HEADER SIGNALING PROTEIN 15-SEP-17 6B0V TITLE CRYSTAL STRUCTURE OF SMALL MOLECULE ARS-107 COVALENTLY BOUND TO K-RAS TITLE 2 G12C COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTPASE KRAS; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-169; COMPND 5 SYNONYM: K-RAS 2,KI-RAS,C-K-RAS,C-KI-RAS; COMPND 6 ENGINEERED: YES; COMPND 7 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: KRAS, KRAS2, RASK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PJEXPRESS411 KEYWDS SMALL GTPASE DOMAIN, COVALENT INHIBITOR BOUND, SWITCH II POCKET, GDP KEYWDS 2 BOUND, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.HANSEN,U.PETERS,A.BABBAR,Y.CHEN,J.FENG,M.R.JANES,L.-S.LI,P.REN, AUTHOR 2 Y.LIU,P.P.ZARRINKAR REVDAT 4 04-OCT-23 6B0V 1 LINK REVDAT 3 07-NOV-18 6B0V 1 JRNL REVDAT 2 30-MAY-18 6B0V 1 SOURCE JRNL REVDAT 1 16-MAY-18 6B0V 0 JRNL AUTH R.HANSEN,U.PETERS,A.BABBAR,Y.CHEN,J.FENG,M.R.JANES,L.S.LI, JRNL AUTH 2 P.REN,Y.LIU,P.P.ZARRINKAR JRNL TITL THE REACTIVITY-DRIVEN BIOCHEMICAL MECHANISM OF COVALENT JRNL TITL 2 KRASG12CINHIBITORS. JRNL REF NAT. STRUCT. MOL. BIOL. V. 25 454 2018 JRNL REFN ESSN 1545-9985 JRNL PMID 29760531 JRNL DOI 10.1038/S41594-018-0061-5 REMARK 2 REMARK 2 RESOLUTION. 1.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 3 NUMBER OF REFLECTIONS : 65427 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3371 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) : 1.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.32 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4699 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 237 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2642 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 114 REMARK 3 SOLVENT ATOMS : 402 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : 0.92000 REMARK 3 B33 (A**2) : -0.66000 REMARK 3 B12 (A**2) : -0.38000 REMARK 3 B13 (A**2) : 0.38000 REMARK 3 B23 (A**2) : 1.08000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.062 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.066 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.048 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.292 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2886 ; 0.023 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2709 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3932 ; 2.478 ; 2.004 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6242 ; 2.199 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 355 ; 5.840 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 136 ;34.079 ;24.485 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 501 ;13.735 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;13.681 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 439 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3264 ; 0.015 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 653 ; 0.002 ; 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): 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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 167 REMARK 3 RESIDUE RANGE : A 201 A 204 REMARK 3 ORIGIN FOR THE GROUP (A): -18.236 9.863 6.664 REMARK 3 T TENSOR REMARK 3 T11: 0.0080 T22: 0.0070 REMARK 3 T33: 0.0108 T12: -0.0055 REMARK 3 T13: 0.0031 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 0.7404 L22: 0.0953 REMARK 3 L33: 0.8196 L12: -0.0350 REMARK 3 L13: -0.0653 L23: -0.2315 REMARK 3 S TENSOR REMARK 3 S11: -0.0386 S12: 0.0260 S13: 0.0054 REMARK 3 S21: 0.0033 S22: -0.0073 S23: -0.0251 REMARK 3 S31: 0.0062 S32: -0.0033 S33: 0.0459 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 167 REMARK 3 RESIDUE RANGE : B 201 B 204 REMARK 3 ORIGIN FOR THE GROUP (A): -2.055 -2.517 34.946 REMARK 3 T TENSOR REMARK 3 T11: 0.0056 T22: 0.0188 REMARK 3 T33: 0.0077 T12: -0.0023 REMARK 3 T13: -0.0009 T23: 0.0055 REMARK 3 L TENSOR REMARK 3 L11: 0.1792 L22: 0.3481 REMARK 3 L33: 0.6153 L12: -0.0610 REMARK 3 L13: 0.1375 L23: -0.2187 REMARK 3 S TENSOR REMARK 3 S11: -0.0020 S12: -0.0182 S13: 0.0236 REMARK 3 S21: -0.0192 S22: -0.0082 S23: -0.0061 REMARK 3 S31: 0.0358 S32: -0.0181 S33: 0.0102 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6B0V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1000229850. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999995 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68823 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 REMARK 200 RESOLUTION RANGE LOW (A) : 32.171 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.34100 REMARK 200 R SYM FOR SHELL (I) : 0.34100 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: 5F2E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 29% PEG 4000, 0.2 M CACL2, 0.1 M TRIS REMARK 280 PH=8.5, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 0 REMARK 465 GLU A 168 REMARK 465 LYS A 169 REMARK 465 GLY B 0 REMARK 465 GLU B 168 REMARK 465 LYS B 169 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 ASP A 30 CG OD1 OD2 REMARK 470 SER A 122 OG REMARK 470 ASP A 126 CG OD1 OD2 REMARK 470 MET B 1 CG SD CE REMARK 470 GLU B 31 CG CD OE1 OE2 REMARK 470 ARG B 41 CG CD NE CZ NH1 NH2 REMARK 470 MET B 67 CG SD CE REMARK 470 ASP B 126 CG OD1 OD2 REMARK 470 LYS B 167 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 OE1 GLN B 43 O HOH B 301 2.01 REMARK 500 OE1 GLU A 3 O LEU A 52 2.14 REMARK 500 OE2 GLU A 62 O HOH A 302 2.17 REMARK 500 OG SER B 106 O HOH B 302 2.18 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 GLU B 143 CD GLU B 143 OE1 0.066 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 ASP A 33 CB - CG - OD1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ASP A 33 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 97 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 135 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 161 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP B 33 CB - CG - OD1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG B 97 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 97 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B 135 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 TYR B 137 CB - CG - CD1 ANGL. DEV. = 3.6 DEGREES REMARK 500 PHE B 141 CB - CG - CD1 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG B 161 NE - CZ - NH2 ANGL. DEV. = -3.1 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 LYS B 117 36.06 72.63 REMARK 500 LYS B 117 35.30 72.63 REMARK 500 PRO B 121 43.46 -91.95 REMARK 500 SER B 122 59.40 -147.77 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 A 487 DISTANCE = 6.15 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 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 GDP A 204 O1B 83.8 REMARK 620 3 HOH A 313 O 77.9 88.3 REMARK 620 4 HOH A 324 O 161.5 83.3 114.8 REMARK 620 5 HOH A 349 O 85.7 82.0 161.8 79.4 REMARK 620 6 HOH A 354 O 84.3 162.2 102.0 104.8 84.0 REMARK 620 7 HOH A 375 O 133.4 124.5 68.1 65.0 129.9 73.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 63 OE1 REMARK 620 2 GLU A 63 OE2 51.7 REMARK 620 3 GLY A 138 O 48.1 3.9 REMARK 620 4 HOH A 305 O 48.6 7.2 7.8 REMARK 620 5 HOH A 337 O 52.2 1.2 4.8 6.6 REMARK 620 6 HOH A 373 O 45.1 7.0 4.9 5.1 7.3 REMARK 620 7 HOH A 457 O 50.5 3.7 5.4 3.5 3.1 5.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 17 OG REMARK 620 2 GDP B 204 O3B 85.4 REMARK 620 3 HOH B 342 O 163.3 82.7 REMARK 620 4 HOH B 347 O 79.6 85.9 111.1 REMARK 620 5 HOH B 354 O 87.4 84.4 79.8 164.3 REMARK 620 6 HOH B 374 O 84.3 163.9 104.5 104.3 82.8 REMARK 620 7 HOH B 382 O 131.3 123.9 65.4 66.6 129.1 72.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 63 OE1 REMARK 620 2 GLU B 63 OE2 52.3 REMARK 620 3 GLY B 138 O 48.1 4.3 REMARK 620 4 HOH B 337 O 52.5 1.2 4.9 REMARK 620 5 HOH B 356 O 49.6 7.3 7.7 6.3 REMARK 620 6 HOH B 415 O 45.5 7.9 5.4 7.6 4.9 REMARK 620 7 HOH B 468 O 50.7 3.9 5.2 3.0 3.4 5.2 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C8G A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide C8G B 203 and CYS B REMARK 800 12 DBREF 6B0V A 1 169 UNP P01116 RASK_HUMAN 1 169 DBREF 6B0V B 1 169 UNP P01116 RASK_HUMAN 1 169 SEQADV 6B0V GLY A 0 UNP P01116 EXPRESSION TAG SEQADV 6B0V CYS A 12 UNP P01116 GLY 12 ENGINEERED MUTATION SEQADV 6B0V SER A 51 UNP P01116 CYS 51 ENGINEERED MUTATION SEQADV 6B0V LEU A 80 UNP P01116 CYS 80 ENGINEERED MUTATION SEQADV 6B0V SER A 118 UNP P01116 CYS 118 ENGINEERED MUTATION SEQADV 6B0V GLY B 0 UNP P01116 EXPRESSION TAG SEQADV 6B0V CYS B 12 UNP P01116 GLY 12 ENGINEERED MUTATION SEQADV 6B0V SER B 51 UNP P01116 CYS 51 ENGINEERED MUTATION SEQADV 6B0V LEU B 80 UNP P01116 CYS 80 ENGINEERED MUTATION SEQADV 6B0V SER B 118 UNP P01116 CYS 118 ENGINEERED MUTATION SEQRES 1 A 170 GLY MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA CYS SEQRES 2 A 170 GLY VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN SEQRES 3 A 170 ASN HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SEQRES 4 A 170 SER TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR SER SEQRES 5 A 170 LEU LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SEQRES 6 A 170 SER ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY SEQRES 7 A 170 PHE LEU LEU VAL PHE ALA ILE ASN ASN THR LYS SER PHE SEQRES 8 A 170 GLU ASP ILE HIS HIS TYR ARG GLU GLN ILE LYS ARG VAL SEQRES 9 A 170 LYS ASP SER GLU ASP VAL PRO MET VAL LEU VAL GLY ASN SEQRES 10 A 170 LYS SER ASP LEU PRO SER ARG THR VAL ASP THR LYS GLN SEQRES 11 A 170 ALA GLN ASP LEU ALA ARG SER TYR GLY ILE PRO PHE ILE SEQRES 12 A 170 GLU THR SER ALA LYS THR ARG GLN GLY VAL ASP ASP ALA SEQRES 13 A 170 PHE TYR THR LEU VAL ARG GLU ILE ARG LYS HIS LYS GLU SEQRES 14 A 170 LYS SEQRES 1 B 170 GLY MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA CYS SEQRES 2 B 170 GLY VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN SEQRES 3 B 170 ASN HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SEQRES 4 B 170 SER TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR SER SEQRES 5 B 170 LEU LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SEQRES 6 B 170 SER ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY SEQRES 7 B 170 PHE LEU LEU VAL PHE ALA ILE ASN ASN THR LYS SER PHE SEQRES 8 B 170 GLU ASP ILE HIS HIS TYR ARG GLU GLN ILE LYS ARG VAL SEQRES 9 B 170 LYS ASP SER GLU ASP VAL PRO MET VAL LEU VAL GLY ASN SEQRES 10 B 170 LYS SER ASP LEU PRO SER ARG THR VAL ASP THR LYS GLN SEQRES 11 B 170 ALA GLN ASP LEU ALA ARG SER TYR GLY ILE PRO PHE ILE SEQRES 12 B 170 GLU THR SER ALA LYS THR ARG GLN GLY VAL ASP ASP ALA SEQRES 13 B 170 PHE TYR THR LEU VAL ARG GLU ILE ARG LYS HIS LYS GLU SEQRES 14 B 170 LYS HET CA A 201 1 HET CA A 202 1 HET C8G A 203 27 HET GDP A 204 28 HET CA B 201 1 HET CA B 202 1 HET C8G B 203 27 HET GDP B 204 28 HETNAM CA CALCIUM ION HETNAM C8G 1-[3-(4-{[(4,5-DICHLORO-2-HYDROXYPHENYL) HETNAM 2 C8G AMINO]ACETYL}PIPERAZIN-1-YL)AZETIDIN-1-YL]PROPAN-1-ONE HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 3 CA 4(CA 2+) FORMUL 5 C8G 2(C18 H24 CL2 N4 O3) FORMUL 6 GDP 2(C10 H15 N5 O11 P2) FORMUL 11 HOH *402(H2 O) HELIX 1 AA1 GLY A 15 ASN A 26 1 12 HELIX 2 AA2 SER A 65 ARG A 73 1 9 HELIX 3 AA3 ASN A 86 ASP A 105 1 20 HELIX 4 AA4 ASP A 126 GLY A 138 1 13 HELIX 5 AA5 GLY A 151 LYS A 167 1 17 HELIX 6 AA6 GLY B 15 ASN B 26 1 12 HELIX 7 AA7 SER B 65 ARG B 73 1 9 HELIX 8 AA8 ASN B 86 LYS B 104 1 19 HELIX 9 AA9 ASP B 126 GLY B 138 1 13 HELIX 10 AB1 GLY B 151 LYS B 167 1 17 SHEET 1 AA1 6 ASP A 38 ILE A 46 0 SHEET 2 AA1 6 GLU A 49 ASP A 57 -1 O ILE A 55 N TYR A 40 SHEET 3 AA1 6 THR A 2 VAL A 9 1 N VAL A 8 O LEU A 56 SHEET 4 AA1 6 GLY A 77 ALA A 83 1 O VAL A 81 N VAL A 9 SHEET 5 AA1 6 MET A 111 ASN A 116 1 O VAL A 114 N LEU A 80 SHEET 6 AA1 6 PHE A 141 GLU A 143 1 O ILE A 142 N LEU A 113 SHEET 1 AA2 6 ASP B 38 ILE B 46 0 SHEET 2 AA2 6 GLU B 49 ASP B 57 -1 O ILE B 55 N TYR B 40 SHEET 3 AA2 6 GLU B 3 VAL B 9 1 N LEU B 6 O LEU B 56 SHEET 4 AA2 6 GLY B 77 ALA B 83 1 O VAL B 81 N VAL B 9 SHEET 5 AA2 6 MET B 111 ASN B 116 1 O ASN B 116 N PHE B 82 SHEET 6 AA2 6 PHE B 141 GLU B 143 1 O ILE B 142 N LEU B 113 LINK SG CYS A 12 C12 C8G A 203 1555 1555 1.68 LINK SG CYS B 12 C12 C8G B 203 1555 1555 1.70 LINK OG SER A 17 CA CA A 201 1555 1555 2.46 LINK OE1 GLU A 63 CA CA A 202 1555 1655 2.52 LINK OE2 GLU A 63 CA CA A 202 1555 1655 2.47 LINK O GLY A 138 CA CA A 202 1555 1555 2.29 LINK CA CA A 201 O1B GDP A 204 1555 1555 2.35 LINK CA CA A 201 O HOH A 313 1555 1555 2.42 LINK CA CA A 201 O HOH A 324 1555 1555 2.44 LINK CA CA A 201 O HOH A 349 1555 1555 2.37 LINK CA CA A 201 O HOH A 354 1555 1555 2.40 LINK CA CA A 201 O HOH A 375 1555 1555 2.51 LINK CA CA A 202 O HOH A 305 1555 1555 2.25 LINK CA CA A 202 O HOH A 337 1555 1555 2.45 LINK CA CA A 202 O HOH A 373 1555 1555 2.49 LINK CA CA A 202 O HOH A 457 1555 1555 2.44 LINK OG SER B 17 CA CA B 201 1555 1555 2.37 LINK OE1 GLU B 63 CA CA B 202 1555 1455 2.49 LINK OE2 GLU B 63 CA CA B 202 1555 1455 2.45 LINK O GLY B 138 CA CA B 202 1555 1555 2.24 LINK CA CA B 201 O3B GDP B 204 1555 1555 2.31 LINK CA CA B 201 O HOH B 342 1555 1555 2.41 LINK CA CA B 201 O HOH B 347 1555 1555 2.38 LINK CA CA B 201 O HOH B 354 1555 1555 2.41 LINK CA CA B 201 O HOH B 374 1555 1555 2.39 LINK CA CA B 201 O HOH B 382 1555 1555 2.58 LINK CA CA B 202 O HOH B 337 1555 1555 2.41 LINK CA CA B 202 O HOH B 356 1555 1555 2.34 LINK CA CA B 202 O HOH B 415 1555 1555 2.44 LINK CA CA B 202 O HOH B 468 1555 1555 2.38 SITE 1 AC1 7 SER A 17 GDP A 204 HOH A 313 HOH A 324 SITE 2 AC1 7 HOH A 349 HOH A 354 HOH A 375 SITE 1 AC2 6 GLU A 63 GLY A 138 HOH A 305 HOH A 337 SITE 2 AC2 6 HOH A 373 HOH A 457 SITE 1 AC3 15 GLY A 10 CYS A 12 LYS A 16 ALA A 59 SITE 2 AC3 15 GLY A 60 GLN A 61 GLU A 63 ARG A 68 SITE 3 AC3 15 ASP A 69 TYR A 96 GLN A 99 VAL A 103 SITE 4 AC3 15 GDP A 204 HOH A 324 HOH A 421 SITE 1 AC4 26 GLY A 13 VAL A 14 GLY A 15 LYS A 16 SITE 2 AC4 26 SER A 17 ALA A 18 PHE A 28 VAL A 29 SITE 3 AC4 26 ASP A 30 ASN A 116 LYS A 117 ASP A 119 SITE 4 AC4 26 LEU A 120 SER A 145 ALA A 146 LYS A 147 SITE 5 AC4 26 CA A 201 C8G A 203 HOH A 306 HOH A 324 SITE 6 AC4 26 HOH A 349 HOH A 364 HOH A 366 HOH A 374 SITE 7 AC4 26 HOH A 388 HOH A 397 SITE 1 AC5 7 SER B 17 GDP B 204 HOH B 342 HOH B 347 SITE 2 AC5 7 HOH B 354 HOH B 374 HOH B 382 SITE 1 AC6 6 GLU B 63 GLY B 138 HOH B 337 HOH B 356 SITE 2 AC6 6 HOH B 415 HOH B 468 SITE 1 AC7 24 GLY B 13 VAL B 14 GLY B 15 LYS B 16 SITE 2 AC7 24 SER B 17 ALA B 18 PHE B 28 VAL B 29 SITE 3 AC7 24 ASP B 30 ASN B 116 LYS B 117 ASP B 119 SITE 4 AC7 24 LEU B 120 SER B 145 ALA B 146 LYS B 147 SITE 5 AC7 24 CA B 201 HOH B 328 HOH B 342 HOH B 354 SITE 6 AC7 24 HOH B 365 HOH B 376 HOH B 385 HOH B 433 SITE 1 AC8 21 GLY B 10 ALA B 11 GLY B 13 VAL B 14 SITE 2 AC8 21 LYS B 16 ALA B 59 GLY B 60 GLN B 61 SITE 3 AC8 21 GLU B 63 TYR B 64 ARG B 68 ASP B 69 SITE 4 AC8 21 MET B 72 TYR B 96 GLN B 99 VAL B 103 SITE 5 AC8 21 HOH B 342 HOH B 377 HOH B 411 HOH B 417 SITE 6 AC8 21 HOH B 458 CRYST1 33.140 39.880 62.430 77.00 81.24 77.58 P 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.030175 -0.006645 -0.003394 0.00000 SCALE2 0.000000 0.025676 -0.005217 0.00000 SCALE3 0.000000 0.000000 0.016538 0.00000