PDB Short entry for 5AR3 HEADER TRANSFERASE 23-SEP-15 5AR3 TITLE RIP2 KINASE CATALYTIC DOMAIN (1 - 310) COMPLEX WITH AMP-PCP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: KINASE DOMAIN, UNP RESIDUES 1-310; COMPND 5 SYNONYM: CARD-CONTAINING INTERLEUKIN-1 BETA-CONVERTING ENZYME- COMPND 6 ASSOCIATED KINASE, CARD-CONTAINING IL-1 BETA ICE-KINASE, RIP-LIKE- COMPND 7 INTERACTING CLARP KINASE, RECEPTOR-INTERACTING PROTEIN 2, RIP-2, COMPND 8 TYROSINE-PROTEIN KINASE RIPK2, RECEPTOR-INTERACTING SERINE THREONINE- COMPND 9 PROTEIN KINASE 2; COMPND 10 EC: 2.7.11.1; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS TRANSFERASE, KINASE INHIBITOR, STRUCTURE-BASED DRUG DESIGN, INHIBITOR KEYWDS 2 SELECTIVITY EXPDTA X-RAY DIFFRACTION AUTHOR A.K.CHARNLEY,M.A.CONVERY,A.LAKDAWALA SHAH,E.JONES,P.HARDWICKE, AUTHOR 2 A.BRIDGES,B.J.VOTTA,P.J.GOUGH,R.W.MARQUIS,J.BERTIN,L.CASILLAS REVDAT 3 04-APR-18 5AR3 1 REMARK REVDAT 2 09-DEC-15 5AR3 1 JRNL REVDAT 1 21-OCT-15 5AR3 0 JRNL AUTH A.K.CHARNLEY,M.A.CONVERY,A.LAKDAWALA SHAH,E.JONES, JRNL AUTH 2 P.HARDWICKE,A.BRIDGES,M.OUELLETTE,R.TOTORITIS,B.SCHWARTZ, JRNL AUTH 3 B.W.KING,D.D.WISNOSKI,J.KANG,P.M.EIDAM,B.J.VOTTA,P.J.GOUGH, JRNL AUTH 4 R.W.MARQUIS,J.BERTIN,L.CASILLAS JRNL TITL CRYSTAL STRUCTURES OF HUMAN RIP2 KINASE CATALYTIC DOMAIN JRNL TITL 2 COMPLEXED WITH ATP-COMPETITIVE INHIBITORS: FOUNDATIONS FOR JRNL TITL 3 UNDERSTANDING INHIBITOR SELECTIVITY. JRNL REF BIOORG.MED.CHEM. V. 23 7000 2015 JRNL REFN ISSN 0968-0896 JRNL PMID 26455654 JRNL DOI 10.1016/J.BMC.2015.09.038 REMARK 2 REMARK 2 RESOLUTION. 3.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 3.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 16629 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.100 REMARK 3 FREE R VALUE TEST SET COUNT : 712 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) : 3.23 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.32 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1226 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4476 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.56000 REMARK 3 B22 (A**2) : 1.56000 REMARK 3 B33 (A**2) : -5.05000 REMARK 3 B12 (A**2) : 1.56000 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): 0.440 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.313 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.007 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.899 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4678 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6374 ; 1.224 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 549 ; 2.508 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 211 ;31.269 ;23.365 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 764 ;11.071 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ; 8.024 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 703 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3549 ; 0.005 ; 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): 2217 ; 4.444 ; 8.769 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2759 ; 7.337 ;19.664 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2459 ; 5.191 ; 9.033 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 5AR3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1290065146. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMICS HF REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72012 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.230 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2M NAKTARTRATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 71.05467 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 35.52733 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.52733 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 71.05467 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A -15 REMARK 465 ASP A -14 REMARK 465 TYR A -13 REMARK 465 LYS A -12 REMARK 465 ASP A -11 REMARK 465 ASP A -10 REMARK 465 ASP A -9 REMARK 465 ASP A -8 REMARK 465 LYS A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 GLY A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 GLY A 3 REMARK 465 GLU A 4 REMARK 465 ALA A 5 REMARK 465 ILE A 51 REMARK 465 HIS A 52 REMARK 465 THR A 53 REMARK 465 PRO A 54 REMARK 465 LEU A 55 REMARK 465 MET A 173 REMARK 465 SER A 174 REMARK 465 LEU A 175 REMARK 465 SER A 176 REMARK 465 GLN A 177 REMARK 465 SER A 178 REMARK 465 ARG A 179 REMARK 465 SER A 180 REMARK 465 SER A 181 REMARK 465 LYS A 182 REMARK 465 SER A 183 REMARK 465 ALA A 184 REMARK 465 PRO A 185 REMARK 465 GLU A 186 REMARK 465 GLU A 199 REMARK 465 PRO A 200 REMARK 465 GLY A 201 REMARK 465 GLN A 202 REMARK 465 LYS A 203 REMARK 465 SER A 204 REMARK 465 ARG A 205 REMARK 465 MET B -15 REMARK 465 ASP B -14 REMARK 465 TYR B -13 REMARK 465 LYS B -12 REMARK 465 ASP B -11 REMARK 465 ASP B -10 REMARK 465 ASP B -9 REMARK 465 ASP B -8 REMARK 465 LYS B -7 REMARK 465 GLU B -6 REMARK 465 ASN B -5 REMARK 465 LEU B -4 REMARK 465 TYR B -3 REMARK 465 PHE B -2 REMARK 465 GLN B -1 REMARK 465 GLY B 0 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 GLY B 3 REMARK 465 GLU B 4 REMARK 465 ALA B 5 REMARK 465 ILE B 51 REMARK 465 HIS B 52 REMARK 465 THR B 53 REMARK 465 PRO B 54 REMARK 465 LEU B 55 REMARK 465 LEU B 56 REMARK 465 ASP B 57 REMARK 465 SER B 58 REMARK 465 MET B 173 REMARK 465 SER B 174 REMARK 465 LEU B 175 REMARK 465 SER B 176 REMARK 465 GLN B 177 REMARK 465 SER B 178 REMARK 465 ARG B 179 REMARK 465 SER B 180 REMARK 465 SER B 181 REMARK 465 LYS B 182 REMARK 465 SER B 183 REMARK 465 ALA B 184 REMARK 465 PRO B 185 REMARK 465 GLU B 186 REMARK 465 GLY B 187 REMARK 465 GLY B 188 REMARK 465 GLY B 201 REMARK 465 GLN B 202 REMARK 465 LYS B 203 REMARK 465 SER B 204 REMARK 465 ARG B 205 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 ARG A 26 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 49 CG CD1 CD2 REMARK 470 HIS A 50 CG ND1 CD2 CE1 NE2 REMARK 470 LEU A 56 CG CD1 CD2 REMARK 470 ASP A 57 CG OD1 OD2 REMARK 470 GLU A 59 CG CD OE1 OE2 REMARK 470 LYS A 61 CG CD CE NZ REMARK 470 LYS A 169 CG CD CE NZ REMARK 470 ARG B 26 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 50 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 59 CG CD OE1 OE2 REMARK 470 ARG B 60 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 61 CG CD CE NZ REMARK 470 LYS B 169 CG CD CE NZ REMARK 470 MET B 172 CG SD CE 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 TYR A 15 -38.14 -39.01 REMARK 500 LEU A 21 97.42 -60.52 REMARK 500 SER A 29 -16.56 92.84 REMARK 500 SER A 76 -37.87 -38.96 REMARK 500 HIS A 145 8.75 51.84 REMARK 500 ASP A 146 33.99 -141.38 REMARK 500 ASP A 164 76.24 72.21 REMARK 500 PHE A 165 34.32 -97.68 REMARK 500 PHE A 229 68.42 63.66 REMARK 500 ASN B 86 72.13 -105.33 REMARK 500 HIS B 145 8.54 55.58 REMARK 500 ASP B 164 78.10 65.93 REMARK 500 PHE B 165 35.33 -98.91 REMARK 500 LYS B 209 26.17 -72.08 REMARK 500 ASN B 251 -159.10 -96.00 REMARK 500 TRP B 273 30.82 -87.14 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 B2002 DISTANCE = 7.60 ANGSTROMS REMARK 525 HOH B2033 DISTANCE = 8.41 ANGSTROMS REMARK 525 HOH B2034 DISTANCE = 7.61 ANGSTROMS 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 A1312 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ACP A1311 O1A REMARK 620 2 ACP A1311 O2B 86.9 REMARK 620 3 ASN A 151 OD1 88.0 170.9 REMARK 620 4 HOH A2023 O 159.3 76.4 106.8 REMARK 620 5 ASP A 164 OD2 98.1 106.8 81.4 98.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1312 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ACP B1311 O2B REMARK 620 2 ACP B1311 O1A 88.1 REMARK 620 3 ASN B 151 OD1 170.0 100.6 REMARK 620 4 ASP B 164 OD2 88.8 89.0 96.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACP A 1311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACP B 1311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1312 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AR2 RELATED DB: PDB REMARK 900 RIP2 KINASE CATALYTIC DOMAIN (1 - 310) REMARK 900 RELATED ID: 5AR4 RELATED DB: PDB REMARK 900 RIP2 KINASE CATALYTIC DOMAIN (1 - 310) COMPLEX WITH SB -203580 REMARK 900 RELATED ID: 5AR5 RELATED DB: PDB REMARK 900 RIP2 KINASE CATALYTIC DOMAIN (1 - 310) COMPLEX WITH BENZIMIDAZOLE REMARK 900 RELATED ID: 5AR7 RELATED DB: PDB REMARK 900 RIP2 KINASE CATALYTIC DOMAIN (1 - 310) COMPLEX WITH BIARYL UREA REMARK 900 RELATED ID: 5AR8 RELATED DB: PDB REMARK 900 RIP2 KINASE CATALYTIC DOMAIN (1 - 310) COMPLEX WITH REMARK 900 BIPHENYLSULFONAMIDE DBREF 5AR3 A 1 310 UNP O43353 RIPK2_HUMAN 1 310 DBREF 5AR3 B 1 310 UNP O43353 RIPK2_HUMAN 1 310 SEQADV 5AR3 MET A -15 UNP O43353 EXPRESSION TAG SEQADV 5AR3 ASP A -14 UNP O43353 EXPRESSION TAG SEQADV 5AR3 TYR A -13 UNP O43353 EXPRESSION TAG SEQADV 5AR3 LYS A -12 UNP O43353 EXPRESSION TAG SEQADV 5AR3 ASP A -11 UNP O43353 EXPRESSION TAG SEQADV 5AR3 ASP A -10 UNP O43353 EXPRESSION TAG SEQADV 5AR3 ASP A -9 UNP O43353 EXPRESSION TAG SEQADV 5AR3 ASP A -8 UNP O43353 EXPRESSION TAG SEQADV 5AR3 LYS A -7 UNP O43353 EXPRESSION TAG SEQADV 5AR3 GLU A -6 UNP O43353 EXPRESSION TAG SEQADV 5AR3 ASN A -5 UNP O43353 EXPRESSION TAG SEQADV 5AR3 LEU A -4 UNP O43353 EXPRESSION TAG SEQADV 5AR3 TYR A -3 UNP O43353 EXPRESSION TAG SEQADV 5AR3 PHE A -2 UNP O43353 EXPRESSION TAG SEQADV 5AR3 GLN A -1 UNP O43353 EXPRESSION TAG SEQADV 5AR3 GLY A 0 UNP O43353 EXPRESSION TAG SEQADV 5AR3 MET B -15 UNP O43353 EXPRESSION TAG SEQADV 5AR3 ASP B -14 UNP O43353 EXPRESSION TAG SEQADV 5AR3 TYR B -13 UNP O43353 EXPRESSION TAG SEQADV 5AR3 LYS B -12 UNP O43353 EXPRESSION TAG SEQADV 5AR3 ASP B -11 UNP O43353 EXPRESSION TAG SEQADV 5AR3 ASP B -10 UNP O43353 EXPRESSION TAG SEQADV 5AR3 ASP B -9 UNP O43353 EXPRESSION TAG SEQADV 5AR3 ASP B -8 UNP O43353 EXPRESSION TAG SEQADV 5AR3 LYS B -7 UNP O43353 EXPRESSION TAG SEQADV 5AR3 GLU B -6 UNP O43353 EXPRESSION TAG SEQADV 5AR3 ASN B -5 UNP O43353 EXPRESSION TAG SEQADV 5AR3 LEU B -4 UNP O43353 EXPRESSION TAG SEQADV 5AR3 TYR B -3 UNP O43353 EXPRESSION TAG SEQADV 5AR3 PHE B -2 UNP O43353 EXPRESSION TAG SEQADV 5AR3 GLN B -1 UNP O43353 EXPRESSION TAG SEQADV 5AR3 GLY B 0 UNP O43353 EXPRESSION TAG SEQRES 1 A 326 MET ASP TYR LYS ASP ASP ASP ASP LYS GLU ASN LEU TYR SEQRES 2 A 326 PHE GLN GLY MET ASN GLY GLU ALA ILE CYS SER ALA LEU SEQRES 3 A 326 PRO THR ILE PRO TYR HIS LYS LEU ALA ASP LEU ARG TYR SEQRES 4 A 326 LEU SER ARG GLY ALA SER GLY THR VAL SER SER ALA ARG SEQRES 5 A 326 HIS ALA ASP TRP ARG VAL GLN VAL ALA VAL LYS HIS LEU SEQRES 6 A 326 HIS ILE HIS THR PRO LEU LEU ASP SER GLU ARG LYS ASP SEQRES 7 A 326 VAL LEU ARG GLU ALA GLU ILE LEU HIS LYS ALA ARG PHE SEQRES 8 A 326 SER TYR ILE LEU PRO ILE LEU GLY ILE CYS ASN GLU PRO SEQRES 9 A 326 GLU PHE LEU GLY ILE VAL THR GLU TYR MET PRO ASN GLY SEQRES 10 A 326 SER LEU ASN GLU LEU LEU HIS ARG LYS THR GLU TYR PRO SEQRES 11 A 326 ASP VAL ALA TRP PRO LEU ARG PHE ARG ILE LEU HIS GLU SEQRES 12 A 326 ILE ALA LEU GLY VAL ASN TYR LEU HIS ASN MET THR PRO SEQRES 13 A 326 PRO LEU LEU HIS HIS ASP LEU LYS THR GLN ASN ILE LEU SEQRES 14 A 326 LEU ASP ASN GLU PHE HIS VAL LYS ILE ALA ASP PHE GLY SEQRES 15 A 326 LEU SER LYS TRP ARG MET MET SER LEU SER GLN SER ARG SEQRES 16 A 326 SER SER LYS SER ALA PRO GLU GLY GLY THR ILE ILE TYR SEQRES 17 A 326 MET PRO PRO GLU ASN TYR GLU PRO GLY GLN LYS SER ARG SEQRES 18 A 326 ALA SER ILE LYS HIS ASP ILE TYR SER TYR ALA VAL ILE SEQRES 19 A 326 THR TRP GLU VAL LEU SER ARG LYS GLN PRO PHE GLU ASP SEQRES 20 A 326 VAL THR ASN PRO LEU GLN ILE MET TYR SER VAL SER GLN SEQRES 21 A 326 GLY HIS ARG PRO VAL ILE ASN GLU GLU SER LEU PRO TYR SEQRES 22 A 326 ASP ILE PRO HIS ARG ALA ARG MET ILE SER LEU ILE GLU SEQRES 23 A 326 SER GLY TRP ALA GLN ASN PRO ASP GLU ARG PRO SER PHE SEQRES 24 A 326 LEU LYS CYS LEU ILE GLU LEU GLU PRO VAL LEU ARG THR SEQRES 25 A 326 PHE GLU GLU ILE THR PHE LEU GLU ALA VAL ILE GLN LEU SEQRES 26 A 326 LYS SEQRES 1 B 326 MET ASP TYR LYS ASP ASP ASP ASP LYS GLU ASN LEU TYR SEQRES 2 B 326 PHE GLN GLY MET ASN GLY GLU ALA ILE CYS SER ALA LEU SEQRES 3 B 326 PRO THR ILE PRO TYR HIS LYS LEU ALA ASP LEU ARG TYR SEQRES 4 B 326 LEU SER ARG GLY ALA SER GLY THR VAL SER SER ALA ARG SEQRES 5 B 326 HIS ALA ASP TRP ARG VAL GLN VAL ALA VAL LYS HIS LEU SEQRES 6 B 326 HIS ILE HIS THR PRO LEU LEU ASP SER GLU ARG LYS ASP SEQRES 7 B 326 VAL LEU ARG GLU ALA GLU ILE LEU HIS LYS ALA ARG PHE SEQRES 8 B 326 SER TYR ILE LEU PRO ILE LEU GLY ILE CYS ASN GLU PRO SEQRES 9 B 326 GLU PHE LEU GLY ILE VAL THR GLU TYR MET PRO ASN GLY SEQRES 10 B 326 SER LEU ASN GLU LEU LEU HIS ARG LYS THR GLU TYR PRO SEQRES 11 B 326 ASP VAL ALA TRP PRO LEU ARG PHE ARG ILE LEU HIS GLU SEQRES 12 B 326 ILE ALA LEU GLY VAL ASN TYR LEU HIS ASN MET THR PRO SEQRES 13 B 326 PRO LEU LEU HIS HIS ASP LEU LYS THR GLN ASN ILE LEU SEQRES 14 B 326 LEU ASP ASN GLU PHE HIS VAL LYS ILE ALA ASP PHE GLY SEQRES 15 B 326 LEU SER LYS TRP ARG MET MET SER LEU SER GLN SER ARG SEQRES 16 B 326 SER SER LYS SER ALA PRO GLU GLY GLY THR ILE ILE TYR SEQRES 17 B 326 MET PRO PRO GLU ASN TYR GLU PRO GLY GLN LYS SER ARG SEQRES 18 B 326 ALA SER ILE LYS HIS ASP ILE TYR SER TYR ALA VAL ILE SEQRES 19 B 326 THR TRP GLU VAL LEU SER ARG LYS GLN PRO PHE GLU ASP SEQRES 20 B 326 VAL THR ASN PRO LEU GLN ILE MET TYR SER VAL SER GLN SEQRES 21 B 326 GLY HIS ARG PRO VAL ILE ASN GLU GLU SER LEU PRO TYR SEQRES 22 B 326 ASP ILE PRO HIS ARG ALA ARG MET ILE SER LEU ILE GLU SEQRES 23 B 326 SER GLY TRP ALA GLN ASN PRO ASP GLU ARG PRO SER PHE SEQRES 24 B 326 LEU LYS CYS LEU ILE GLU LEU GLU PRO VAL LEU ARG THR SEQRES 25 B 326 PHE GLU GLU ILE THR PHE LEU GLU ALA VAL ILE GLN LEU SEQRES 26 B 326 LYS HET ACP A1311 31 HET MG A1312 1 HET ACP B1311 31 HET MG B1312 1 HETNAM ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER HETNAM MG MAGNESIUM ION HETSYN ACP ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE FORMUL 3 ACP 2(C11 H18 N5 O12 P3) FORMUL 4 MG 2(MG 2+) FORMUL 7 HOH *79(H2 O) HELIX 1 1 PRO A 14 HIS A 16 5 3 HELIX 2 2 SER A 58 ALA A 73 1 16 HELIX 3 3 SER A 102 ARG A 109 1 8 HELIX 4 4 ALA A 117 ASN A 137 1 21 HELIX 5 5 PRO A 194 TYR A 198 5 5 HELIX 6 6 LYS A 209 ARG A 225 1 17 HELIX 7 7 ASN A 234 GLN A 244 1 11 HELIX 8 8 HIS A 261 TRP A 273 1 13 HELIX 9 9 ASN A 276 ARG A 280 5 5 HELIX 10 10 SER A 282 ARG A 295 1 14 HELIX 11 11 GLU A 298 GLN A 308 1 11 HELIX 12 12 PRO B 14 HIS B 16 5 3 HELIX 13 13 GLU B 59 ALA B 73 1 15 HELIX 14 14 SER B 102 ARG B 109 1 8 HELIX 15 15 ALA B 117 ASN B 137 1 21 HELIX 16 16 LYS B 148 GLN B 150 5 3 HELIX 17 17 PRO B 194 GLU B 199 5 6 HELIX 18 18 LYS B 209 ARG B 225 1 17 HELIX 19 19 ASN B 234 GLN B 244 1 11 HELIX 20 20 HIS B 261 TRP B 273 1 13 HELIX 21 21 SER B 282 THR B 296 1 15 HELIX 22 22 GLU B 298 LYS B 310 1 13 SHEET 1 AA 2 CYS A 7 ALA A 9 0 SHEET 2 AA 2 CYS B 7 ALA B 9 -1 O SER B 8 N SER A 8 SHEET 1 AB 5 LEU A 18 GLY A 27 0 SHEET 2 AB 5 GLY A 30 HIS A 37 -1 O GLY A 30 N GLY A 27 SHEET 3 AB 5 GLN A 43 LEU A 49 -1 O VAL A 44 N ALA A 35 SHEET 4 AB 5 LEU A 91 GLU A 96 -1 O LEU A 91 N LEU A 49 SHEET 5 AB 5 ILE A 81 ASN A 86 -1 N LEU A 82 O VAL A 94 SHEET 1 AC 2 LEU A 142 LEU A 143 0 SHEET 2 AC 2 LYS A 169 TRP A 170 -1 O LYS A 169 N LEU A 143 SHEET 1 AD 2 ILE A 152 LEU A 154 0 SHEET 2 AD 2 VAL A 160 ILE A 162 -1 O LYS A 161 N LEU A 153 SHEET 1 BA 5 LEU B 18 ARG B 26 0 SHEET 2 BA 5 THR B 31 HIS B 37 -1 O VAL B 32 N LEU B 24 SHEET 3 BA 5 GLN B 43 HIS B 48 -1 O VAL B 44 N ALA B 35 SHEET 4 BA 5 PHE B 90 GLU B 96 -1 O ILE B 93 N LYS B 47 SHEET 5 BA 5 ILE B 81 GLU B 87 -1 N LEU B 82 O VAL B 94 SHEET 1 BB 2 LEU B 142 LEU B 143 0 SHEET 2 BB 2 LYS B 169 TRP B 170 -1 O LYS B 169 N LEU B 143 SHEET 1 BC 2 ILE B 152 LEU B 154 0 SHEET 2 BC 2 VAL B 160 ILE B 162 -1 O LYS B 161 N LEU B 153 LINK O1A ACP A1311 MG MG A1312 1555 1555 2.19 LINK O2B ACP A1311 MG MG A1312 1555 1555 2.19 LINK MG MG A1312 OD1 ASN A 151 1555 1555 2.19 LINK MG MG A1312 O HOH A2023 1555 1555 2.31 LINK MG MG A1312 OD2 ASP A 164 1555 1555 2.19 LINK O2B ACP B1311 MG MG B1312 1555 1555 2.18 LINK O1A ACP B1311 MG MG B1312 1555 1555 2.19 LINK MG MG B1312 OD1 ASN B 151 1555 1555 2.18 LINK MG MG B1312 OD2 ASP B 164 1555 1555 2.18 CISPEP 1 THR A 139 PRO A 140 0 2.90 CISPEP 2 THR B 139 PRO B 140 0 -0.39 SITE 1 AC1 19 LEU A 24 ALA A 28 SER A 29 GLY A 30 SITE 2 AC1 19 ALA A 45 LYS A 47 THR A 95 GLU A 96 SITE 3 AC1 19 TYR A 97 MET A 98 GLU A 105 GLN A 150 SITE 4 AC1 19 ASN A 151 LEU A 153 ASP A 164 MG A1312 SITE 5 AC1 19 HOH A2005 HOH A2023 HOH A2045 SITE 1 AC2 16 SER B 25 GLY B 27 ALA B 28 SER B 29 SITE 2 AC2 16 GLY B 30 ALA B 45 LYS B 47 THR B 95 SITE 3 AC2 16 GLU B 96 MET B 98 GLU B 105 ASN B 151 SITE 4 AC2 16 LEU B 153 ASP B 164 MG B1312 HOH B2008 SITE 1 AC3 4 ASN A 151 ASP A 164 ACP A1311 HOH A2023 SITE 1 AC4 3 ASN B 151 ASP B 164 ACP B1311 CRYST1 131.566 131.566 106.582 90.00 90.00 120.00 P 32 2 1 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 0.007601 0.004388 0.000000 0.00000 SCALE2 0.000000 0.008777 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009382 0.00000