HEADER SIGNALING PROTEIN 19-APR-18 6D5W TITLE RAS:SOS:RAS IN COMPLEX WITH A SMALL MOLECULE ACTIVATOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTPASE HRAS; COMPND 3 CHAIN: Q; COMPND 4 SYNONYM: H-RAS-1,HA-RAS,TRANSFORMING PROTEIN P21,C-H-RAS,P21RAS; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: GTPASE HRAS; COMPND 9 CHAIN: R; COMPND 10 SYNONYM: H-RAS-1,HA-RAS,TRANSFORMING PROTEIN P21,C-H-RAS,P21RAS; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: SON OF SEVENLESS HOMOLOG 1; COMPND 14 CHAIN: S; COMPND 15 SYNONYM: SOS-1; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HRAS, HRAS1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: HRAS, HRAS1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 GENE: SOS1; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RAS, SOS, INHIBITOR, ONCOPROTEIN, PROTEIN-PROTEIN COMPLEX, MAPK, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.PHAN,T.HODGES,S.W.FESIK REVDAT 2 04-OCT-23 6D5W 1 REMARK REVDAT 1 27-MAR-19 6D5W 0 JRNL AUTH T.R.HODGES,J.R.ABBOTT,A.J.LITTLE,D.SARKAR,J.M.SALOVICH, JRNL AUTH 2 J.E.HOWES,D.T.AKAN,J.SAI,A.L.ARNOLD,C.BROWNING,M.C.BURNS, JRNL AUTH 3 T.SOBOLIK,Q.SUN,Y.BEESETTY,J.A.COKER,D.SCHARN, JRNL AUTH 4 H.STADTMUELLER,O.W.ROSSANESE,J.PHAN,A.G.WATERSON, JRNL AUTH 5 D.B.MCCONNELL,S.W.FESIK JRNL TITL DISCOVERY AND STRUCTURE-BASED OPTIMIZATION OF JRNL TITL 2 BENZIMIDAZOLE-DERIVED ACTIVATORS OF SOS1-MEDIATED NUCLEOTIDE JRNL TITL 3 EXCHANGE ON RAS. JRNL REF J. MED. CHEM. V. 61 8875 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 30205005 JRNL DOI 10.1021/ACS.JMEDCHEM.8B01108 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.C.BURNS,Q.SUN,R.N.DANIELS,D.CAMPER,J.P.KENNEDY,J.PHAN, REMARK 1 AUTH 2 E.T.OLEJNICZAK,T.LEE,A.G.WATERSON,O.W.ROSSANESE,S.W.FESIK REMARK 1 TITL APPROACH FOR TARGETING RAS WITH SMALL MOLECULES THAT REMARK 1 TITL 2 ACTIVATE SOS-MEDIATED NUCLEOTIDE EXCHANGE. REMARK 1 REF PROC. NATL. ACAD. SCI. V. 111 3401 2014 REMARK 1 REF 2 U.S.A. REMARK 1 REFN ESSN 1091-6490 REMARK 1 PMID 24550516 REMARK 1 DOI 10.1073/PNAS.1315798111 REMARK 2 REMARK 2 RESOLUTION. 2.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 54591 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.640 REMARK 3 FREE R VALUE TEST SET COUNT : 1988 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 43.0394 - 5.9676 1.00 4056 153 0.1777 0.1888 REMARK 3 2 5.9676 - 4.7386 1.00 3905 147 0.1670 0.1876 REMARK 3 3 4.7386 - 4.1401 1.00 3890 148 0.1435 0.1774 REMARK 3 4 4.1401 - 3.7618 0.99 3816 144 0.1676 0.2147 REMARK 3 5 3.7618 - 3.4923 0.92 3540 130 0.2278 0.2654 REMARK 3 6 3.4923 - 3.2865 1.00 3822 148 0.1957 0.2359 REMARK 3 7 3.2865 - 3.1220 1.00 3806 147 0.2078 0.2987 REMARK 3 8 3.1220 - 2.9861 1.00 3817 144 0.2171 0.2756 REMARK 3 9 2.9861 - 2.8712 1.00 3785 145 0.2265 0.2344 REMARK 3 10 2.8712 - 2.7721 1.00 3817 140 0.2274 0.2529 REMARK 3 11 2.7721 - 2.6855 1.00 3791 144 0.2434 0.3078 REMARK 3 12 2.6855 - 2.6087 1.00 3767 148 0.2636 0.2793 REMARK 3 13 2.6087 - 2.5400 1.00 3812 130 0.2660 0.3052 REMARK 3 14 2.5400 - 2.4781 0.79 2979 120 0.2849 0.3497 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 6785 REMARK 3 ANGLE : 1.082 9188 REMARK 3 CHIRALITY : 0.073 1004 REMARK 3 PLANARITY : 0.004 1196 REMARK 3 DIHEDRAL : 17.000 2612 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6D5W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-APR-18. REMARK 100 THE DEPOSITION ID IS D_1000234035. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-12 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 : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54650 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.470 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 14.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.31000 REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.00000 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4NYI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, 2.0 M SODIUM REMARK 280 FORMATE, PH 4.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 93.06250 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 93.06250 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 89.60850 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 93.06250 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 93.06250 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 89.60850 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 93.06250 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 93.06250 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 89.60850 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 93.06250 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 93.06250 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 89.60850 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 93.06250 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 93.06250 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 89.60850 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 93.06250 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 93.06250 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 89.60850 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 93.06250 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 93.06250 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 89.60850 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 93.06250 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 93.06250 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 89.60850 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: Q, R, S 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 S 565 REMARK 465 ASN S 591 REMARK 465 MET S 592 REMARK 465 GLN S 593 REMARK 465 PRO S 594 REMARK 465 LYS S 595 REMARK 465 ALA S 596 REMARK 465 ARG S 744 REMARK 465 ASP S 745 REMARK 465 ASN S 746 REMARK 465 GLY S 747 REMARK 465 PRO S 748 REMARK 465 GLY S 749 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 GLU S 954 O HOH S 1201 1.87 REMARK 500 O HOH S 1230 O HOH S 1311 1.89 REMARK 500 O HOH R 261 O HOH S 1301 1.89 REMARK 500 O HOH S 1247 O HOH S 1275 1.96 REMARK 500 O HOH S 1271 O HOH S 1342 1.96 REMARK 500 OG1 THR S 829 O HOH S 1202 2.00 REMARK 500 O HOH R 221 O HOH R 235 2.06 REMARK 500 NH1 ARG R 73 O ASN S 879 2.08 REMARK 500 O HOH S 1353 O HOH S 1366 2.10 REMARK 500 OG1 THR S 720 O HOH S 1203 2.10 REMARK 500 O HOH S 1386 O HOH S 1394 2.11 REMARK 500 O HOH S 1381 O HOH S 1386 2.12 REMARK 500 O HOH S 1334 O HOH S 1404 2.13 REMARK 500 OG SER R 145 O HOH R 201 2.16 REMARK 500 OD2 ASP S 707 O HOH S 1204 2.16 REMARK 500 O HOH S 1337 O HOH S 1364 2.16 REMARK 500 OH TYR S 681 O HOH S 1205 2.17 REMARK 500 OD1 ASP Q 33 O HOH Q 301 2.18 REMARK 500 O HOH S 1336 O HOH S 1368 2.19 REMARK 500 OE1 GLN S 566 O HOH S 1206 2.19 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 O HOH S 1375 O HOH S 1375 7555 2.08 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 ALA Q 122 73.64 -68.64 REMARK 500 ARG Q 149 -1.68 81.05 REMARK 500 VAL R 14 28.03 -141.53 REMARK 500 SER R 17 -38.25 -39.57 REMARK 500 ASN R 26 78.88 44.61 REMARK 500 HIS R 27 -23.10 93.39 REMARK 500 ASP R 30 11.73 -154.34 REMARK 500 LYS R 42 118.96 -164.83 REMARK 500 ASP R 119 -150.18 -146.35 REMARK 500 ARG R 149 17.60 58.50 REMARK 500 ALA S 572 23.50 -75.23 REMARK 500 TYR S 575 109.53 -170.86 REMARK 500 PHE S 577 32.23 -91.82 REMARK 500 GLU S 583 20.03 -76.08 REMARK 500 THR S 614 38.81 -140.77 REMARK 500 HIS S 700 43.38 -140.22 REMARK 500 HIS S 764 -109.25 -116.19 REMARK 500 LEU S 886 65.15 -68.39 REMARK 500 PRO S 894 150.25 -43.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLN R 25 ASN R 26 -144.06 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 Q 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER Q 17 OG REMARK 620 2 THR Q 35 OG1 82.6 REMARK 620 3 GNP Q 202 O1G 162.9 87.4 REMARK 620 4 GNP Q 202 O1B 98.7 151.7 83.7 REMARK 620 5 HOH Q 307 O 80.5 81.9 84.5 70.6 REMARK 620 6 HOH Q 318 O 98.5 105.0 97.5 102.7 172.8 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 MG Q 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GNP Q 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FVV S 1101 DBREF 6D5W Q 1 166 UNP P01112 RASH_HUMAN 1 166 DBREF 6D5W R 1 166 UNP P01112 RASH_HUMAN 1 166 DBREF 6D5W S 566 1046 UNP Q07889 SOS1_HUMAN 566 1046 SEQADV 6D5W GLY Q 0 UNP P01112 EXPRESSION TAG SEQADV 6D5W ALA Q 64 UNP P01112 TYR 64 ENGINEERED MUTATION SEQADV 6D5W GLY R 0 UNP P01112 EXPRESSION TAG SEQADV 6D5W GLY S 565 UNP Q07889 EXPRESSION TAG SEQRES 1 Q 167 GLY MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA GLY SEQRES 2 Q 167 GLY VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN SEQRES 3 Q 167 ASN HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SEQRES 4 Q 167 SER TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR CYS SEQRES 5 Q 167 LEU LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU ALA SEQRES 6 Q 167 SER ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY SEQRES 7 Q 167 PHE LEU CYS VAL PHE ALA ILE ASN ASN THR LYS SER PHE SEQRES 8 Q 167 GLU ASP ILE HIS GLN TYR ARG GLU GLN ILE LYS ARG VAL SEQRES 9 Q 167 LYS ASP SER ASP ASP VAL PRO MET VAL LEU VAL GLY ASN SEQRES 10 Q 167 LYS CYS ASP LEU ALA ALA ARG THR VAL GLU SER ARG GLN SEQRES 11 Q 167 ALA GLN ASP LEU ALA ARG SER TYR GLY ILE PRO TYR ILE SEQRES 12 Q 167 GLU THR SER ALA LYS THR ARG GLN GLY VAL GLU ASP ALA SEQRES 13 Q 167 PHE TYR THR LEU VAL ARG GLU ILE ARG GLN HIS SEQRES 1 R 167 GLY MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA GLY SEQRES 2 R 167 GLY VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN SEQRES 3 R 167 ASN HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SEQRES 4 R 167 SER TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR CYS SEQRES 5 R 167 LEU LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SEQRES 6 R 167 SER ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY SEQRES 7 R 167 PHE LEU CYS VAL PHE ALA ILE ASN ASN THR LYS SER PHE SEQRES 8 R 167 GLU ASP ILE HIS GLN TYR ARG GLU GLN ILE LYS ARG VAL SEQRES 9 R 167 LYS ASP SER ASP ASP VAL PRO MET VAL LEU VAL GLY ASN SEQRES 10 R 167 LYS CYS ASP LEU ALA ALA ARG THR VAL GLU SER ARG GLN SEQRES 11 R 167 ALA GLN ASP LEU ALA ARG SER TYR GLY ILE PRO TYR ILE SEQRES 12 R 167 GLU THR SER ALA LYS THR ARG GLN GLY VAL GLU ASP ALA SEQRES 13 R 167 PHE TYR THR LEU VAL ARG GLU ILE ARG GLN HIS SEQRES 1 S 482 GLY GLN MET ARG LEU PRO SER ALA ASP VAL TYR ARG PHE SEQRES 2 S 482 ALA GLU PRO ASP SER GLU GLU ASN ILE ILE PHE GLU GLU SEQRES 3 S 482 ASN MET GLN PRO LYS ALA GLY ILE PRO ILE ILE LYS ALA SEQRES 4 S 482 GLY THR VAL ILE LYS LEU ILE GLU ARG LEU THR TYR HIS SEQRES 5 S 482 MET TYR ALA ASP PRO ASN PHE VAL ARG THR PHE LEU THR SEQRES 6 S 482 THR TYR ARG SER PHE CYS LYS PRO GLN GLU LEU LEU SER SEQRES 7 S 482 LEU ILE ILE GLU ARG PHE GLU ILE PRO GLU PRO GLU PRO SEQRES 8 S 482 THR GLU ALA ASP ARG ILE ALA ILE GLU ASN GLY ASP GLN SEQRES 9 S 482 PRO LEU SER ALA GLU LEU LYS ARG PHE ARG LYS GLU TYR SEQRES 10 S 482 ILE GLN PRO VAL GLN LEU ARG VAL LEU ASN VAL CYS ARG SEQRES 11 S 482 HIS TRP VAL GLU HIS HIS PHE TYR ASP PHE GLU ARG ASP SEQRES 12 S 482 ALA TYR LEU LEU GLN ARG MET GLU GLU PHE ILE GLY THR SEQRES 13 S 482 VAL ARG GLY LYS ALA MET LYS LYS TRP VAL GLU SER ILE SEQRES 14 S 482 THR LYS ILE ILE GLN ARG LYS LYS ILE ALA ARG ASP ASN SEQRES 15 S 482 GLY PRO GLY HIS ASN ILE THR PHE GLN SER SER PRO PRO SEQRES 16 S 482 THR VAL GLU TRP HIS ILE SER ARG PRO GLY HIS ILE GLU SEQRES 17 S 482 THR PHE ASP LEU LEU THR LEU HIS PRO ILE GLU ILE ALA SEQRES 18 S 482 ARG GLN LEU THR LEU LEU GLU SER ASP LEU TYR ARG ALA SEQRES 19 S 482 VAL GLN PRO SER GLU LEU VAL GLY SER VAL TRP THR LYS SEQRES 20 S 482 GLU ASP LYS GLU ILE ASN SER PRO ASN LEU LEU LYS MET SEQRES 21 S 482 ILE ARG HIS THR THR ASN LEU THR LEU TRP PHE GLU LYS SEQRES 22 S 482 CYS ILE VAL GLU THR GLU ASN LEU GLU GLU ARG VAL ALA SEQRES 23 S 482 VAL VAL SER ARG ILE ILE GLU ILE LEU GLN VAL PHE GLN SEQRES 24 S 482 GLU LEU ASN ASN PHE ASN GLY VAL LEU GLU VAL VAL SER SEQRES 25 S 482 ALA MET ASN SER SER PRO VAL TYR ARG LEU ASP HIS THR SEQRES 26 S 482 PHE GLU GLN ILE PRO SER ARG GLN LYS LYS ILE LEU GLU SEQRES 27 S 482 GLU ALA HIS GLU LEU SER GLU ASP HIS TYR LYS LYS TYR SEQRES 28 S 482 LEU ALA LYS LEU ARG SER ILE ASN PRO PRO CYS VAL PRO SEQRES 29 S 482 PHE PHE GLY ILE TYR LEU THR ASN ILE LEU LYS THR GLU SEQRES 30 S 482 GLU GLY ASN PRO GLU VAL LEU LYS ARG HIS GLY LYS GLU SEQRES 31 S 482 LEU ILE ASN PHE SER LYS ARG ARG LYS VAL ALA GLU ILE SEQRES 32 S 482 THR GLY GLU ILE GLN GLN TYR GLN ASN GLN PRO TYR CYS SEQRES 33 S 482 LEU ARG VAL GLU SER ASP ILE LYS ARG PHE PHE GLU ASN SEQRES 34 S 482 LEU ASN PRO MET GLY ASN SER MET GLU LYS GLU PHE THR SEQRES 35 S 482 ASP TYR LEU PHE ASN LYS SER LEU GLU ILE GLU PRO ARG SEQRES 36 S 482 ASN PRO LYS PRO LEU PRO ARG PHE PRO LYS LYS TYR SER SEQRES 37 S 482 TYR PRO LEU LYS SER PRO GLY VAL ARG PRO SER ASN PRO SEQRES 38 S 482 ARG HET MG Q 201 1 HET GNP Q 202 32 HET FVV S1101 21 HETNAM MG MAGNESIUM ION HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM FVV 10-[(4-FLUOROPHENYL)METHYL]-2,3,4,10- HETNAM 2 FVV TETRAHYDROPYRIMIDO[1,2-A]BENZIMIDAZOLE FORMUL 4 MG MG 2+ FORMUL 5 GNP C10 H17 N6 O13 P3 FORMUL 6 FVV C17 H16 F N3 FORMUL 7 HOH *323(H2 O) HELIX 1 AA1 GLY Q 15 ASN Q 26 1 12 HELIX 2 AA2 GLN Q 61 MET Q 67 5 7 HELIX 3 AA3 ARG Q 68 GLY Q 75 1 8 HELIX 4 AA4 ASN Q 86 ASP Q 92 1 7 HELIX 5 AA5 ASP Q 92 ASP Q 105 1 14 HELIX 6 AA6 GLU Q 126 GLY Q 138 1 13 HELIX 7 AA7 GLY Q 151 HIS Q 166 1 16 HELIX 8 AA8 SER R 17 ASN R 26 1 10 HELIX 9 AA9 TYR R 64 ALA R 66 5 3 HELIX 10 AB1 MET R 67 ARG R 73 1 7 HELIX 11 AB2 ASN R 86 ASP R 92 1 7 HELIX 12 AB3 ASP R 92 ASP R 105 1 14 HELIX 13 AB4 GLU R 126 TYR R 137 1 12 HELIX 14 AB5 GLY R 151 GLN R 165 1 15 HELIX 15 AB6 TYR S 575 GLU S 579 5 5 HELIX 16 AB7 THR S 605 THR S 614 1 10 HELIX 17 AB8 ASP S 620 TYR S 631 1 12 HELIX 18 AB9 ARG S 632 PHE S 634 5 3 HELIX 19 AC1 LYS S 636 GLU S 649 1 14 HELIX 20 AC2 THR S 656 ASN S 665 1 10 HELIX 21 AC3 SER S 671 TYR S 681 1 11 HELIX 22 AC4 TYR S 681 HIS S 700 1 20 HELIX 23 AC5 PHE S 701 ARG S 706 1 6 HELIX 24 AC6 ASP S 707 THR S 720 1 14 HELIX 25 AC7 MET S 726 ALA S 743 1 18 HELIX 26 AC8 HIS S 780 VAL S 799 1 20 HELIX 27 AC9 GLN S 800 LYS S 811 5 12 HELIX 28 AD1 ASP S 813 SER S 818 1 6 HELIX 29 AD2 SER S 818 GLU S 841 1 24 HELIX 30 AD3 ASN S 844 LEU S 865 1 22 HELIX 31 AD4 ASN S 867 ASN S 879 1 13 HELIX 32 AD5 SER S 880 ARG S 885 1 6 HELIX 33 AD6 LEU S 886 ILE S 893 1 8 HELIX 34 AD7 PRO S 894 LEU S 907 1 14 HELIX 35 AD8 SER S 908 ARG S 920 1 13 HELIX 36 AD9 PHE S 929 ASN S 944 1 16 HELIX 37 AE1 PHE S 958 GLN S 975 1 18 HELIX 38 AE2 GLU S 984 ASN S 993 1 10 HELIX 39 AE3 MET S 1001 GLU S 1017 1 17 SHEET 1 AA1 6 GLU Q 37 ILE Q 46 0 SHEET 2 AA1 6 GLU Q 49 THR Q 58 -1 O LEU Q 53 N LYS Q 42 SHEET 3 AA1 6 THR Q 2 GLY Q 10 1 N TYR Q 4 O ASP Q 54 SHEET 4 AA1 6 GLY Q 77 ALA Q 83 1 O LEU Q 79 N VAL Q 7 SHEET 5 AA1 6 MET Q 111 ASN Q 116 1 O VAL Q 114 N CYS Q 80 SHEET 6 AA1 6 TYR Q 141 GLU Q 143 1 O ILE Q 142 N LEU Q 113 SHEET 1 AA2 6 ARG R 41 ILE R 46 0 SHEET 2 AA2 6 GLU R 49 ASP R 57 -1 O LEU R 53 N LYS R 42 SHEET 3 AA2 6 THR R 2 GLY R 10 1 N THR R 2 O LEU R 52 SHEET 4 AA2 6 GLY R 77 ALA R 83 1 O LEU R 79 N VAL R 9 SHEET 5 AA2 6 MET R 111 LYS R 117 1 O ASN R 116 N PHE R 82 SHEET 6 AA2 6 TYR R 141 SER R 145 1 O ILE R 142 N LEU R 113 SHEET 1 AA3 4 ILE S 586 PHE S 588 0 SHEET 2 AA3 4 ILE S 601 GLY S 604 -1 O ALA S 603 N ILE S 587 SHEET 3 AA3 4 LYS S 953 ASN S 957 -1 O ILE S 956 N GLY S 604 SHEET 4 AA3 4 VAL S 947 ARG S 950 -1 N ARG S 950 O LYS S 953 LINK OG SER Q 17 MG MG Q 201 1555 1555 2.38 LINK OG1 THR Q 35 MG MG Q 201 1555 1555 1.91 LINK MG MG Q 201 O1G GNP Q 202 1555 1555 2.07 LINK MG MG Q 201 O1B GNP Q 202 1555 1555 1.99 LINK MG MG Q 201 O HOH Q 307 1555 1555 2.32 LINK MG MG Q 201 O HOH Q 318 1555 1555 2.12 CISPEP 1 ASN R 26 HIS R 27 0 26.85 CISPEP 2 PRO S 924 PRO S 925 0 4.41 CISPEP 3 ASN S 1020 PRO S 1021 0 7.85 SITE 1 AC1 5 SER Q 17 THR Q 35 GNP Q 202 HOH Q 307 SITE 2 AC1 5 HOH Q 318 SITE 1 AC2 23 GLY Q 12 GLY Q 13 VAL Q 14 GLY Q 15 SITE 2 AC2 23 LYS Q 16 SER Q 17 ALA Q 18 PHE Q 28 SITE 3 AC2 23 VAL Q 29 ASP Q 30 TYR Q 32 PRO Q 34 SITE 4 AC2 23 THR Q 35 GLY Q 60 GLN Q 61 ASN Q 116 SITE 5 AC2 23 LYS Q 117 ASP Q 119 LEU Q 120 SER Q 145 SITE 6 AC2 23 ALA Q 146 MG Q 201 HOH Q 307 SITE 1 AC3 9 VAL S 852 MET S 878 VAL S 883 TYR S 884 SITE 2 AC3 9 LEU S 886 THR S 889 PHE S 890 LEU S 901 SITE 3 AC3 9 GLU S 902 CRYST1 186.125 186.125 179.217 90.00 90.00 90.00 I 4 2 2 16 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 0.005373 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005373 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005580 0.00000