PDB Short entry for 3IMD HEADER SIGNALING PROTEIN/PEPTIDE 10-AUG-09 3IMD TITLE CRYSTAL STRUCTURE OF THE GRB2 SH2 DOMAIN IN COMPLEX WITH A FLEXIBLE TITLE 2 AC-PY-Q-N-NH2 TRIPEPTIDE MIMIC COMPND MOL_ID: 1; COMPND 2 MOLECULE: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SH2 DOMAIN; COMPND 5 SYNONYM: ADAPTER PROTEIN GRB2, SH2/SH3 ADAPTER GRB2, PROTEIN ASH; 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: GRB2, ASH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SG13009; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE-60 KEYWDS LIGAND PREORGANIZATION, PEPTIDE MIMICS, GOLGI APPARATUS, HOST-VIRUS KEYWDS 2 INTERACTION, PHOSPHOPROTEIN, SH2 DOMAIN, SIGNALING PROTEIN, KEYWDS 3 SIGNALING PROTEIN-PSEUDOPEPTIDE LIGAND COMPLEX, SIGNALING PROTEIN- KEYWDS 4 PEPTIDE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.H.CLEMENTS REVDAT 5 06-SEP-23 3IMD 1 REMARK SEQADV REVDAT 4 01-NOV-17 3IMD 1 REMARK REVDAT 3 13-JUL-11 3IMD 1 VERSN REVDAT 2 01-DEC-09 3IMD 1 JRNL REVDAT 1 17-NOV-09 3IMD 0 JRNL AUTH J.E.DELORBE,J.H.CLEMENTS,M.G.TERESK,A.P.BENFIELD,H.R.PLAKE, JRNL AUTH 2 L.E.MILLSPAUGH,S.F.MARTIN JRNL TITL THERMODYNAMIC AND STRUCTURAL EFFECTS OF CONFORMATIONAL JRNL TITL 2 CONSTRAINTS IN PROTEIN-LIGAND INTERACTIONS. ENTROPIC JRNL TITL 3 PARADOXY ASSOCIATED WITH LIGAND PREORGANIZATION. JRNL REF J.AM.CHEM.SOC. V. 131 16758 2009 JRNL REFN ISSN 0002-7863 JRNL PMID 19886660 JRNL DOI 10.1021/JA904698Q REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.P.BENFIELD,M.G.TERESK,H.R.PLAKE,J.E.DELORBE, REMARK 1 AUTH 2 L.E.MILLSPAUGH,S.F.MARTIN REMARK 1 TITL LIGAND PREORGANIZATION MAY BE ACCOMPANIED BY ENTROPIC REMARK 1 TITL 2 PENALTIES IN PROTEIN-LIGAND INTERACTIONS REMARK 1 REF ANGEW.CHEM.INT.ED.ENGL. V. 45 6830 2006 REMARK 1 REFN ISSN 1433-7851 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 12970 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 SET) : 0.199 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 641 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1664 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 81 REMARK 3 SOLVENT ATOMS : 191 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00500 REMARK 3 B22 (A**2) : 0.04900 REMARK 3 B33 (A**2) : -0.05500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.114 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.663 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.776 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.528 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 11.41 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : CNS_TOPPAR:ION.PARAM REMARK 3 PARAMETER FILE 5 : FPYQN.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : CNS_TOPPAR:PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CNS_TOPPAR:DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : CNS_TOPPAR:WATER.TOP REMARK 3 TOPOLOGY FILE 4 : CNS_TOPPAR:ION.TOP REMARK 3 TOPOLOGY FILE 5 : FPYQN.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3IMD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000054591. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : BLUE MAX-FLUX CONFOCAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18279 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 50.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.08400 REMARK 200 R SYM FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3C7I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LIGAND IN LYPHILIZED POWDER FORM WAS REMARK 280 DISSOLVED IN A 9.1 MG/ML SOLUTION OF GRB2 SH2 IN WATER SUCH TO REMARK 280 GIVE A PROTEIN/LIGAND MOLAR RATIO OF 2:1. 3 UL OF THIS SOLUTION REMARK 280 WAS MIXED WITH 4 UL OF 0.2 M MGCL2 X 6H2O, 30% W/V PEG MW4000, REMARK 280 0.1 M TRIS, PH 8.5 TO CREATE THE HANGING DROP, WHICH YIELDED REMARK 280 CRYSTALS OF THE PROTEIN-LIGAND COMPLEX IN THE PRESENCE OF THE REMARK 280 ABOVE-MENTIONED SOLUTION AFTER FOUR WEEKS AT ROOM TEMPERATURE., REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 21.11950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.19200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.12150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.19200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.11950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.12150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 ILE A 53 REMARK 465 GLU A 54 REMARK 465 GLN A 156 REMARK 465 GLN A 157 REMARK 465 PRO A 158 REMARK 465 THR A 159 REMARK 465 TYR A 160 REMARK 465 VAL A 161 REMARK 465 GLN A 162 REMARK 465 ALA A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 ILE B 53 REMARK 465 GLU B 54 REMARK 465 GLN B 156 REMARK 465 GLN B 157 REMARK 465 PRO B 158 REMARK 465 THR B 159 REMARK 465 TYR B 160 REMARK 465 VAL B 161 REMARK 465 GLN B 162 REMARK 465 ALA B 163 REMARK 465 HIS B 164 REMARK 465 HIS B 165 REMARK 465 HIS B 166 REMARK 465 HIS B 167 REMARK 465 HIS B 168 REMARK 465 HIS B 169 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 ARG B 112 CZ ARG B 112 NH1 -0.207 REMARK 500 ARG B 112 CZ ARG B 112 NH2 -0.165 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 B 112 NH1 - CZ - NH2 ANGL. DEV. = -15.3 DEGREES REMARK 500 ARG B 112 NE - CZ - NH1 ANGL. DEV. = 16.9 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 TRP A 121 -79.72 -127.29 REMARK 500 TRP A 121 -79.45 -127.29 REMARK 500 VAL A 122 -52.79 -120.93 REMARK 500 TRP B 121 -75.82 -125.80 REMARK 500 VAL B 122 -53.99 -124.16 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 ARG B 112 0.25 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: N~2~-{(2R)-4-(METHYLAMINO)-4-OXO-2-[4-(PHOSPHONOOXY) REMARK 630 BENZYL]BUTANOYL}-L-GLUTAMINYL-L-ASPARTAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 FYQ A 1 REMARK 630 FYQ B 1 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: FY0 GLN ASN NH2 REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FYQ A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FYQ B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 170 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3C7I RELATED DB: PDB REMARK 900 RELATED ID: 2HUW RELATED DB: PDB REMARK 900 RELATED ID: 3IMJ RELATED DB: PDB REMARK 900 RELATED ID: 3IN7 RELATED DB: PDB REMARK 900 RELATED ID: 3IN8 RELATED DB: PDB DBREF 3IMD A 53 163 UNP P62993 GRB2_HUMAN 53 163 DBREF 3IMD B 53 163 UNP P62993 GRB2_HUMAN 53 163 SEQADV 3IMD HIS A 164 UNP P62993 EXPRESSION TAG SEQADV 3IMD HIS A 165 UNP P62993 EXPRESSION TAG SEQADV 3IMD HIS A 166 UNP P62993 EXPRESSION TAG SEQADV 3IMD HIS A 167 UNP P62993 EXPRESSION TAG SEQADV 3IMD HIS A 168 UNP P62993 EXPRESSION TAG SEQADV 3IMD HIS A 169 UNP P62993 EXPRESSION TAG SEQADV 3IMD HIS B 164 UNP P62993 EXPRESSION TAG SEQADV 3IMD HIS B 165 UNP P62993 EXPRESSION TAG SEQADV 3IMD HIS B 166 UNP P62993 EXPRESSION TAG SEQADV 3IMD HIS B 167 UNP P62993 EXPRESSION TAG SEQADV 3IMD HIS B 168 UNP P62993 EXPRESSION TAG SEQADV 3IMD HIS B 169 UNP P62993 EXPRESSION TAG SEQRES 1 A 117 ILE GLU MET LYS PRO HIS PRO TRP PHE PHE GLY LYS ILE SEQRES 2 A 117 PRO ARG ALA LYS ALA GLU GLU MET LEU SER LYS GLN ARG SEQRES 3 A 117 HIS ASP GLY ALA PHE LEU ILE ARG GLU SER GLU SER ALA SEQRES 4 A 117 PRO GLY ASP PHE SER LEU SER VAL LYS PHE GLY ASN ASP SEQRES 5 A 117 VAL GLN HIS PHE LYS VAL LEU ARG ASP GLY ALA GLY LYS SEQRES 6 A 117 TYR PHE LEU TRP VAL VAL LYS PHE ASN SER LEU ASN GLU SEQRES 7 A 117 LEU VAL ASP TYR HIS ARG SER THR SER VAL SER ARG ASN SEQRES 8 A 117 GLN GLN ILE PHE LEU ARG ASP ILE GLU GLN VAL PRO GLN SEQRES 9 A 117 GLN PRO THR TYR VAL GLN ALA HIS HIS HIS HIS HIS HIS SEQRES 1 B 117 ILE GLU MET LYS PRO HIS PRO TRP PHE PHE GLY LYS ILE SEQRES 2 B 117 PRO ARG ALA LYS ALA GLU GLU MET LEU SER LYS GLN ARG SEQRES 3 B 117 HIS ASP GLY ALA PHE LEU ILE ARG GLU SER GLU SER ALA SEQRES 4 B 117 PRO GLY ASP PHE SER LEU SER VAL LYS PHE GLY ASN ASP SEQRES 5 B 117 VAL GLN HIS PHE LYS VAL LEU ARG ASP GLY ALA GLY LYS SEQRES 6 B 117 TYR PHE LEU TRP VAL VAL LYS PHE ASN SER LEU ASN GLU SEQRES 7 B 117 LEU VAL ASP TYR HIS ARG SER THR SER VAL SER ARG ASN SEQRES 8 B 117 GLN GLN ILE PHE LEU ARG ASP ILE GLU GLN VAL PRO GLN SEQRES 9 B 117 GLN PRO THR TYR VAL GLN ALA HIS HIS HIS HIS HIS HIS HET FYQ A 1 38 HET CL A 2 1 HET MG A 4 1 HET CL A 5 1 HET CL A 6 1 HET FYQ B 1 38 HET CL B 170 1 HETNAM FYQ N~2~-{(2R)-4-(METHYLAMINO)-4-OXO-2-[4-(PHOSPHONOOXY) HETNAM 2 FYQ BENZYL]BUTANOYL}-L-GLUTAMINYL-L-ASPARTAMIDE HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION FORMUL 3 FYQ 2(C21 H31 N6 O10 P) FORMUL 4 CL 4(CL 1-) FORMUL 5 MG MG 2+ FORMUL 10 HOH *191(H2 O) HELIX 1 1 PRO A 66 SER A 75 1 10 HELIX 2 2 SER A 127 HIS A 135 1 9 HELIX 3 3 PRO B 66 SER B 75 1 10 HELIX 4 4 SER B 127 HIS B 135 1 9 SHEET 1 A 5 PHE A 61 GLY A 63 0 SHEET 2 A 5 PHE A 83 GLU A 87 1 O GLU A 87 N GLY A 63 SHEET 3 A 5 PHE A 95 PHE A 101 -1 O SER A 96 N ARG A 86 SHEET 4 A 5 ASP A 104 ARG A 112 -1 O GLN A 106 N VAL A 99 SHEET 5 A 5 TYR A 118 PHE A 119 -1 O PHE A 119 N LEU A 111 SHEET 1 B 4 PHE B 83 GLU B 87 0 SHEET 2 B 4 PHE B 95 PHE B 101 -1 O SER B 96 N ARG B 86 SHEET 3 B 4 ASP B 104 ARG B 112 -1 O PHE B 108 N LEU B 97 SHEET 4 B 4 TYR B 118 PHE B 119 -1 O PHE B 119 N LEU B 111 SITE 1 AC1 19 ARG A 67 ARG A 86 SER A 88 SER A 90 SITE 2 AC1 19 SER A 96 HIS A 107 PHE A 108 LYS A 109 SITE 3 AC1 19 LEU A 120 TRP A 121 HOH A 171 HOH A 177 SITE 4 AC1 19 HOH A 178 HOH A 186 HOH A 187 ARG B 78 SITE 5 AC1 19 VAL B 154 PRO B 155 HOH B 207 SITE 1 AC2 3 SER A 139 GLN A 145 HOH A 195 SITE 1 AC3 3 HIS A 58 ASN A 129 ASP A 133 SITE 1 AC4 3 ARG A 78 GLU A 152 LYS B 109 SITE 1 AC5 3 LYS A 109 ARG B 78 GLU B 152 SITE 1 AC6 21 ARG A 78 GLU A 152 VAL A 154 PRO A 155 SITE 2 AC6 21 HOH B 5 HOH B 7 HOH B 8 HOH B 13 SITE 3 AC6 21 HOH B 27 ARG B 67 ARG B 86 SER B 88 SITE 4 AC6 21 SER B 90 SER B 96 HIS B 107 PHE B 108 SITE 5 AC6 21 LYS B 109 LEU B 120 TRP B 121 HOH B 196 SITE 6 AC6 21 HOH B 206 SITE 1 AC7 2 SER B 139 GLN B 145 CRYST1 42.239 42.243 110.384 90.00 90.00 90.00 P 21 21 21 8 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 0.023675 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023673 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009059 0.00000