HEADER PEPTIDE BINDING PROTEIN 24-APR-20 6WO2 TITLE CRYSTAL STRUCTURE OF THE GRB2 SH2 DOMAIN IN COMPLEX WITH A TRIPEPTIDE: TITLE 2 AC-PY-AC6C-N-ISOHEXYL 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,PROTEIN ASH,SH2/SH3 ADAPTER GRB2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ACE-PTR-02K-ASN-U67; COMPND 9 CHAIN: C, D; COMPND 10 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; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS GRB2 SH2 LIGAND PREORGANIZATION, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.F.MARTIN,J.H.CLEMENTS REVDAT 4 15-NOV-23 6WO2 1 REMARK REVDAT 3 18-OCT-23 6WO2 1 REMARK REVDAT 2 23-SEP-20 6WO2 1 JRNL REVDAT 1 02-SEP-20 6WO2 0 JRNL AUTH D.L.CRAMER,B.CHENG,J.TIAN,J.H.CLEMENTS,R.M.WYPYCH,S.F.MARTIN JRNL TITL SOME THERMODYNAMIC EFFECTS OF VARYING NONPOLAR SURFACES IN JRNL TITL 2 PROTEIN-LIGAND INTERACTIONS. JRNL REF EUR.J.MED.CHEM. V. 208 12771 2020 JRNL REFN ISSN 0223-5234 JRNL PMID 32916312 JRNL DOI 10.1016/J.EJMECH.2020.112771 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 11844 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 645 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 822 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.2140 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.2870 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1754 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 74 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.65000 REMARK 3 B22 (A**2) : -1.47000 REMARK 3 B33 (A**2) : -1.18000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.265 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.224 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.150 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.243 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.938 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.886 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1809 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2417 ; 1.887 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 204 ; 7.868 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;33.213 ;23.222 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 302 ;18.638 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;15.948 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 242 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1377 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 : NULL 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 : 1.40 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 6WO2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-20. REMARK 100 THE DEPOSITION ID IS D_1000248708. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 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 : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17182 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 51.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.54400 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: PHASER REMARK 200 STARTING MODEL: 4P9V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AN AQUEOUS SOLUTION CONTAINING A 1.5 REMARK 280 MOLAR RATIO OF LIGAND TO PROTEIN, CA. 10 MG/ML, WAS PREPARED. REMARK 280 4.0 UL OF THIS SOLUTION WAS MIXED WITH 3.0 UL OF A PRECIPITANT REMARK 280 SOLUTION CONTAINING 0.2 M SODIUM CITRATE TRIBASIC DIHYDRATE, 0.1 REMARK 280 M HEPES, AND 20% V/V 2-PROPANOL (HAMPTON CRYSTAL SCREEN I, REMARK 280 CONDITION NO. 27), AND ALLOWED TO EQUILIBRATE WITH 350 UL OF THE REMARK 280 AFOREMENTIONED PRECIPITANT WELL SOLUTION. USABLE CRYSTALS GREW REMARK 280 AFTER 4 WEEKS, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 16.11250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.06850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.36000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.06850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.11250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.36000 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 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 PRO A 155 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 PRO B 155 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 54 CB CG CD OE1 OE2 REMARK 480 GLN A 153 CB CG REMARK 480 TRP B 121 CG CD1 CD2 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 NH2 ARG B 112 O GLY B 116 2.13 REMARK 500 O MET B 55 O HOH B 301 2.19 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 GLU A 54 CA GLU A 54 CB -0.196 REMARK 500 GLN A 153 CG GLN A 153 CD 0.164 REMARK 500 TRP B 121 CD1 TRP B 121 NE1 -0.340 REMARK 500 TRP B 121 CE2 TRP B 121 CD2 -0.296 REMARK 500 TRP B 121 CD2 TRP B 121 CE3 0.387 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 GLU A 54 N - CA - CB ANGL. DEV. = 11.8 DEGREES REMARK 500 GLN A 153 CG - CD - OE1 ANGL. DEV. = 15.5 DEGREES REMARK 500 GLN A 153 CG - CD - NE2 ANGL. DEV. = -16.4 DEGREES REMARK 500 TRP B 121 CD1 - NE1 - CE2 ANGL. DEV. = 5.6 DEGREES REMARK 500 TRP B 121 CE2 - CD2 - CE3 ANGL. DEV. = 11.8 DEGREES REMARK 500 TRP B 121 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 TRP B 121 CG - CD2 - CE3 ANGL. DEV. = -6.4 DEGREES REMARK 500 TRP B 121 CD2 - CE3 - CZ3 ANGL. DEV. = -14.4 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 MET A 55 90.90 -60.57 REMARK 500 ASN A 103 5.14 -68.14 REMARK 500 TRP A 121 -103.28 -132.34 REMARK 500 MET B 55 -95.80 -141.94 REMARK 500 LYS B 56 136.05 37.28 REMARK 500 TRP B 121 -87.89 -138.19 REMARK 500 VAL B 122 -67.12 -94.07 REMARK 500 GLN B 144 104.91 42.58 REMARK 500 GLN B 145 45.38 147.56 REMARK 500 GLN B 153 -109.19 1.33 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 ASN A 103 ASP A 104 -138.01 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 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 152 OE1 REMARK 620 2 GLU A 152 OE2 57.0 REMARK 620 3 GLU B 152 OE1 49.7 27.0 REMARK 620 4 GLU B 152 OE2 45.3 28.4 4.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 201 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 54 OE1 REMARK 620 2 GLU B 54 OE2 48.9 REMARK 620 3 HOH B 301 O 82.5 124.1 REMARK 620 4 HOH B 305 O 107.0 58.1 148.5 REMARK 620 5 HOH B 330 O 97.6 74.9 88.7 60.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IPA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IPA B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand U67 E 5 bound to ASN E 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand U67 F 5 bound to ASN F 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues ACE E 1 and PTR E 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues PTR E 2 and 02K E 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide 02K E 3 and ASN E 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues ACE F 1 and PTR F 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues PTR F 2 and 02K F 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide 02K F 3 and ASN F 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4P9V RELATED DB: PDB REMARK 900 RELATED ID: 6WM1 RELATED DB: PDB DBREF 6WO2 A 53 163 UNP P62993 GRB2_HUMAN 53 163 DBREF 6WO2 B 53 163 UNP P62993 GRB2_HUMAN 53 163 DBREF 6WO2 C 1 5 PDB 6WO2 6WO2 1 5 DBREF 6WO2 D 1 5 PDB 6WO2 6WO2 1 5 SEQADV 6WO2 HIS A 164 UNP P62993 EXPRESSION TAG SEQADV 6WO2 HIS A 165 UNP P62993 EXPRESSION TAG SEQADV 6WO2 HIS A 166 UNP P62993 EXPRESSION TAG SEQADV 6WO2 HIS A 167 UNP P62993 EXPRESSION TAG SEQADV 6WO2 HIS A 168 UNP P62993 EXPRESSION TAG SEQADV 6WO2 HIS A 169 UNP P62993 EXPRESSION TAG SEQADV 6WO2 HIS B 164 UNP P62993 EXPRESSION TAG SEQADV 6WO2 HIS B 165 UNP P62993 EXPRESSION TAG SEQADV 6WO2 HIS B 166 UNP P62993 EXPRESSION TAG SEQADV 6WO2 HIS B 167 UNP P62993 EXPRESSION TAG SEQADV 6WO2 HIS B 168 UNP P62993 EXPRESSION TAG SEQADV 6WO2 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 SEQRES 1 C 5 ACE PTR 02K ASN U67 SEQRES 1 D 5 ACE PTR 02K ASN U67 HET ACE C 1 3 HET PTR C 2 16 HET 02K C 3 9 HET U67 C 5 7 HET ACE D 1 3 HET PTR D 2 16 HET 02K D 3 9 HET U67 D 5 7 HET CA A 201 1 HET IPA A 202 4 HET NA B 201 1 HET IPA B 202 4 HETNAM ACE ACETYL GROUP HETNAM PTR O-PHOSPHOTYROSINE HETNAM 02K 1-AMINOCYCLOHEXANECARBOXYLIC ACID HETNAM U67 4-METHYLPENTAN-1-AMINE HETNAM CA CALCIUM ION HETNAM IPA ISOPROPYL ALCOHOL HETNAM NA SODIUM ION HETSYN PTR PHOSPHONOTYROSINE HETSYN IPA 2-PROPANOL FORMUL 3 ACE 2(C2 H4 O) FORMUL 3 PTR 2(C9 H12 N O6 P) FORMUL 3 02K 2(C7 H13 N O2) FORMUL 3 U67 2(C6 H15 N) FORMUL 5 CA CA 2+ FORMUL 6 IPA 2(C3 H8 O) FORMUL 7 NA NA 1+ FORMUL 9 HOH *74(H2 O) HELIX 1 AA1 PRO A 66 LYS A 76 1 11 HELIX 2 AA2 SER A 127 THR A 138 1 12 HELIX 3 AA3 PRO B 66 LYS B 76 1 11 HELIX 4 AA4 SER B 127 HIS B 135 1 9 SHEET 1 AA1 6 LYS A 124 PHE A 125 0 SHEET 2 AA1 6 TYR A 118 PHE A 119 -1 N TYR A 118 O PHE A 125 SHEET 3 AA1 6 ASP A 104 ARG A 112 -1 N LEU A 111 O PHE A 119 SHEET 4 AA1 6 PHE A 95 PHE A 101 -1 N LEU A 97 O PHE A 108 SHEET 5 AA1 6 ALA A 82 GLU A 87 -1 N ARG A 86 O SER A 96 SHEET 6 AA1 6 ARG A 149 ASP A 150 1 O ARG A 149 N PHE A 83 SHEET 1 AA2 6 LYS B 124 PHE B 125 0 SHEET 2 AA2 6 TYR B 118 PHE B 119 -1 N TYR B 118 O PHE B 125 SHEET 3 AA2 6 ASP B 104 ARG B 112 -1 N LEU B 111 O PHE B 119 SHEET 4 AA2 6 PHE B 95 PHE B 101 -1 N PHE B 95 O VAL B 110 SHEET 5 AA2 6 ALA B 82 GLU B 87 -1 N ARG B 86 O SER B 96 SHEET 6 AA2 6 ARG B 149 ASP B 150 1 O ARG B 149 N PHE B 83 LINK C ACE C 1 N PTR C 2 1555 1555 1.34 LINK C PTR C 2 N 02K C 3 1555 1555 1.35 LINK C 02K C 3 N ASN C 4 1555 1555 1.29 LINK C ASN C 4 NAK U67 C 5 1555 1555 1.34 LINK C ACE D 1 N PTR D 2 1555 1555 1.33 LINK C PTR D 2 N 02K D 3 1555 1555 1.34 LINK C 02K D 3 N ASN D 4 1555 1555 1.37 LINK C ASN D 4 NAK U67 D 5 1555 1555 1.33 LINK OE1 GLU A 152 CA CA A 201 1555 1555 2.42 LINK OE2 GLU A 152 CA CA A 201 1555 1555 2.13 LINK CA CA A 201 OE1 GLU B 152 4445 1555 2.13 LINK CA CA A 201 OE2 GLU B 152 4445 1555 2.51 LINK OE1 GLU B 54 NA NA B 201 1555 1555 2.50 LINK OE2 GLU B 54 NA NA B 201 1555 1555 2.75 LINK NA NA B 201 O HOH B 301 1555 1555 2.00 LINK NA NA B 201 O HOH B 305 1555 1555 2.27 LINK NA NA B 201 O HOH B 330 1555 1555 2.37 CISPEP 1 GLN B 144 GLN B 145 0 0.47 CISPEP 2 GLN B 153 VAL B 154 0 8.23 SITE 1 AC1 5 HIS A 79 GLU A 152 HIS B 79 ARG B 149 SITE 2 AC1 5 GLU B 152 SITE 1 AC2 5 VAL A 105 GLN A 106 VAL A 122 02K C 3 SITE 2 AC2 5 HOH C 101 SITE 1 AC3 6 GLU B 54 MET B 55 HIS B 58 HOH B 301 SITE 2 AC3 6 HOH B 305 HOH B 330 SITE 1 AC4 3 GLU B 54 HIS B 58 ASP B 150 SITE 1 AC5 6 GLU A 89 LYS A 109 THR A 138 PTR C 2 SITE 2 AC5 6 02K C 3 ASN C 4 SITE 1 AC6 6 GLU A 72 SER A 75 LYS A 76 PTR D 2 SITE 2 AC6 6 02K D 3 ASN D 4 SITE 1 AC7 13 ARG A 67 ARG A 86 SER A 88 SER A 90 SITE 2 AC7 13 SER A 96 HIS A 107 LYS A 109 TRP A 121 SITE 3 AC7 13 ARG A 142 02K C 3 ASN C 4 U67 C 5 SITE 4 AC7 13 HOH C 101 SITE 1 AC8 15 ARG A 67 ARG A 86 SER A 88 SER A 90 SITE 2 AC8 15 SER A 96 GLN A 106 HIS A 107 PHE A 108 SITE 3 AC8 15 LYS A 109 TRP A 121 ARG A 142 IPA A 202 SITE 4 AC8 15 ACE C 1 ASN C 4 U67 C 5 SITE 1 AC9 10 SER A 90 GLN A 106 HIS A 107 PHE A 108 SITE 2 AC9 10 LYS A 109 LEU A 120 TRP A 121 IPA A 202 SITE 3 AC9 10 PTR C 2 U67 C 5 SITE 1 AD1 14 SER A 75 ARG B 67 ARG B 86 SER B 88 SITE 2 AD1 14 GLU B 89 SER B 90 SER B 96 HIS B 107 SITE 3 AD1 14 LYS B 109 HOH B 317 02K D 3 ASN D 4 SITE 4 AD1 14 U67 D 5 HOH D 102 SITE 1 AD2 18 SER A 75 ASN A 103 ASP A 104 ARG B 67 SITE 2 AD2 18 ARG B 86 SER B 88 GLU B 89 SER B 90 SITE 3 AD2 18 SER B 96 GLN B 106 HIS B 107 PHE B 108 SITE 4 AD2 18 LYS B 109 ACE D 1 ASN D 4 U67 D 5 SITE 5 AD2 18 HOH D 101 HOH D 102 SITE 1 AD3 14 SER A 75 ARG A 78 ASN A 103 ASP A 104 SITE 2 AD3 14 GLN B 106 HIS B 107 PHE B 108 LYS B 109 SITE 3 AD3 14 LEU B 111 LEU B 120 TRP B 121 PTR D 2 SITE 4 AD3 14 U67 D 5 HOH D 101 CRYST1 32.225 62.720 90.137 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 0.031032 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015944 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011094 0.00000