 REMARK 465 SER A 1209 REMARK 465 GLY B 1006 REMARK 465 ALA B 1007 REMARK 465 MET B 1008 REMARK 465 GLY B 1009 REMARK 465 GLY B 1010 REMARK 465 SER B 1011 REMARK 465 GLU B 1012 REMARK 465 PHE B 1013 REMARK 465 PRO B 1014 REMARK 465 LYS B 1015 REMARK 465 SER B 1016 REMARK 465 GLY B 1060 REMARK 465 ASP B 1061 REMARK 465 SER B 1062 REMARK 465 GLU B 1063 REMARK 465 GLN B 1183 REMARK 465 SER B 1184 REMARK 465 VAL B 1185 REMARK 465 HIS B 1186 REMARK 465 SER B 1187 REMARK 465 VAL B 1188 REMARK 465 SER B 1189 REMARK 465 GLY B 1190 REMARK 465 GLU B 1206 REMARK 465 GLU B 1207 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 THR A1066 OG1 CG2 REMARK 470 LYS A1120 O REMARK 470 LYS B1120 O REMARK 470 LYS B1277 CG CD CE NZ 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 LEU A 1045 O ASP A 1048 1.42 REMARK 500 OD2 ASP B 1177 MG MG B 1302 1.44 REMARK 500 OD2 ASP A 1154 MG MG A 1302 1.63 REMARK 500 O ALA A 1199 OG1 THR A 1202 1.67 REMARK 500 O ILE A 1058 NZ LYS A 1071 1.78 REMARK 500 OD1 ASP B 1048 OG SER B 1050 1.86 REMARK 500 O ASP A 1154 ND2 ASN A 1159 1.93 REMARK 500 O TYR A 1224 OG1 THR A 1228 1.93 REMARK 500 N LYS B 1092 OE2 GLU B 1106 2.06 REMARK 500 OD1 ASN A 1159 OD2 ASP A 1177 2.08 REMARK 500 O MET A 1068 N GLU A 1070 2.08 REMARK 500 O LEU A 1270 OG SER A 1273 2.12 REMARK 500 O SER A 1273 NH2 ARG A 1279 2.13 REMARK 500 O VAL B 1079 OG SER B 1083 2.14 REMARK 500 CD2 LEU A 1192 NE2 GLN A 1196 2.17 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 HIS A1152 NE2 HIS A1152 CD2 -0.066 REMARK 500 TYR A1217 CE1 TYR A1217 CZ -0.083 REMARK 500 ASN B1245 N ASN B1245 CA 0.143 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 HIS A1098 N - CA - C ANGL. DEV. = 18.2 DEGREES REMARK 500 ASP A1177 N - CA - C ANGL. DEV. = 19.2 DEGREES REMARK 500 GLY A1179 N - CA - C ANGL. DEV. = -21.6 DEGREES REMARK 500 PHE A1195 N - CA - CB ANGL. DEV. = -26.9 DEGREES REMARK 500 PHE A1195 N - CA - C ANGL. DEV. = 31.2 DEGREES REMARK 500 GLY B1035 N - CA - C ANGL. DEV. = -32.4 DEGREES REMARK 500 GLU B1065 N - CA - C ANGL. DEV. = 19.6 DEGREES REMARK 500 ALA B1176 N - CA - C ANGL. DEV. = 22.9 DEGREES REMARK 500 GLY B1179 N - CA - C ANGL. DEV. = -20.3 DEGREES REMARK 500 ASN B1245 C - N - CA ANGL. DEV. = 18.6 DEGREES REMARK 500 ASN B1245 C - N - CA ANGL. DEV. = 18.1 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 GLU A1067 1.43 81.44 REMARK 500 ILE A1069 51.52 -67.88 REMARK 500 ASN A1086 84.40 -150.49 REMARK 500 ARG A1153 -2.12 76.35 REMARK 500 ASP A1154 44.10 -143.16 REMARK 500 PHE A1178 21.92 -76.55 REMARK 500 ASN A1194 -169.80 -75.84 REMARK 500 PHE A1195 10.04 -60.69 REMARK 500 ARG B1153 -7.00 76.23 REMARK 500 ASP B1154 56.99 -144.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4K4 A 1301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4K4 B 1301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 1302 DBREF 4YZM A 1019 1292 UNP Q6XHB2 ROCO4_DICDI 1019 1292 DBREF 4YZM B 1019 1292 UNP Q6XHB2 ROCO4_DICDI 1019 1292 SEQADV 4YZM GLY A 1006 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM ALA A 1007 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM MET A 1008 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM GLY A 1009 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM GLY A 1010 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM SER A 1011 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM GLU A 1012 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM PHE A 1013 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM PRO A 1014 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM LYS A 1015 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM SER A 1016 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM ARG A 1017 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM LEU A 1018 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM LEU A 1107 UNP Q6XHB2 PHE 1107 ENGINEERED MUTATION SEQADV 4YZM LEU A 1161 UNP Q6XHB2 PHE 1161 ENGINEERED MUTATION SEQADV 4YZM GLY B 1006 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM ALA B 1007 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM MET B 1008 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM GLY B 1009 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM GLY B 1010 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM SER B 1011 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM GLU B 1012 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM PHE B 1013 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM PRO B 1014 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM LYS B 1015 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM SER B 1016 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM ARG B 1017 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM LEU B 1018 UNP Q6XHB2 EXPRESSION TAG SEQADV 4YZM LEU B 1107 UNP Q6XHB2 PHE 1107 ENGINEERED MUTATION SEQADV 4YZM LEU B 1161 UNP Q6XHB2 PHE 1161 ENGINEERED MUTATION SEQRES 1 A 287 GLY ALA MET GLY GLY SER GLU PHE PRO LYS SER ARG LEU SEQRES 2 A 287 PRO THR LEU ALA ASP ASN GLU ILE GLU TYR GLU LYS GLN SEQRES 3 A 287 ILE GLY LYS GLY GLY PHE GLY LEU VAL HIS LYS GLY ARG SEQRES 4 A 287 LEU VAL LYS ASP LYS SER VAL VAL ALA ILE LYS SER LEU SEQRES 5 A 287 ILE LEU GLY ASP SER GLU GLY GLU THR GLU MET ILE GLU SEQRES 6 A 287 LYS PHE GLN GLU PHE GLN ARG GLU VAL PHE ILE MET SER SEQRES 7 A 287 ASN LEU ASN HIS PRO ASN ILE VAL LYS LEU TYR GLY LEU SEQRES 8 A 287 MET HIS ASN PRO PRO ARG MET VAL MET GLU LEU VAL PRO SEQRES 9 A 287 CYS GLY ASP LEU TYR HIS ARG LEU LEU ASP LYS ALA HIS SEQRES 10 A 287 PRO ILE LYS TRP SER VAL LYS LEU ARG LEU MET LEU ASP SEQRES 11 A 287 ILE ALA LEU GLY ILE GLU TYR MET GLN ASN GLN ASN PRO SEQRES 12 A 287 PRO ILE VAL HIS ARG ASP LEU ARG SER PRO ASN ILE LEU SEQRES 13 A 287 LEU GLN SER LEU ASP GLU ASN ALA PRO VAL CYS ALA LYS SEQRES 14 A 287 VAL ALA ASP PHE GLY LEU SER GLN GLN SER VAL HIS SER SEQRES 15 A 287 VAL SER GLY LEU LEU GLY ASN PHE GLN TRP MET ALA PRO SEQRES 16 A 287 GLU THR ILE GLY ALA GLU GLU GLU SER TYR THR GLU LYS SEQRES 17 A 287 ALA ASP THR TYR SER PHE ALA MET ILE LEU TYR THR ILE SEQRES 18 A 287 LEU THR GLY GLU GLY PRO PHE ASP GLU TYR SER TYR GLY SEQRES 19 A 287 LYS ILE LYS PHE ILE ASN MET ILE ARG GLU GLU GLY LEU SEQRES 20 A 287 ARG PRO THR ILE PRO GLU ASP CYS PRO PRO ARG LEU ARG SEQRES 21 A 287 ASN VAL ILE GLU LEU CYS TRP SER GLY ASP PRO LYS LYS SEQRES 22 A 287 ARG PRO HIS PHE SER TYR ILE VAL LYS GLU LEU SER GLU SEQRES 23 A 287 LEU SEQRES 1 B 287 GLY ALA MET GLY GLY SER GLU PHE PRO LYS SER ARG LEU SEQRES 2 B 287 PRO THR LEU ALA ASP ASN GLU ILE GLU TYR GLU LYS GLN SEQRES 3 B 287 ILE GLY LYS GLY GLY PHE GLY LEU VAL HIS LYS GLY ARG SEQRES 4 B 287 LEU VAL LYS ASP LYS SER VAL VAL ALA ILE LYS SER LEU SEQRES 5 B 287 ILE LEU GLY ASP SER GLU GLY GLU THR GLU MET ILE GLU SEQRES 6 B 287 LYS PHE GLN GLU PHE GLN ARG GLU VAL PHE ILE MET SER SEQRES 7 B 287 ASN LEU ASN HIS PRO ASN ILE VAL LYS LEU TYR GLY LEU SEQRES 8 B 287 MET HIS ASN PRO PRO ARG MET VAL MET GLU LEU VAL PRO SEQRES 9 B 287 CYS GLY ASP LEU TYR HIS ARG LEU LEU ASP LYS ALA HIS SEQRES 10 B 287 PRO ILE LYS TRP SER VAL LYS LEU ARG LEU MET LEU ASP SEQRES 11 B 287 ILE ALA LEU GLY ILE GLU TYR MET GLN ASN GLN ASN PRO SEQRES 12 B 287 PRO ILE VAL HIS ARG ASP LEU ARG SER PRO ASN ILE LEU SEQRES 13 B 287 LEU GLN SER LEU ASP GLU ASN ALA PRO VAL CYS ALA LYS SEQRES 14 B 287 VAL ALA ASP PHE GLY LEU SER GLN GLN SER VAL HIS SER SEQRES 15 B 287 VAL SER GLY LEU LEU GLY ASN PHE GLN TRP MET ALA PRO SEQRES 16 B 287 GLU THR ILE GLY ALA GLU GLU GLU SER TYR THR GLU LYS SEQRES 17 B 287 ALA ASP THR TYR SER PHE ALA MET ILE LEU TYR THR ILE SEQRES 18 B 287 LEU THR GLY GLU GLY PRO PHE ASP GLU TYR SER TYR GLY SEQRES 19 B 287 LYS ILE LYS PHE ILE ASN MET ILE ARG GLU GLU GLY LEU SEQRES 20 B 287 ARG PRO THR ILE PRO GLU ASP CYS PRO PRO ARG LEU ARG SEQRES 21 B 287 ASN VAL ILE GLU LEU CYS TRP SER GLY ASP PRO LYS LYS SEQRES 22 B 287 ARG PRO HIS PHE SER TYR ILE VAL LYS GLU LEU SER GLU SEQRES 23 B 287 LEU HET 4K4 A1301 42 HET MG A1302 1 HET 4K4 B1301 42 HET MG B1302 1 HETNAM 4K4 2-[(2-METHOXY-4-{[4-(4-METHYLPIPERAZIN-1-YL)PIPERIDIN- HETNAM 2 4K4 1-YL]CARBONYL}PHENYL)AMINO]-5,11-DIMETHYL-5,11- HETNAM 3 4K4 DIHYDRO-6H-PYRIMIDO[4,5-B][1,4]BENZODIAZEPIN-6-ONE HETNAM MG MAGNESIUM ION FORMUL 3 4K4 2(C31 H38 N8 O3) FORMUL 4 MG 2(MG 2+) FORMUL 7 HOH *36(H2 O) HELIX 1 AA1 ALA A 1022 ASN A 1024 5 3 HELIX 2 AA2 GLU A 1070 LEU A 1085 1 16 HELIX 3 AA3 ASP A 1112 LEU A 1117 1 6 HELIX 4 AA4 LYS A 1125 GLN A 1144 1 20 HELIX 5 AA5 ARG A 1156 PRO A 1158 5 3 HELIX 6 AA6 ASN A 1194 MET A 1198 5 5 HELIX 7 AA7 ALA A 1199 ILE A 1203 5 5 HELIX 8 AA8 GLU A 1212 GLY A 1229 1 18 HELIX 9 AA9 GLY A 1239 GLU A 1249 1 11 HELIX 10 AB1 PRO A 1261 TRP A 1272 1 12 HELIX 11 AB2 ASP A 1275 ARG A 1279 5 5 HELIX 12 AB3 HIS A 1281 LEU A 1292 1 12 HELIX 13 AB4 ALA B 1022 ASN B 1024 5 3 HELIX 14 AB5 GLU B 1067 LEU B 1085 1 19 HELIX 15 AB6 ASP B 1112 LEU B 1117 1 6 HELIX 16 AB7 LYS B 1125 ASN B 1145 1 21 HELIX 17 AB8 ARG B 1156 PRO B 1158 5 3 HELIX 18 AB9 ALA B 1199 ILE B 1203 5 5 HELIX 19 AC1 THR B 1211 GLY B 1229 1 19 HELIX 20 AC2 GLY B 1239 GLY B 1251 1 13 HELIX 21 AC3 PRO B 1261 TRP B 1272 1 12 HELIX 22 AC4 ASP B 1275 ARG B 1279 5 5 HELIX 23 AC5 HIS B 1281 GLU B 1291 1 11 SHEET 1 AA1 5 ILE A1026 GLY A1035 0 SHEET 2 AA1 5 GLY A1038 LEU A1045 -1 O LYS A1042 N LYS A1030 SHEET 3 AA1 5 VAL A1051 SER A1056 -1 O VAL A1052 N GLY A1043 SHEET 4 AA1 5 ARG A1102 MET A1105 -1 O MET A1105 N ALA A1053 SHEET 5 AA1 5 LEU A1093 MET A1097 -1 N TYR A1094 O VAL A1104 SHEET 1 AA2 2 ILE A1160 LEU A1162 0 SHEET 2 AA2 2 ALA A1173 VAL A1175 -1 O LYS A1174 N LEU A1161 SHEET 1 AA3 5 ILE B1026 GLN B1031 0 SHEET 2 AA3 5 LEU B1039 LEU B1045 -1 O ARG B1044 N GLU B1027 SHEET 3 AA3 5 VAL B1051 SER B1056 -1 O VAL B1052 N GLY B1043 SHEET 4 AA3 5 ARG B1102 MET B1105 -1 O MET B1105 N ALA B1053 SHEET 5 AA3 5 LEU B1093 MET B1097 -1 N TYR B1094 O VAL B1104 SHEET 1 AA4 2 ILE B1160 LEU B1162 0 SHEET 2 AA4 2 ALA B1173 VAL B1175 -1 O LYS B1174 N LEU B1161 LINK OD1 ASP A1177 MG MG A1302 1555 1555 2.46 LINK OD2 ASP B1154 MG MG B1302 1555 1555 2.32 CISPEP 1 ASN A 1099 PRO A 1100 0 -1.34 CISPEP 2 ASN A 1147 PRO A 1148 0 -3.46 CISPEP 3 ASN B 1099 PRO B 1100 0 1.45 CISPEP 4 ASN B 1147 PRO B 1148 0 -0.21 SITE 1 AC1 11 ILE A1032 GLY A1035 LYS A1055 MET A1105 SITE 2 AC1 11 GLU A1106 LEU A1107 VAL A1108 PRO A1109 SITE 3 AC1 11 GLY A1111 PRO A1158 LEU A1161 SITE 1 AC2 3 ASP A1154 ASP A1177 SER A1181 SITE 1 AC3 9 VAL B1040 LYS B1055 GLU B1106 LEU B1107 SITE 2 AC3 9 VAL B1108 PRO B1109 GLY B1111 PRO B1158 SITE 3 AC3 9 LEU B1161 SITE 1 AC4 3 ASP B1154 ASP B1177 LEU B1191 CRYST1 43.030 89.070 177.710 90.00 90.00 90.00 P 21 21 21 8 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 0.023240 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011227 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005627 0.00000