HEADER SIGNALING PROTEIN 19-APR-18 6D5V 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 3 04-OCT-23 6D5V 1 REMARK REVDAT 2 07-NOV-18 6D5V 1 JRNL REVDAT 1 19-SEP-18 6D5V 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. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 94992 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 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 35.8599 - 4.9132 1.00 6955 148 0.1758 0.1823 REMARK 3 2 4.9132 - 3.9012 1.00 6750 146 0.1351 0.1326 REMARK 3 3 3.9012 - 3.4085 1.00 6686 145 0.1454 0.1520 REMARK 3 4 3.4085 - 3.0971 1.00 6665 142 0.1662 0.1833 REMARK 3 5 3.0971 - 2.8752 1.00 6639 145 0.1779 0.2263 REMARK 3 6 2.8752 - 2.7057 1.00 6636 140 0.1845 0.2246 REMARK 3 7 2.7057 - 2.5703 1.00 6599 146 0.1851 0.2019 REMARK 3 8 2.5703 - 2.4584 1.00 6601 141 0.1771 0.2057 REMARK 3 9 2.4584 - 2.3638 1.00 6611 139 0.1783 0.2514 REMARK 3 10 2.3638 - 2.2822 1.00 6601 136 0.1805 0.2136 REMARK 3 11 2.2822 - 2.2109 1.00 6548 148 0.1782 0.2132 REMARK 3 12 2.2109 - 2.1477 1.00 6593 140 0.1765 0.2023 REMARK 3 13 2.1477 - 2.0912 1.00 6560 142 0.1843 0.2137 REMARK 3 14 2.0912 - 2.0402 1.00 6550 140 0.1940 0.2144 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.150 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 6781 REMARK 3 ANGLE : 1.062 9188 REMARK 3 CHIRALITY : 0.043 1006 REMARK 3 PLANARITY : 0.004 1194 REMARK 3 DIHEDRAL : 14.007 2618 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 6D5V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-APR-18. REMARK 100 THE DEPOSITION ID IS D_1000234034. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-14 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 : 95040 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 18.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 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) : NULL 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 91.41100 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 91.41100 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 88.93300 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 91.41100 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 91.41100 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 88.93300 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 91.41100 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 91.41100 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 88.93300 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 91.41100 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 91.41100 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 88.93300 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 91.41100 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 91.41100 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 88.93300 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 91.41100 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 91.41100 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 88.93300 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 91.41100 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 91.41100 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 88.93300 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 91.41100 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 91.41100 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 88.93300 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: 7060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 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 S1627 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 GLY Q 0 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 465 HIS S 750 REMARK 465 ARG S 1046 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 TRP S 809 O REMARK 470 ARG S1026 O 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 S 1668 O HOH S 1699 1.85 REMARK 500 O HOH R 272 O HOH R 288 1.89 REMARK 500 NH2 ARG S 982 O HOH S 1201 1.90 REMARK 500 O HOH R 330 O HOH R 355 1.92 REMARK 500 O HOH S 1256 O HOH S 1500 1.93 REMARK 500 O HOH S 1704 O HOH S 1718 1.94 REMARK 500 O HOH R 258 O HOH R 281 1.95 REMARK 500 OE2 GLU S 843 O HOH S 1202 1.96 REMARK 500 O HOH S 1536 O HOH S 1756 1.97 REMARK 500 O HOH R 272 O HOH R 300 1.99 REMARK 500 O HOH S 1380 O HOH S 1728 1.99 REMARK 500 O HOH Q 403 O HOH Q 457 1.99 REMARK 500 O HOH Q 408 O HOH Q 449 2.01 REMARK 500 O HOH S 1514 O HOH S 1721 2.01 REMARK 500 O GLN Q 70 O HOH Q 301 2.02 REMARK 500 O HOH S 1219 O HOH S 1497 2.04 REMARK 500 OD2 ASP S 620 O HOH S 1203 2.04 REMARK 500 O HOH S 1494 O HOH S 1723 2.05 REMARK 500 NH2 ARG S 722 O HOH S 1204 2.05 REMARK 500 O HOH Q 311 O HOH Q 446 2.05 REMARK 500 O HOH R 259 O HOH S 1666 2.06 REMARK 500 ND1 HIS S 951 O HOH S 1205 2.06 REMARK 500 NZ LYS S 899 O HOH S 1206 2.07 REMARK 500 O HOH S 1475 O HOH S 1721 2.08 REMARK 500 O HOH Q 451 O HOH Q 456 2.08 REMARK 500 OE1 GLU S 579 O HOH S 1207 2.09 REMARK 500 O HOH Q 407 O HOH Q 422 2.09 REMARK 500 O HOH R 343 O HOH R 353 2.10 REMARK 500 O HOH R 257 O HOH R 285 2.11 REMARK 500 O HOH S 1341 O HOH S 1372 2.12 REMARK 500 NH2 ARG Q 102 O HOH Q 302 2.12 REMARK 500 O HOH S 1474 O HOH S 1628 2.13 REMARK 500 O HOH S 1698 O HOH S 1708 2.14 REMARK 500 O HOH Q 382 O HOH Q 407 2.14 REMARK 500 O HOH Q 312 O HOH Q 431 2.14 REMARK 500 O HOH R 283 O HOH S 1445 2.15 REMARK 500 OE2 GLU Q 31 O HOH Q 303 2.15 REMARK 500 O HOH S 1739 O HOH S 1774 2.16 REMARK 500 O HOH S 1501 O HOH S 1718 2.17 REMARK 500 O PRO S 1045 O HOH S 1208 2.19 REMARK 500 NZ LYS S 988 O HOH S 1209 2.19 REMARK 500 O HOH S 1217 O HOH S 1388 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 R 352 O HOH S 1716 4555 1.94 REMARK 500 O HOH R 348 O HOH S 1580 4555 2.01 REMARK 500 O HOH R 344 O HOH S 1460 4555 2.14 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 S 647 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG S 647 NE - CZ - NH2 ANGL. DEV. = -4.5 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 ILE Q 36 -62.40 -103.06 REMARK 500 ARG Q 149 -2.31 77.96 REMARK 500 ASN R 26 -87.88 15.60 REMARK 500 ASP R 30 93.56 -58.47 REMARK 500 TYR R 32 135.23 -172.03 REMARK 500 ASP R 38 -0.97 97.76 REMARK 500 TYR R 40 13.37 -143.71 REMARK 500 HIS S 764 -119.85 -120.01 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 78.5 REMARK 620 3 GNP Q 202 O1G 166.0 87.5 REMARK 620 4 GNP Q 202 O1B 95.1 172.2 98.8 REMARK 620 5 HOH Q 331 O 86.3 88.0 93.7 96.1 REMARK 620 6 HOH Q 341 O 87.0 85.8 91.6 89.4 171.6 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 FVY S 1101 DBREF 6D5V Q 1 166 UNP P01112 RASH_HUMAN 1 166 DBREF 6D5V R 1 166 UNP P01112 RASH_HUMAN 1 166 DBREF 6D5V S 566 1046 UNP Q07889 SOS1_HUMAN 566 1046 SEQADV 6D5V GLY Q 0 UNP P01112 EXPRESSION TAG SEQADV 6D5V ALA Q 64 UNP P01112 TYR 64 CONFLICT SEQADV 6D5V GLY R 0 UNP P01112 EXPRESSION TAG SEQADV 6D5V 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 FVY S1101 21 HETNAM MG MAGNESIUM ION HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM FVY 1-[(3-CHLORO-4-FLUOROPHENYL)METHYL]-5,6-DIMETHYL-1H- HETNAM 2 FVY BENZIMIDAZOL-2-AMINE FORMUL 4 MG MG 2+ FORMUL 5 GNP C10 H17 N6 O13 P3 FORMUL 6 FVY C16 H15 CL F N3 FORMUL 7 HOH *914(H2 O) HELIX 1 AA1 GLY Q 15 ASN Q 26 1 12 HELIX 2 AA2 GLN Q 61 ALA Q 66 5 6 HELIX 3 AA3 MET Q 67 GLY Q 75 1 9 HELIX 4 AA4 ASN Q 86 ASP Q 105 1 20 HELIX 5 AA5 GLU Q 126 GLY Q 138 1 13 HELIX 6 AA6 GLY Q 151 HIS Q 166 1 16 HELIX 7 AA7 SER R 17 GLN R 25 1 9 HELIX 8 AA8 TYR R 64 ALA R 66 5 3 HELIX 9 AA9 MET R 67 THR R 74 1 8 HELIX 10 AB1 ASN R 86 ASP R 92 1 7 HELIX 11 AB2 ASP R 92 ASP R 105 1 14 HELIX 12 AB3 GLU R 126 GLY R 138 1 13 HELIX 13 AB4 GLY R 151 GLN R 165 1 15 HELIX 14 AB5 TYR S 575 GLU S 579 5 5 HELIX 15 AB6 THR S 605 THR S 614 1 10 HELIX 16 AB7 ASP S 620 TYR S 631 1 12 HELIX 17 AB8 ARG S 632 PHE S 634 5 3 HELIX 18 AB9 LYS S 636 GLU S 649 1 14 HELIX 19 AC1 THR S 656 ASN S 665 1 10 HELIX 20 AC2 SER S 671 TYR S 681 1 11 HELIX 21 AC3 TYR S 681 HIS S 700 1 20 HELIX 22 AC4 PHE S 701 ASP S 707 1 7 HELIX 23 AC5 ASP S 707 THR S 720 1 14 HELIX 24 AC6 MET S 726 ILE S 742 1 17 HELIX 25 AC7 HIS S 770 PHE S 774 5 5 HELIX 26 AC8 HIS S 780 ALA S 798 1 19 HELIX 27 AC9 GLN S 800 VAL S 808 5 9 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 GLY S 943 1 15 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 CYS Q 51 N VAL Q 44 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 VAL Q 81 N VAL Q 9 SHEET 5 AA1 6 MET Q 111 ASN Q 116 1 O ASN Q 116 N PHE Q 82 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 TYR R 4 O LEU R 52 SHEET 4 AA2 6 GLY R 77 ALA R 83 1 O VAL R 81 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 THR R 144 N LYS R 117 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 LEU S 948 O LEU S 955 LINK OG SER Q 17 MG MG Q 201 1555 1555 2.14 LINK OG1 THR Q 35 MG MG Q 201 1555 1555 2.15 LINK MG MG Q 201 O1G GNP Q 202 1555 1555 1.97 LINK MG MG Q 201 O1B GNP Q 202 1555 1555 1.92 LINK MG MG Q 201 O HOH Q 331 1555 1555 2.02 LINK MG MG Q 201 O HOH Q 341 1555 1555 2.12 CISPEP 1 ASN R 26 HIS R 27 0 21.77 CISPEP 2 PHE S 754 GLN S 755 0 -12.64 CISPEP 3 PRO S 924 PRO S 925 0 8.43 CISPEP 4 ASN S 1020 PRO S 1021 0 7.79 SITE 1 AC1 5 SER Q 17 THR Q 35 GNP Q 202 HOH Q 331 SITE 2 AC1 5 HOH Q 341 SITE 1 AC2 29 GLY Q 12 GLY Q 13 VAL Q 14 GLY Q 15 SITE 2 AC2 29 LYS Q 16 SER Q 17 ALA Q 18 PHE Q 28 SITE 3 AC2 29 VAL Q 29 ASP Q 30 GLU Q 31 PRO Q 34 SITE 4 AC2 29 THR Q 35 GLY Q 60 GLN Q 61 ASN Q 116 SITE 5 AC2 29 LYS Q 117 ASP Q 119 LEU Q 120 SER Q 145 SITE 6 AC2 29 ALA Q 146 LYS Q 147 MG Q 201 HOH Q 331 SITE 7 AC2 29 HOH Q 341 HOH Q 349 HOH Q 356 HOH Q 359 SITE 8 AC2 29 HOH Q 402 SITE 1 AC3 15 VAL S 852 MET S 878 ASN S 879 VAL S 883 SITE 2 AC3 15 TYR S 884 LEU S 886 THR S 889 PHE S 890 SITE 3 AC3 15 ILE S 893 LEU S 901 GLU S 902 HIS S 905 SITE 4 AC3 15 HOH S1244 HOH S1360 HOH S1363 CRYST1 182.822 182.822 177.866 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 0.005470 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005470 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005622 0.00000