HEADER TRANSFERASE/TRANSFERASE INHIBITOR 09-JAN-18 6C3E TITLE CRYSTAL STRUCTURE OF RIP1 KINASE BOUND TO INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CELL DEATH PROTEIN RIP,RECEPTOR-INTERACTING PROTEIN 1,RIP-1, COMPND 5 SERINE/THREONINE-PROTEIN KINASE RIP; COMPND 6 EC: 2.7.11.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RIPK1, RIP, RIP1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS HUMAN RIP1 KINASE, CELL CYCLE, TRANSFERASE-TRANSFERASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.S.SAIKATENDU,M.YOSHIKAWA REVDAT 3 13-MAR-24 6C3E 1 REMARK REVDAT 2 04-APR-18 6C3E 1 JRNL REVDAT 1 21-MAR-18 6C3E 0 JRNL AUTH M.YOSHIKAWA,M.SAITOH,T.KATOH,T.SEKI,S.V.BIGI,Y.SHIMIZU, JRNL AUTH 2 T.ISHII,T.OKAI,M.KUNO,H.HATTORI,E.WATANABE,K.S.SAIKATENDU, JRNL AUTH 3 H.ZOU,M.NAKAKARIYA,T.TATAMIYA,Y.NAKADA,T.YOGO JRNL TITL DISCOVERY OF 7-OXO-2,4,5,7-TETRAHYDRO-6 H-PYRAZOLO[3,4- JRNL TITL 2 C]PYRIDINE DERIVATIVES AS POTENT, ORALLY AVAILABLE, AND JRNL TITL 3 BRAIN-PENETRATING RECEPTOR INTERACTING PROTEIN 1 (RIP1) JRNL TITL 4 KINASE INHIBITORS: ANALYSIS OF STRUCTURE-KINETIC JRNL TITL 5 RELATIONSHIPS. JRNL REF J. MED. CHEM. V. 61 2384 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 29485864 JRNL DOI 10.1021/ACS.JMEDCHEM.7B01647 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 15970 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) : 0.261 REMARK 3 R VALUE (WORKING SET) : 0.259 REMARK 3 FREE R VALUE : 0.307 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 810 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1120 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.2940 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.4370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4117 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 32 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.34000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.37000 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): 0.420 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.375 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 39.409 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.895 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.855 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4249 ; 0.005 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4155 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5720 ; 1.036 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9603 ; 0.748 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 512 ; 5.711 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 177 ;34.359 ;24.633 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 805 ;16.207 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;14.804 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 630 ; 0.062 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4650 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 892 ; 0.001 ; 0.020 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): 2066 ; 0.458 ; 1.209 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2065 ; 0.453 ; 1.209 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2572 ; 0.631 ; 1.813 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2573 ; 0.631 ; 1.813 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2183 ; 0.366 ; 1.226 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2172 ; 0.366 ; 1.226 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3137 ; 0.463 ; 1.833 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4699 ; 0.777 ; 9.431 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4690 ; 0.778 ; 9.426 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 8404 ; 0.429 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 14 ;20.790 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 8336 ; 1.472 ; 5.000 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 : 4 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 9 A 293 REMARK 3 ORIGIN FOR THE GROUP (A): 9.8138 -3.6097 -23.4933 REMARK 3 T TENSOR REMARK 3 T11: 0.2535 T22: 0.3852 REMARK 3 T33: 0.0194 T12: 0.0023 REMARK 3 T13: 0.0119 T23: 0.0262 REMARK 3 L TENSOR REMARK 3 L11: 1.7583 L22: 3.0559 REMARK 3 L33: 1.7964 L12: 0.0827 REMARK 3 L13: -0.3234 L23: 0.3231 REMARK 3 S TENSOR REMARK 3 S11: 0.1016 S12: -0.0386 S13: -0.0752 REMARK 3 S21: 0.0941 S22: 0.0229 S23: 0.0831 REMARK 3 S31: -0.1331 S32: -0.0553 S33: -0.1245 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 294 REMARK 3 ORIGIN FOR THE GROUP (A): 22.0310 -2.5051 -55.3044 REMARK 3 T TENSOR REMARK 3 T11: 0.3123 T22: 0.3819 REMARK 3 T33: 0.1236 T12: -0.0252 REMARK 3 T13: 0.0136 T23: 0.0276 REMARK 3 L TENSOR REMARK 3 L11: 1.4566 L22: 3.4034 REMARK 3 L33: 3.2959 L12: 0.0455 REMARK 3 L13: 0.8612 L23: -1.2599 REMARK 3 S TENSOR REMARK 3 S11: -0.0079 S12: 0.1471 S13: 0.1002 REMARK 3 S21: -0.3868 S22: 0.0046 S23: -0.0503 REMARK 3 S31: 0.0407 S32: -0.0594 S33: 0.0033 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 301 A 301 REMARK 3 RESIDUE RANGE : B 301 B 301 REMARK 3 ORIGIN FOR THE GROUP (A): 11.4304 -2.8196 -42.2127 REMARK 3 T TENSOR REMARK 3 T11: 0.1352 T22: 0.3738 REMARK 3 T33: 0.3135 T12: 0.1326 REMARK 3 T13: -0.1319 T23: -0.0250 REMARK 3 L TENSOR REMARK 3 L11: 1.8244 L22: 7.6769 REMARK 3 L33: 0.1489 L12: 2.5058 REMARK 3 L13: 0.3263 L23: 0.0022 REMARK 3 S TENSOR REMARK 3 S11: -0.0861 S12: 0.0120 S13: -0.0563 REMARK 3 S21: 0.1254 S22: -0.0409 S23: -0.4376 REMARK 3 S31: -0.1056 S32: -0.0513 S33: 0.1270 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 401 A 420 REMARK 3 RESIDUE RANGE : B 401 B 412 REMARK 3 ORIGIN FOR THE GROUP (A): 17.2101 -6.1868 -34.3648 REMARK 3 T TENSOR REMARK 3 T11: 0.2801 T22: 0.2783 REMARK 3 T33: 0.0237 T12: -0.0135 REMARK 3 T13: -0.0640 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 1.8288 L22: 1.8031 REMARK 3 L33: 1.3580 L12: 0.3016 REMARK 3 L13: -1.4956 L23: 0.2275 REMARK 3 S TENSOR REMARK 3 S11: 0.0476 S12: -0.0412 S13: 0.1072 REMARK 3 S21: -0.2246 S22: 0.0236 S23: 0.1188 REMARK 3 S31: -0.0633 S32: 0.0469 S33: -0.0712 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6C3E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1000232007. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15973 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 (%) : 95.7 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.66 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.25 M AMMONIUM IODIDE, 0.03 M GLYCYL REMARK 280 -GLYCYL-GLYCINE AND POLYETHYLENE GLYCOL (PEG) 3350, PH 7.0, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 277K 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 21.13100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.22200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.54700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 67.22200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.13100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.54700 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 21.13100 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 67.22200 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 -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 GLY A 1 REMARK 465 GLN A 2 REMARK 465 PRO A 3 REMARK 465 ASP A 4 REMARK 465 MET A 5 REMARK 465 SER A 6 REMARK 465 LEU A 7 REMARK 465 ASN A 8 REMARK 465 GLY A 50 REMARK 465 PRO A 51 REMARK 465 ASN A 52 REMARK 465 CYS A 53 REMARK 465 GLU A 171 REMARK 465 GLU A 172 REMARK 465 HIS A 173 REMARK 465 ASN A 174 REMARK 465 GLU A 175 REMARK 465 LEU A 176 REMARK 465 ARG A 177 REMARK 465 GLU A 178 REMARK 465 VAL A 179 REMARK 465 ASP A 180 REMARK 465 GLY A 181 REMARK 465 THR A 182 REMARK 465 ALA A 183 REMARK 465 LYS A 184 REMARK 465 LYS A 185 REMARK 465 ASN A 186 REMARK 465 GLY A 187 REMARK 465 ASN A 199 REMARK 465 ASP A 200 REMARK 465 VAL A 201 REMARK 465 ASN A 202 REMARK 465 ALA A 203 REMARK 465 LYS A 204 REMARK 465 GLU A 294 REMARK 465 GLY B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 GLY B 1 REMARK 465 GLN B 2 REMARK 465 PRO B 3 REMARK 465 ASP B 4 REMARK 465 MET B 5 REMARK 465 SER B 6 REMARK 465 LEU B 7 REMARK 465 ASN B 8 REMARK 465 VAL B 9 REMARK 465 LEU B 23 REMARK 465 ASP B 24 REMARK 465 SER B 25 REMARK 465 GLY B 26 REMARK 465 GLY B 27 REMARK 465 PHE B 28 REMARK 465 GLY B 29 REMARK 465 ASN B 169 REMARK 465 ASN B 170 REMARK 465 GLU B 171 REMARK 465 GLU B 172 REMARK 465 HIS B 173 REMARK 465 ASN B 174 REMARK 465 GLU B 175 REMARK 465 LEU B 176 REMARK 465 ARG B 177 REMARK 465 GLU B 178 REMARK 465 VAL B 179 REMARK 465 ASP B 180 REMARK 465 GLY B 181 REMARK 465 THR B 182 REMARK 465 ALA B 183 REMARK 465 LYS B 184 REMARK 465 LYS B 185 REMARK 465 ASN B 186 REMARK 465 GLY B 187 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 ILE A 54 CG1 CG2 CD1 REMARK 470 GLU A 55 CG CD OE1 OE2 REMARK 470 LYS B 30 CG CD CE NZ REMARK 470 HIS B 56 CG ND1 CD2 CE1 NE2 REMARK 470 PHE B 162 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU B 294 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 55 -86.30 -12.24 REMARK 500 GLU A 85 -114.23 57.30 REMARK 500 SER A 109 46.68 -97.75 REMARK 500 ASP A 138 56.53 -161.45 REMARK 500 ASP A 251 45.23 -91.65 REMARK 500 LEU A 252 -33.41 -172.21 REMARK 500 GLU B 19 -85.36 42.46 REMARK 500 SER B 20 140.31 85.69 REMARK 500 PRO B 51 -71.30 -44.12 REMARK 500 ASN B 52 -54.91 158.33 REMARK 500 CYS B 53 -27.82 3.65 REMARK 500 GLU B 85 -74.71 -49.40 REMARK 500 ASP B 138 54.91 -144.80 REMARK 500 ASP B 200 76.97 -160.10 REMARK 500 TRP B 268 31.38 -97.01 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 EJY A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EJY B 301 DBREF 6C3E A 2 294 UNP Q13546 RIPK1_HUMAN 2 294 DBREF 6C3E B 2 294 UNP Q13546 RIPK1_HUMAN 2 294 SEQADV 6C3E GLY A -2 UNP Q13546 EXPRESSION TAG SEQADV 6C3E GLY A -1 UNP Q13546 EXPRESSION TAG SEQADV 6C3E SER A 0 UNP Q13546 EXPRESSION TAG SEQADV 6C3E GLY A 1 UNP Q13546 EXPRESSION TAG SEQADV 6C3E ALA A 34 UNP Q13546 CYS 34 CONFLICT SEQADV 6C3E ALA A 127 UNP Q13546 CYS 127 CONFLICT SEQADV 6C3E ALA A 233 UNP Q13546 CYS 233 CONFLICT SEQADV 6C3E ALA A 240 UNP Q13546 CYS 240 CONFLICT SEQADV 6C3E LEU A 252 UNP Q13546 ILE 252 CONFLICT SEQADV 6C3E GLY B -2 UNP Q13546 EXPRESSION TAG SEQADV 6C3E GLY B -1 UNP Q13546 EXPRESSION TAG SEQADV 6C3E SER B 0 UNP Q13546 EXPRESSION TAG SEQADV 6C3E GLY B 1 UNP Q13546 EXPRESSION TAG SEQADV 6C3E ALA B 34 UNP Q13546 CYS 34 CONFLICT SEQADV 6C3E ALA B 127 UNP Q13546 CYS 127 CONFLICT SEQADV 6C3E ALA B 233 UNP Q13546 CYS 233 CONFLICT SEQADV 6C3E ALA B 240 UNP Q13546 CYS 240 CONFLICT SEQADV 6C3E LEU B 252 UNP Q13546 ILE 252 CONFLICT SEQRES 1 A 297 GLY GLY SER GLY GLN PRO ASP MET SER LEU ASN VAL ILE SEQRES 2 A 297 LYS MET LYS SER SER ASP PHE LEU GLU SER ALA GLU LEU SEQRES 3 A 297 ASP SER GLY GLY PHE GLY LYS VAL SER LEU ALA PHE HIS SEQRES 4 A 297 ARG THR GLN GLY LEU MET ILE MET LYS THR VAL TYR LYS SEQRES 5 A 297 GLY PRO ASN CYS ILE GLU HIS ASN GLU ALA LEU LEU GLU SEQRES 6 A 297 GLU ALA LYS MET MET ASN ARG LEU ARG HIS SER ARG VAL SEQRES 7 A 297 VAL LYS LEU LEU GLY VAL ILE ILE GLU GLU GLY LYS TYR SEQRES 8 A 297 SER LEU VAL MET GLU TYR MET GLU LYS GLY ASN LEU MET SEQRES 9 A 297 HIS VAL LEU LYS ALA GLU MET SER THR PRO LEU SER VAL SEQRES 10 A 297 LYS GLY ARG ILE ILE LEU GLU ILE ILE GLU GLY MET ALA SEQRES 11 A 297 TYR LEU HIS GLY LYS GLY VAL ILE HIS LYS ASP LEU LYS SEQRES 12 A 297 PRO GLU ASN ILE LEU VAL ASP ASN ASP PHE HIS ILE LYS SEQRES 13 A 297 ILE ALA ASP LEU GLY LEU ALA SER PHE LYS MET TRP SER SEQRES 14 A 297 LYS LEU ASN ASN GLU GLU HIS ASN GLU LEU ARG GLU VAL SEQRES 15 A 297 ASP GLY THR ALA LYS LYS ASN GLY GLY THR LEU TYR TYR SEQRES 16 A 297 MET ALA PRO GLU HIS LEU ASN ASP VAL ASN ALA LYS PRO SEQRES 17 A 297 THR GLU LYS SER ASP VAL TYR SER PHE ALA VAL VAL LEU SEQRES 18 A 297 TRP ALA ILE PHE ALA ASN LYS GLU PRO TYR GLU ASN ALA SEQRES 19 A 297 ILE ALA GLU GLN GLN LEU ILE MET ALA ILE LYS SER GLY SEQRES 20 A 297 ASN ARG PRO ASP VAL ASP ASP LEU THR GLU TYR CYS PRO SEQRES 21 A 297 ARG GLU ILE ILE SER LEU MET LYS LEU CYS TRP GLU ALA SEQRES 22 A 297 ASN PRO GLU ALA ARG PRO THR PHE PRO GLY ILE GLU GLU SEQRES 23 A 297 LYS PHE ARG PRO PHE TYR LEU SER GLN LEU GLU SEQRES 1 B 297 GLY GLY SER GLY GLN PRO ASP MET SER LEU ASN VAL ILE SEQRES 2 B 297 LYS MET LYS SER SER ASP PHE LEU GLU SER ALA GLU LEU SEQRES 3 B 297 ASP SER GLY GLY PHE GLY LYS VAL SER LEU ALA PHE HIS SEQRES 4 B 297 ARG THR GLN GLY LEU MET ILE MET LYS THR VAL TYR LYS SEQRES 5 B 297 GLY PRO ASN CYS ILE GLU HIS ASN GLU ALA LEU LEU GLU SEQRES 6 B 297 GLU ALA LYS MET MET ASN ARG LEU ARG HIS SER ARG VAL SEQRES 7 B 297 VAL LYS LEU LEU GLY VAL ILE ILE GLU GLU GLY LYS TYR SEQRES 8 B 297 SER LEU VAL MET GLU TYR MET GLU LYS GLY ASN LEU MET SEQRES 9 B 297 HIS VAL LEU LYS ALA GLU MET SER THR PRO LEU SER VAL SEQRES 10 B 297 LYS GLY ARG ILE ILE LEU GLU ILE ILE GLU GLY MET ALA SEQRES 11 B 297 TYR LEU HIS GLY LYS GLY VAL ILE HIS LYS ASP LEU LYS SEQRES 12 B 297 PRO GLU ASN ILE LEU VAL ASP ASN ASP PHE HIS ILE LYS SEQRES 13 B 297 ILE ALA ASP LEU GLY LEU ALA SER PHE LYS MET TRP SER SEQRES 14 B 297 LYS LEU ASN ASN GLU GLU HIS ASN GLU LEU ARG GLU VAL SEQRES 15 B 297 ASP GLY THR ALA LYS LYS ASN GLY GLY THR LEU TYR TYR SEQRES 16 B 297 MET ALA PRO GLU HIS LEU ASN ASP VAL ASN ALA LYS PRO SEQRES 17 B 297 THR GLU LYS SER ASP VAL TYR SER PHE ALA VAL VAL LEU SEQRES 18 B 297 TRP ALA ILE PHE ALA ASN LYS GLU PRO TYR GLU ASN ALA SEQRES 19 B 297 ILE ALA GLU GLN GLN LEU ILE MET ALA ILE LYS SER GLY SEQRES 20 B 297 ASN ARG PRO ASP VAL ASP ASP LEU THR GLU TYR CYS PRO SEQRES 21 B 297 ARG GLU ILE ILE SER LEU MET LYS LEU CYS TRP GLU ALA SEQRES 22 B 297 ASN PRO GLU ALA ARG PRO THR PHE PRO GLY ILE GLU GLU SEQRES 23 B 297 LYS PHE ARG PRO PHE TYR LEU SER GLN LEU GLU HET EJY A 301 19 HET EJY B 301 19 HETNAM EJY 2-BENZYL-5-NITRO-1H-BENZIMIDAZOLE FORMUL 3 EJY 2(C14 H11 N3 O2) FORMUL 5 HOH *32(H2 O) HELIX 1 AA1 LYS A 13 SER A 15 5 3 HELIX 2 AA2 ASP A 24 GLY A 29 1 6 HELIX 3 AA3 HIS A 56 ARG A 69 1 14 HELIX 4 AA4 ASN A 99 GLU A 107 1 9 HELIX 5 AA5 PRO A 111 LYS A 132 1 22 HELIX 6 AA6 LYS A 140 GLU A 142 5 3 HELIX 7 AA7 PHE A 162 ASN A 170 1 9 HELIX 8 AA8 ALA A 194 LEU A 198 5 5 HELIX 9 AA9 LYS A 208 ASN A 224 1 17 HELIX 10 AB1 ALA A 233 SER A 243 1 11 HELIX 11 AB2 ASP A 248 LEU A 252 5 5 HELIX 12 AB3 PRO A 257 TRP A 268 1 12 HELIX 13 AB4 THR A 277 LEU A 293 1 17 HELIX 14 AB5 LYS B 13 SER B 15 5 3 HELIX 15 AB6 HIS B 56 ARG B 69 1 14 HELIX 16 AB7 LEU B 100 ALA B 106 1 7 HELIX 17 AB8 PRO B 111 LYS B 132 1 22 HELIX 18 AB9 LYS B 140 GLU B 142 5 3 HELIX 19 AC1 PHE B 162 LYS B 167 1 6 HELIX 20 AC2 THR B 189 MET B 193 5 5 HELIX 21 AC3 ALA B 194 LEU B 198 5 5 HELIX 22 AC4 THR B 206 ASN B 224 1 19 HELIX 23 AC5 ALA B 233 SER B 243 1 11 HELIX 24 AC6 PRO B 257 TRP B 268 1 12 HELIX 25 AC7 THR B 277 LEU B 293 1 17 SHEET 1 AA1 5 PHE A 17 GLU A 22 0 SHEET 2 AA1 5 SER A 32 HIS A 36 -1 O LEU A 33 N ALA A 21 SHEET 3 AA1 5 GLY A 40 TYR A 48 -1 O GLY A 40 N HIS A 36 SHEET 4 AA1 5 LYS A 87 GLU A 93 -1 O LEU A 90 N LYS A 45 SHEET 5 AA1 5 LEU A 78 GLU A 84 -1 N LEU A 79 O VAL A 91 SHEET 1 AA2 2 ILE A 144 VAL A 146 0 SHEET 2 AA2 2 ILE A 152 ILE A 154 -1 O LYS A 153 N LEU A 145 SHEET 1 AA3 5 PHE B 17 LEU B 18 0 SHEET 2 AA3 5 VAL B 31 HIS B 36 -1 O PHE B 35 N LEU B 18 SHEET 3 AA3 5 LEU B 41 TYR B 48 -1 O MET B 44 N SER B 32 SHEET 4 AA3 5 LYS B 87 GLU B 93 -1 O TYR B 88 N VAL B 47 SHEET 5 AA3 5 LEU B 78 GLU B 84 -1 N GLY B 80 O VAL B 91 SHEET 1 AA4 3 GLY B 98 ASN B 99 0 SHEET 2 AA4 3 ILE B 144 VAL B 146 -1 O VAL B 146 N GLY B 98 SHEET 3 AA4 3 ILE B 152 ILE B 154 -1 O LYS B 153 N LEU B 145 SITE 1 AC1 8 LYS A 45 MET A 92 LEU A 129 HIS A 136 SITE 2 AC1 8 ALA A 155 ASP A 156 SER A 161 PHE A 162 SITE 1 AC2 12 LYS B 45 LEU B 70 VAL B 75 VAL B 76 SITE 2 AC2 12 LEU B 90 MET B 92 HIS B 136 ILE B 154 SITE 3 AC2 12 ALA B 155 ASP B 156 LEU B 157 SER B 161 CRYST1 42.262 95.094 134.444 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 0.023662 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010516 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007438 0.00000