HEADER HYDROLASE 05-MAY-17 5VPI TITLE CRYSTAL STRUCTURE OF HUMAN KRAS G12A MUTANT IN COMPLEX WITH GTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTPASE KRAS; COMPND 3 CHAIN: A, B; 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,S.NI,M.A.KENNEDY REVDAT 3 13-MAR-24 5VPI 1 LINK REVDAT 2 20-DEC-17 5VPI 1 JRNL REVDAT 1 06-DEC-17 5VPI 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. 1.62 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 49025 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2580 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) : 1.62 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.66 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3629 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3370 REMARK 3 BIN FREE R VALUE SET COUNT : 172 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2546 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 163 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.73000 REMARK 3 B22 (A**2) : -0.73000 REMARK 3 B33 (A**2) : 2.37000 REMARK 3 B12 (A**2) : -0.37000 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): 0.085 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.086 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.446 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2746 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2492 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3728 ; 1.606 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5791 ; 0.802 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 330 ; 6.965 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 137 ;37.352 ;24.234 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 489 ;12.918 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;16.242 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 411 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3032 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 556 ; 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 B 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 B 0 B 169 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT THERMAL 1 A (A**2): 1319 ; 1.550 ; 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 : 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 : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5VPI 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_1000227812. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-17 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 : 51590 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 68.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.88900 REMARK 200 R SYM FOR SHELL (I) : 0.88900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 MOL/L SODIUM ACETATE, 0.1 MOL/L REMARK 280 TRIS PH 8.5, 24% 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 47.39600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.36409 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.49333 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 47.39600 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 27.36409 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 40.49333 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 47.39600 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 27.36409 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.49333 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 54.72819 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 80.98667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 54.72819 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 80.98667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 54.72819 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 80.98667 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 379 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 380 LIES ON A SPECIAL POSITION. 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 THR A 35 REMARK 465 ILE A 36 REMARK 465 GLY A 60 REMARK 465 GLN A 61 REMARK 465 GLU A 62 REMARK 465 GLU A 63 REMARK 465 TYR A 64 REMARK 465 SER A 65 REMARK 465 ALA A 66 REMARK 465 MET A 67 REMARK 465 ARG A 68 REMARK 465 THR B 35 REMARK 465 ILE B 36 REMARK 465 GLY B 60 REMARK 465 GLN B 61 REMARK 465 GLU B 62 REMARK 465 GLU B 63 REMARK 465 TYR B 64 REMARK 465 SER B 65 REMARK 465 ALA B 66 REMARK 465 MET B 67 REMARK 465 ARG B 68 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 131 O HOH B 301 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLN A 25 OE1 GLN B 25 6445 1.57 REMARK 500 OE1 GLN A 25 CD GLN B 25 6445 2.10 REMARK 500 CD GLN A 25 OE1 GLN B 25 6445 2.12 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 78.97 -114.52 REMARK 500 LYS A 117 36.00 73.62 REMARK 500 ASP B 33 79.24 -116.64 REMARK 500 LYS B 117 34.63 73.14 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 GTP A 201 O3G 173.7 REMARK 620 3 GTP A 201 O2B 92.7 90.9 REMARK 620 4 HOH A 310 O 88.0 97.0 92.5 REMARK 620 5 HOH A 355 O 89.4 85.4 91.3 175.5 REMARK 620 6 HOH A 362 O 82.9 93.4 175.6 88.0 88.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 17 OG REMARK 620 2 GTP B 201 O3G 175.9 REMARK 620 3 GTP B 201 O1B 88.8 92.6 REMARK 620 4 HOH B 315 O 87.9 95.8 91.8 REMARK 620 5 HOH B 344 O 88.2 88.0 89.0 176.0 REMARK 620 6 HOH B 371 O 86.9 91.6 175.2 90.2 88.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GTP 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 GTP B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VP7 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 5VPI A 1 169 UNP P01116 RASK_HUMAN 1 169 DBREF 5VPI B 1 169 UNP P01116 RASK_HUMAN 1 169 SEQADV 5VPI HIS A 0 UNP P01116 EXPRESSION TAG SEQADV 5VPI ALA A 12 UNP P01116 GLY 12 ENGINEERED MUTATION SEQADV 5VPI SER A 118 UNP P01116 CYS 118 ENGINEERED MUTATION SEQADV 5VPI HIS B 0 UNP P01116 EXPRESSION TAG SEQADV 5VPI ALA B 12 UNP P01116 GLY 12 ENGINEERED MUTATION SEQADV 5VPI SER B 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 B 170 HIS MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA ALA 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 CYS 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 CYS 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 GTP A 201 32 HET MG A 202 1 HET GTP B 201 32 HET MG B 202 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 3 GTP 2(C10 H16 N5 O14 P3) FORMUL 4 MG 2(MG 2+) FORMUL 7 HOH *163(H2 O) HELIX 1 AA1 GLY A 15 ASN A 26 1 12 HELIX 2 AA2 GLN A 70 GLY A 75 1 6 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 B 15 ASN B 26 1 12 HELIX 8 AA8 GLN B 70 GLY B 75 1 6 HELIX 9 AA9 ASN B 86 ASP B 92 1 7 HELIX 10 AB1 ASP B 92 ASP B 105 1 14 HELIX 11 AB2 ASP B 126 GLY B 138 1 13 HELIX 12 AB3 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 LEU A 53 N LYS A 42 SHEET 3 AA1 6 THR A 2 VAL A 9 1 N THR A 2 O LEU A 52 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 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 B 38 ILE B 46 0 SHEET 2 AA2 6 GLU B 49 ASP B 57 -1 O LEU B 53 N LYS B 42 SHEET 3 AA2 6 THR B 2 VAL B 9 1 N LEU B 6 O ASP B 54 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 OG SER A 17 MG MG A 202 1555 1555 2.18 LINK O3G GTP A 201 MG MG A 202 1555 1555 2.05 LINK O2B GTP A 201 MG MG A 202 1555 1555 2.14 LINK MG MG A 202 O HOH A 310 1555 1555 2.02 LINK MG MG A 202 O HOH A 355 1555 1555 2.24 LINK MG MG A 202 O HOH A 362 1555 1555 2.10 LINK OG SER B 17 MG MG B 202 1555 1555 2.23 LINK O3G GTP B 201 MG MG B 202 1555 1555 2.00 LINK O1B GTP B 201 MG MG B 202 1555 1555 2.22 LINK MG MG B 202 O HOH B 315 1555 1555 2.00 LINK MG MG B 202 O HOH B 344 1555 1555 2.26 LINK MG MG B 202 O HOH B 371 1555 1555 2.21 SITE 1 AC1 24 ALA A 12 GLY A 13 VAL A 14 GLY A 15 SITE 2 AC1 24 LYS A 16 SER A 17 ALA A 18 PHE A 28 SITE 3 AC1 24 VAL A 29 ASP A 30 TYR A 32 ASN A 116 SITE 4 AC1 24 LYS A 117 ASP A 119 LEU A 120 SER A 145 SITE 5 AC1 24 ALA A 146 LYS A 147 MG A 202 HOH A 310 SITE 6 AC1 24 HOH A 355 HOH A 359 HOH A 362 HOH A 365 SITE 1 AC2 5 SER A 17 GTP A 201 HOH A 310 HOH A 355 SITE 2 AC2 5 HOH A 362 SITE 1 AC3 25 ALA B 12 GLY B 13 VAL B 14 GLY B 15 SITE 2 AC3 25 LYS B 16 SER B 17 ALA B 18 PHE B 28 SITE 3 AC3 25 VAL B 29 ASP B 30 TYR B 32 PRO B 34 SITE 4 AC3 25 ALA B 59 ASN B 116 LYS B 117 ASP B 119 SITE 5 AC3 25 LEU B 120 SER B 145 ALA B 146 LYS B 147 SITE 6 AC3 25 MG B 202 HOH B 315 HOH B 344 HOH B 347 SITE 7 AC3 25 HOH B 371 SITE 1 AC4 5 SER B 17 GTP B 201 HOH B 315 HOH B 344 SITE 2 AC4 5 HOH B 371 CRYST1 94.792 94.792 121.480 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 0.010549 0.006091 0.000000 0.00000 SCALE2 0.000000 0.012181 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008232 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 -0.499707 0.866194 -0.000229 0.00555 1 MTRIX2 2 0.866194 0.499707 -0.000163 -0.00386 1 MTRIX3 2 -0.000027 -0.000280 -1.000000 0.00136 1