PDB Short entry for 1RAX HEADER RAS-BINDING DOMAIN 13-MAR-99 1RAX TITLE RA-DOMAIN OF RAL GUANOSINE-NUCLEOTIDE DISSOCIATION STIMULATOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (RA-DOMAIN OF RAL GUANOSINE DISSOCIATION COMPND 3 STIMULATOR); COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: RAS-BINDING DOMAIN; COMPND 6 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: RALGDS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DH5ALPHA; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-2T; SOURCE 10 EXPRESSION_SYSTEM_GENE: HUMAN RALGDS GENE (RALGDS) KEYWDS RAS-BINDING DOMAIN, RALGEF, RALGDS, RAS, RA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR T.D.MUELLER,L.HANDEL,P.SCHMIEDER,H.OSCHKINAT REVDAT 5 27-OCT-21 1RAX 1 SOURCE REMARK REVDAT 4 06-NOV-19 1RAX 1 JRNL REMARK REVDAT 3 24-FEB-09 1RAX 1 VERSN REVDAT 2 26-SEP-01 1RAX 3 ATOM REVDAT 1 19-MAR-99 1RAX 0 JRNL AUTH T.D.MUELLER,L.HANDEL,P.SCHMIEDER,H.OSCHKINAT JRNL TITL HIGH-RESOLUTION STRUCTURE OF THE RA-DOMAIN OF HUMAN RALGDS JRNL TITL 2 AND A DYNAMICS STUDY OF ITS BINDING LOOP TO RAS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.HUANG,X.WENG,F.HOFER,G.S.MARTIN,S.H.KIM REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF THE RAS-INTERACTING DOMAIN OF REMARK 1 TITL 2 RALGDS. REMARK 1 REF NAT.STRUCT.BIOL. V. 4 609 1997 REMARK 1 REFN ISSN 1072-8368 REMARK 1 PMID 9253406 REMARK 1 DOI 10.1038/NSB0897-609 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.GEYER,C.HERRMANN,S.WOHLGEMUTH,A.WITTINGHOFER,H.R.KALBITZER REMARK 1 TITL STRUCTURE OF THE RAS-BINDING DOMAIN OF RALGEF AND REMARK 1 TITL 2 IMPLICATIONS FOR RAS BINDING AND SIGNALLING. REMARK 1 REF NAT.STRUCT.BIOL. V. 4 694 1997 REMARK 1 REFN ISSN 1072-8368 REMARK 1 PMID 9302994 REMARK 1 DOI 10.1038/NSB0997-694 REMARK 1 REFERENCE 3 REMARK 1 AUTH C.HERRMANN,G.HORN,M.SPAARGAREN,A.WITTINGHOFER REMARK 1 TITL DIFFERENTIAL INTERACTION OF THE RAS FAMILY GTP-BINDING REMARK 1 TITL 2 PROTEINS H-RAS, RAP1A, AND R-RAS WITH THE PUTATIVE EFFECTOR REMARK 1 TITL 3 MOLECULES RAF KINASE AND RAL-GUANINE NUCLEOTIDE EXCHANGE REMARK 1 TITL 4 FACTOR. REMARK 1 REF J.BIOL.CHEM. V. 271 6794 1996 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 8636102 REMARK 1 DOI 10.1074/JBC.271.12.6794 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.SPAARGAREN,J.R.BISCHOFF REMARK 1 TITL IDENTIFICATION OF THE GUANINE NUCLEOTIDE DISSOCIATION REMARK 1 TITL 2 STIMULATOR FOR RAL AS A PUTATIVE EFFECTOR MOLECULE OF R-RAS, REMARK 1 TITL 3 H-RAS, K-RAS, AND RAP. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 91 12609 1994 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 7809086 REMARK 1 DOI 10.1073/PNAS.91.26.12609 REMARK 1 REFERENCE 5 REMARK 1 AUTH F.HOFER,S.FIELDS,C.SCHNEIDER,G.S.MARTIN REMARK 1 TITL ACTIVATED RAS INTERACTS WITH THE RAL GUANINE NUCLEOTIDE REMARK 1 TITL 2 DISSOCIATION STIMULATOR. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 91 11089 1994 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 7972015 REMARK 1 DOI 10.1073/PNAS.91.23.11089 REMARK 1 REFERENCE 6 REMARK 1 AUTH C.F.ALBRIGHT,B.W.GIDDINGS,J.LIU,M.VITO,R.A.WEINBERG REMARK 1 TITL CHARACTERIZATION OF A GUANINE NUCLEOTIDE DISSOCIATION REMARK 1 TITL 2 STIMULATOR FOR A RAS-RELATED GTPASE. REMARK 1 REF EMBO J. V. 12 339 1993 REMARK 1 REFN ISSN 0261-4189 REMARK 1 PMID 8094051 REMARK 1 DOI 10.1002/J.1460-2075.1993.TB05662.X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1RAX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-99. REMARK 100 THE DEPOSITION ID IS D_1000000646. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H; 13C; 15N REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AURELIA 2.1, X-PLOR 3.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST TOTAL REMARK 210 ENERGY AND NOE ENERGY WERE REMARK 210 SELECTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A 1 REMARK 465 SER A 2 REMARK 465 PRO A 3 REMARK 465 HIS A 4 REMARK 465 MET A 5 REMARK 465 LEU A 6 REMARK 465 SER A 7 REMARK 465 GLY A 8 REMARK 465 SER A 9 REMARK 465 GLY A 10 REMARK 465 LEU A 11 REMARK 465 CYS A 12 REMARK 465 ASN A 13 REMARK 465 SER A 14 REMARK 465 SER A 15 REMARK 465 SER A 16 REMARK 465 ALA A 17 REMARK 465 LEU A 18 REMARK 465 PRO A 19 REMARK 465 LEU A 20 REMARK 465 TYR A 21 REMARK 465 ASN A 22 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 3 HIS A 65 CG HIS A 65 CD2 0.056 REMARK 500 7 HIS A 65 CG HIS A 65 CD2 0.070 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 1 GLN A 24 171.60 63.37 REMARK 500 1 ASP A 27 114.33 175.73 REMARK 500 1 ASP A 36 69.05 -69.52 REMARK 500 1 VAL A 37 -82.19 -104.57 REMARK 500 1 ASP A 38 -73.33 168.30 REMARK 500 1 ASN A 41 -149.35 -153.45 REMARK 500 1 SER A 50 -53.02 -24.26 REMARK 500 1 ASP A 52 108.11 -28.63 REMARK 500 1 LEU A 81 -77.22 -106.74 REMARK 500 1 ASP A 83 45.88 -78.67 REMARK 500 1 ASP A 84 -31.89 168.57 REMARK 500 1 ASN A 94 100.12 -43.52 REMARK 500 1 ALA A 103 -149.65 -103.43 REMARK 500 1 PHE A 114 63.66 -62.46 REMARK 500 2 ASP A 27 85.19 173.96 REMARK 500 2 ASP A 38 -82.83 66.59 REMARK 500 2 ASN A 39 162.20 -43.85 REMARK 500 2 TYR A 43 121.52 63.02 REMARK 500 2 SER A 50 -58.23 -28.74 REMARK 500 2 ASP A 74 33.89 -96.23 REMARK 500 2 LEU A 81 -75.18 -100.77 REMARK 500 2 ASP A 83 63.92 31.16 REMARK 500 2 ASP A 84 -29.94 84.40 REMARK 500 2 ASN A 94 104.12 -42.26 REMARK 500 2 ALA A 103 -144.73 -78.88 REMARK 500 2 TYR A 105 54.46 -91.73 REMARK 500 2 THR A 113 173.40 -52.19 REMARK 500 2 PHE A 114 69.77 -61.49 REMARK 500 3 ASP A 36 53.93 -105.06 REMARK 500 3 ASP A 38 -14.90 78.21 REMARK 500 3 ASN A 41 144.77 168.04 REMARK 500 3 GLN A 51 -29.87 175.54 REMARK 500 3 LEU A 81 -90.23 -114.40 REMARK 500 3 ASP A 83 -64.69 -29.14 REMARK 500 3 ASN A 92 21.60 -149.09 REMARK 500 3 ASN A 94 107.17 -41.27 REMARK 500 3 ASN A 100 98.57 -41.26 REMARK 500 3 TYR A 105 49.19 -89.40 REMARK 500 3 ARG A 112 64.36 -62.20 REMARK 500 3 PHE A 114 104.04 63.87 REMARK 500 4 ASP A 27 107.80 72.07 REMARK 500 4 VAL A 37 -75.93 -103.91 REMARK 500 4 ASP A 38 -73.39 167.72 REMARK 500 4 TYR A 43 105.02 62.27 REMARK 500 4 SER A 50 -58.16 -28.39 REMARK 500 4 ASP A 74 30.36 -91.68 REMARK 500 4 SER A 82 174.72 172.53 REMARK 500 4 ASN A 94 107.32 -53.13 REMARK 500 4 ASN A 100 96.64 -43.10 REMARK 500 4 PHE A 114 116.20 -163.20 REMARK 500 REMARK 500 THIS ENTRY HAS 139 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 32 0.24 SIDE CHAIN REMARK 500 1 ARG A 59 0.24 SIDE CHAIN REMARK 500 1 ARG A 85 0.30 SIDE CHAIN REMARK 500 1 ARG A 112 0.27 SIDE CHAIN REMARK 500 2 ARG A 32 0.12 SIDE CHAIN REMARK 500 2 ARG A 59 0.19 SIDE CHAIN REMARK 500 2 ARG A 85 0.09 SIDE CHAIN REMARK 500 2 ARG A 112 0.19 SIDE CHAIN REMARK 500 3 ARG A 32 0.29 SIDE CHAIN REMARK 500 3 ARG A 59 0.22 SIDE CHAIN REMARK 500 3 ARG A 85 0.12 SIDE CHAIN REMARK 500 3 ARG A 112 0.32 SIDE CHAIN REMARK 500 4 ARG A 32 0.20 SIDE CHAIN REMARK 500 4 ARG A 59 0.14 SIDE CHAIN REMARK 500 4 ARG A 85 0.32 SIDE CHAIN REMARK 500 4 ARG A 112 0.32 SIDE CHAIN REMARK 500 5 ARG A 32 0.31 SIDE CHAIN REMARK 500 5 ARG A 59 0.22 SIDE CHAIN REMARK 500 5 ARG A 85 0.14 SIDE CHAIN REMARK 500 5 ARG A 112 0.22 SIDE CHAIN REMARK 500 6 ARG A 32 0.33 SIDE CHAIN REMARK 500 6 ARG A 59 0.31 SIDE CHAIN REMARK 500 6 ARG A 85 0.24 SIDE CHAIN REMARK 500 6 ARG A 112 0.28 SIDE CHAIN REMARK 500 7 ARG A 32 0.30 SIDE CHAIN REMARK 500 7 ARG A 59 0.32 SIDE CHAIN REMARK 500 7 ARG A 85 0.28 SIDE CHAIN REMARK 500 7 ARG A 112 0.14 SIDE CHAIN REMARK 500 8 ARG A 32 0.12 SIDE CHAIN REMARK 500 8 ARG A 59 0.31 SIDE CHAIN REMARK 500 8 ARG A 85 0.21 SIDE CHAIN REMARK 500 8 ARG A 112 0.22 SIDE CHAIN REMARK 500 9 ARG A 32 0.14 SIDE CHAIN REMARK 500 9 ARG A 59 0.31 SIDE CHAIN REMARK 500 9 ARG A 85 0.31 SIDE CHAIN REMARK 500 9 ARG A 112 0.32 SIDE CHAIN REMARK 500 10 ARG A 32 0.25 SIDE CHAIN REMARK 500 10 ARG A 59 0.30 SIDE CHAIN REMARK 500 10 ARG A 85 0.12 SIDE CHAIN REMARK 500 10 ARG A 112 0.24 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1RAX A 1 115 UNP Q12967 GNDS_HUMAN 185 300 SEQRES 1 A 115 GLY SER PRO HIS MET LEU SER GLY SER GLY LEU CYS ASN SEQRES 2 A 115 SER SER SER ALA LEU PRO LEU TYR ASN GLN GLN VAL GLY SEQRES 3 A 115 ASP CYS CYS ILE ILE ARG VAL SER LEU ASP VAL ASP ASN SEQRES 4 A 115 GLY ASN MET TYR LYS SER ILE LEU VAL THR SER GLN ASP SEQRES 5 A 115 LYS ALA PRO ALA VAL ILE ARG LYS ALA MET ASP LYS HIS SEQRES 6 A 115 ASN LEU GLU GLU GLU GLU PRO GLU ASP TYR GLU LEU LEU SEQRES 7 A 115 GLN ILE LEU SER ASP ASP ARG LYS LEU LYS ILE PRO GLU SEQRES 8 A 115 ASN ALA ASN VAL PHE TYR ALA MET ASN SER THR ALA ASN SEQRES 9 A 115 TYR ASP PHE VAL LEU LYS LYS ARG THR PHE THR HELIX 1 1 ALA A 54 HIS A 65 1 12 HELIX 2 2 VAL A 95 ALA A 98 1 4 SHEET 1 A 5 LYS A 44 THR A 49 0 SHEET 2 A 5 CYS A 28 LEU A 35 -1 N VAL A 33 O LYS A 44 SHEET 3 A 5 ASP A 106 LYS A 111 1 N PHE A 107 O ARG A 32 SHEET 4 A 5 TYR A 75 ILE A 80 -1 N ILE A 80 O ASP A 106 SHEET 5 A 5 LYS A 86 ILE A 89 -1 N ILE A 89 O LEU A 77 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000