HEADER HYDROLASE 04-MAY-17 5VP7 TITLE CRYSTAL STRUCTURE OF HUMAN KRAS G12A MUTANT IN COMPLEX WITH GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTPASE KRAS; COMPND 3 CHAIN: A, F; COMPND 4 FRAGMENT: 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: 562 KEYWDS ONCOGENIC MUTANT, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.XU,B.LONG,G.BORIS,A.CHEN,S.NI,M.A.KENNEDY REVDAT 3 04-OCT-23 5VP7 1 REMARK LINK REVDAT 2 20-DEC-17 5VP7 1 JRNL REVDAT 1 06-DEC-17 5VP7 0 JRNL AUTH S.XU,B.N.LONG,G.H.BORIS,A.CHEN,S.NI,M.A.KENNEDY JRNL TITL STRUCTURAL INSIGHT INTO THE REARRANGEMENT OF THE SWITCH I JRNL TITL 2 REGION IN GTP-BOUND G12A K-RAS. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 73 970 2017 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 29199977 JRNL DOI 10.1107/S2059798317015418 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.07 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 40983 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2251 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3025 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.87 REMARK 3 BIN R VALUE (WORKING SET) : 0.3340 REMARK 3 BIN FREE R VALUE SET COUNT : 157 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2722 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 70 REMARK 3 SOLVENT ATOMS : 201 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.79000 REMARK 3 B22 (A**2) : -0.79000 REMARK 3 B33 (A**2) : 2.57000 REMARK 3 B12 (A**2) : -0.40000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.096 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.097 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.646 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2869 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2623 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3860 ; 1.615 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6063 ; 0.793 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 342 ; 6.206 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 142 ;39.264 ;24.366 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 510 ;12.143 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;18.651 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 428 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3128 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 572 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A F REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 0 A 169 1 REMARK 3 1 F 0 F 169 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT THERMAL 1 A (A**2): 1368 ; 0.920 ; 0.500 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5VP7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000227803. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97931 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43235 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 28.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : 0.08200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.87300 REMARK 200 R SYM FOR SHELL (I) : 0.03300 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4I8G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 MOL L-1 SODIUM ACETATE, 0.1 MOL L REMARK 280 -1 TRIS PH 8.5, 26% PEG 3,350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.88650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.06993 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.97267 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 46.88650 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 27.06993 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 39.97267 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 46.88650 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 27.06993 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.97267 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 54.13987 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 79.94533 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 54.13987 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 79.94533 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 54.13987 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 79.94533 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: F 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 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 HOH F 395 O HOH F 399 2.10 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 A 0 N HIS A 0 CA 0.126 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 123 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 135 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG F 123 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG F 123 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG F 135 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG F 135 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 ASP A 33 120.57 -39.25 REMARK 500 LYS A 117 36.37 72.40 REMARK 500 ARG A 149 -1.62 79.89 REMARK 500 ARG F 149 0.23 80.39 REMARK 500 REMARK 500 REMARK: NULL 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 A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 GDP A 201 O3B 91.9 REMARK 620 3 HOH A 305 O 83.1 98.0 REMARK 620 4 HOH A 311 O 92.1 88.5 172.0 REMARK 620 5 HOH A 341 O 173.3 93.7 92.5 91.7 REMARK 620 6 HOH A 360 O 92.4 168.7 92.9 80.9 82.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 204 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 18 O REMARK 620 2 HIS A 27 O 130.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG F 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER F 17 OG REMARK 620 2 GDP F 201 O2B 93.4 REMARK 620 3 HOH F 304 O 83.2 97.8 REMARK 620 4 HOH F 316 O 92.5 87.1 173.7 REMARK 620 5 HOH F 346 O 173.9 92.0 93.3 90.6 REMARK 620 6 HOH F 352 O 93.8 166.6 94.3 81.3 81.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA F 203 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA F 18 O REMARK 620 2 HIS F 27 O 128.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP F 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG F 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA F 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VPI RELATED DB: PDB REMARK 900 RELATED ID: 5VPY RELATED DB: PDB REMARK 900 RELATED ID: 5VPZ RELATED DB: PDB REMARK 900 RELATED ID: 5VQ0 RELATED DB: PDB REMARK 900 RELATED ID: 5VQ1 RELATED DB: PDB REMARK 900 RELATED ID: 5VQ2 RELATED DB: PDB REMARK 900 RELATED ID: 5VQ6 RELATED DB: PDB REMARK 900 RELATED ID: 5VQ8 RELATED DB: PDB DBREF 5VP7 A 1 169 UNP P01116 RASK_HUMAN 1 169 DBREF 5VP7 F 1 169 UNP P01116 RASK_HUMAN 1 169 SEQADV 5VP7 HIS A 0 UNP P01116 EXPRESSION TAG SEQADV 5VP7 ALA A 12 UNP P01116 GLY 12 ENGINEERED MUTATION SEQADV 5VP7 SER A 118 UNP P01116 CYS 118 ENGINEERED MUTATION SEQADV 5VP7 HIS F 0 UNP P01116 EXPRESSION TAG SEQADV 5VP7 ALA F 12 UNP P01116 GLY 12 ENGINEERED MUTATION SEQADV 5VP7 SER F 118 UNP P01116 CYS 118 ENGINEERED MUTATION SEQRES 1 A 170 HIS MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA ALA 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 CYS 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 CYS 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 F 170 HIS MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA ALA SEQRES 2 F 170 GLY VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN SEQRES 3 F 170 ASN HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SEQRES 4 F 170 SER TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR CYS SEQRES 5 F 170 LEU LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SEQRES 6 F 170 SER ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY SEQRES 7 F 170 PHE LEU CYS VAL PHE ALA ILE ASN ASN THR LYS SER PHE SEQRES 8 F 170 GLU ASP ILE HIS HIS TYR ARG GLU GLN ILE LYS ARG VAL SEQRES 9 F 170 LYS ASP SER GLU ASP VAL PRO MET VAL LEU VAL GLY ASN SEQRES 10 F 170 LYS SER ASP LEU PRO SER ARG THR VAL ASP THR LYS GLN SEQRES 11 F 170 ALA GLN ASP LEU ALA ARG SER TYR GLY ILE PRO PHE ILE SEQRES 12 F 170 GLU THR SER ALA LYS THR ARG GLN GLY VAL ASP ASP ALA SEQRES 13 F 170 PHE TYR THR LEU VAL ARG GLU ILE ARG LYS HIS LYS GLU SEQRES 14 F 170 LYS HET GDP A 201 28 HET MG A 202 1 HET PGE A 203 10 HET NA A 204 1 HET GDP F 201 28 HET MG F 202 1 HET NA F 203 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM PGE TRIETHYLENE GLYCOL HETNAM NA SODIUM ION FORMUL 3 GDP 2(C10 H15 N5 O11 P2) FORMUL 4 MG 2(MG 2+) FORMUL 5 PGE C6 H14 O4 FORMUL 6 NA 2(NA 1+) FORMUL 10 HOH *201(H2 O) HELIX 1 AA1 GLY A 15 ASN A 26 1 12 HELIX 2 AA2 SER A 65 GLY A 75 1 11 HELIX 3 AA3 ASN A 86 ASP A 92 1 7 HELIX 4 AA4 ASP A 92 ASP A 105 1 14 HELIX 5 AA5 ASP A 126 GLY A 138 1 13 HELIX 6 AA6 GLY A 151 LYS A 167 1 17 HELIX 7 AA7 GLY F 15 ASN F 26 1 12 HELIX 8 AA8 SER F 65 GLY F 75 1 11 HELIX 9 AA9 ASN F 86 ASP F 92 1 7 HELIX 10 AB1 ASP F 92 ASP F 105 1 14 HELIX 11 AB2 ASP F 126 GLY F 138 1 13 HELIX 12 AB3 GLY F 151 LYS F 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 LEU A 53 N LYS A 42 SHEET 3 AA1 6 THR A 2 GLY A 10 1 N THR A 2 O LEU A 52 SHEET 4 AA1 6 GLY A 77 ALA A 83 1 O LEU A 79 N VAL A 9 SHEET 5 AA1 6 MET A 111 ASN A 116 1 O ASN A 116 N PHE A 82 SHEET 6 AA1 6 PHE A 141 GLU A 143 1 O ILE A 142 N LEU A 113 SHEET 1 AA2 6 ASP F 38 ILE F 46 0 SHEET 2 AA2 6 GLU F 49 ASP F 57 -1 O LEU F 53 N LYS F 42 SHEET 3 AA2 6 THR F 2 GLY F 10 1 N THR F 2 O LEU F 52 SHEET 4 AA2 6 GLY F 77 ALA F 83 1 O VAL F 81 N VAL F 9 SHEET 5 AA2 6 MET F 111 ASN F 116 1 O ASN F 116 N PHE F 82 SHEET 6 AA2 6 PHE F 141 GLU F 143 1 O ILE F 142 N LEU F 113 LINK OG SER A 17 MG MG A 202 1555 1555 2.03 LINK O ALA A 18 NA NA A 204 1555 1555 2.61 LINK O HIS A 27 NA NA A 204 1555 1555 2.58 LINK O3B GDP A 201 MG MG A 202 1555 1555 2.03 LINK MG MG A 202 O HOH A 305 1555 1555 2.14 LINK MG MG A 202 O HOH A 311 1555 1555 2.17 LINK MG MG A 202 O HOH A 341 1555 1555 2.15 LINK MG MG A 202 O HOH A 360 1555 1555 2.18 LINK OG SER F 17 MG MG F 202 1555 1555 2.03 LINK O ALA F 18 NA NA F 203 1555 1555 2.62 LINK O HIS F 27 NA NA F 203 1555 1555 2.59 LINK O2B GDP F 201 MG MG F 202 1555 1555 2.03 LINK MG MG F 202 O HOH F 304 1555 1555 2.15 LINK MG MG F 202 O HOH F 316 1555 1555 2.16 LINK MG MG F 202 O HOH F 346 1555 1555 2.16 LINK MG MG F 202 O HOH F 352 1555 1555 2.19 SITE 1 AC1 22 GLY A 13 VAL A 14 GLY A 15 LYS A 16 SITE 2 AC1 22 SER A 17 ALA A 18 PHE A 28 VAL A 29 SITE 3 AC1 22 ASP A 30 ASN A 116 LYS A 117 ASP A 119 SITE 4 AC1 22 LEU A 120 SER A 145 ALA A 146 LYS A 147 SITE 5 AC1 22 MG A 202 HOH A 311 HOH A 318 HOH A 339 SITE 6 AC1 22 HOH A 341 HOH A 372 SITE 1 AC2 6 SER A 17 GDP A 201 HOH A 305 HOH A 311 SITE 2 AC2 6 HOH A 341 HOH A 360 SITE 1 AC3 3 ASP A 154 ASP F 153 ASP F 154 SITE 1 AC4 6 ALA A 18 ILE A 21 GLN A 22 HIS A 27 SITE 2 AC4 6 PHE A 28 VAL A 29 SITE 1 AC5 21 GLY F 13 VAL F 14 GLY F 15 LYS F 16 SITE 2 AC5 21 SER F 17 ALA F 18 PHE F 28 VAL F 29 SITE 3 AC5 21 ASP F 30 ASN F 116 LYS F 117 ASP F 119 SITE 4 AC5 21 LEU F 120 SER F 145 ALA F 146 LYS F 147 SITE 5 AC5 21 MG F 202 HOH F 316 HOH F 324 HOH F 346 SITE 6 AC5 21 HOH F 375 SITE 1 AC6 6 SER F 17 GDP F 201 HOH F 304 HOH F 316 SITE 2 AC6 6 HOH F 346 HOH F 352 SITE 1 AC7 6 ALA F 18 ILE F 21 GLN F 22 HIS F 27 SITE 2 AC7 6 PHE F 28 VAL F 29 CRYST1 93.773 93.773 119.918 90.00 90.00 120.00 H 3 18 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 0.010664 0.006157 0.000000 0.00000 SCALE2 0.000000 0.012314 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008339 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 1.000000 -0.000015 -0.000827 -0.02321 1 MTRIX2 2 -0.000015 -1.000000 0.000175 -54.13287 1 MTRIX3 2 -0.000827 -0.000175 -1.000000 -23.19203 1