HEADER PEPTIDE BINDING PROTEIN 20-APR-20 6WM1 TITLE CRYSTAL STRUCTURE OF THE GRB2 SH2 DOMAIN IN COMPLEX WITH A TRIPEPTIDE: TITLE 2 AC-PY-AC6C-N-PHENYLPROPYL COMPND MOL_ID: 1; COMPND 2 MOLECULE: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2; COMPND 3 CHAIN: A, C; 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-PRA; COMPND 9 CHAIN: B, 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 5 23-OCT-24 6WM1 1 REMARK REVDAT 4 15-NOV-23 6WM1 1 REMARK REVDAT 3 18-OCT-23 6WM1 1 REMARK REVDAT 2 23-SEP-20 6WM1 1 JRNL REVDAT 1 02-SEP-20 6WM1 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.4 REMARK 3 NUMBER OF REFLECTIONS : 15867 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 850 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1227 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 64 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1744 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.90000 REMARK 3 B22 (A**2) : -2.40000 REMARK 3 B33 (A**2) : -0.50000 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): 0.169 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.166 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.092 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.888 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1853 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2496 ; 2.019 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 210 ; 6.140 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 92 ;30.585 ;23.261 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 314 ;15.747 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;13.322 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 245 ; 0.164 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1442 ; 0.011 ; 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 6WM1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-APR-20. REMARK 100 THE DEPOSITION ID IS D_1000248559. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16789 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 51.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.6 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 46.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 10.50 REMARK 200 R MERGE FOR SHELL (I) : 0.11300 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 2.1.4 REMARK 200 STARTING MODEL: 4P9V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AN AQUEOUS SOLUTION CONTAINING A 1.5 REMARK 280 MOLAR RATIO OF LIGAND TO PROTEIN, 10 MG/ML, WAS PREPARED. 4.0 UL REMARK 280 OF THIS SOLUTION WAS MIXED WITH 3.0 UL PRECIPITANT SOLUTION REMARK 280 CONTAINING 0.1 M HEPES, PH 7.5, AND 25% W/V POLYETHYLENE GLYCOL, REMARK 280 MW 10,000, AND ALLOWED TO EQUILIBRATE WITH 350 UL OF THE REMARK 280 AFOREMENTIONED PRECIPITANT WELL SOLUTION AT 298 K. USEABLE REMARK 280 CRYSTALS GREW AFTER 4 WEEKS, VAPOR DIFFUSION, HANGING DROP 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 18.00500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.44450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.48850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.44450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.00500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.48850 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, 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: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 GLU A 54 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 C 53 REMARK 465 VAL C 154 REMARK 465 PRO C 155 REMARK 465 GLN C 156 REMARK 465 GLN C 157 REMARK 465 PRO C 158 REMARK 465 THR C 159 REMARK 465 TYR C 160 REMARK 465 VAL C 161 REMARK 465 GLN C 162 REMARK 465 ALA C 163 REMARK 465 HIS C 164 REMARK 465 HIS C 165 REMARK 465 HIS C 166 REMARK 465 HIS C 167 REMARK 465 HIS C 168 REMARK 465 HIS C 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 ARG A 78 CG CD NE CZ NH1 NH2 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 OE2 GLU C 152 CA CA C 202 1.41 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 OE2 GLU A 152 OE2 GLU C 152 4455 2.09 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 ARG A 78 CB ARG A 78 CG -0.220 REMARK 500 TYR C 118 CD1 TYR C 118 CE1 0.093 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 GLN A 144 CB - CA - C ANGL. DEV. = -12.2 DEGREES REMARK 500 ASP C 113 CB - CG - OD1 ANGL. DEV. = 6.0 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 LYS A 56 141.66 11.28 REMARK 500 ASN A 103 45.90 -102.77 REMARK 500 TRP A 121 -91.15 -119.47 REMARK 500 ALA C 91 74.11 -119.45 REMARK 500 TRP C 121 -76.90 -127.65 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 C 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 152 OE1 REMARK 620 2 GLU A 152 OE2 53.2 REMARK 620 3 GLU C 152 OE1 51.7 24.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL C 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand PRA 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 PRA 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 GRB2 SH2 COMPLEXED WITH AC-PY-AC6C-N TRIPEPTIDE DBREF 6WM1 A 53 163 UNP P62993 GRB2_HUMAN 53 163 DBREF 6WM1 C 53 163 UNP P62993 GRB2_HUMAN 53 163 DBREF 6WM1 B 1 5 PDB 6WM1 6WM1 1 5 DBREF 6WM1 D 1 5 PDB 6WM1 6WM1 1 5 SEQADV 6WM1 HIS A 164 UNP P62993 EXPRESSION TAG SEQADV 6WM1 HIS A 165 UNP P62993 EXPRESSION TAG SEQADV 6WM1 HIS A 166 UNP P62993 EXPRESSION TAG SEQADV 6WM1 HIS A 167 UNP P62993 EXPRESSION TAG SEQADV 6WM1 HIS A 168 UNP P62993 EXPRESSION TAG SEQADV 6WM1 HIS A 169 UNP P62993 EXPRESSION TAG SEQADV 6WM1 HIS C 164 UNP P62993 EXPRESSION TAG SEQADV 6WM1 HIS C 165 UNP P62993 EXPRESSION TAG SEQADV 6WM1 HIS C 166 UNP P62993 EXPRESSION TAG SEQADV 6WM1 HIS C 167 UNP P62993 EXPRESSION TAG SEQADV 6WM1 HIS C 168 UNP P62993 EXPRESSION TAG SEQADV 6WM1 HIS C 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 C 117 ILE GLU MET LYS PRO HIS PRO TRP PHE PHE GLY LYS ILE SEQRES 2 C 117 PRO ARG ALA LYS ALA GLU GLU MET LEU SER LYS GLN ARG SEQRES 3 C 117 HIS ASP GLY ALA PHE LEU ILE ARG GLU SER GLU SER ALA SEQRES 4 C 117 PRO GLY ASP PHE SER LEU SER VAL LYS PHE GLY ASN ASP SEQRES 5 C 117 VAL GLN HIS PHE LYS VAL LEU ARG ASP GLY ALA GLY LYS SEQRES 6 C 117 TYR PHE LEU TRP VAL VAL LYS PHE ASN SER LEU ASN GLU SEQRES 7 C 117 LEU VAL ASP TYR HIS ARG SER THR SER VAL SER ARG ASN SEQRES 8 C 117 GLN GLN ILE PHE LEU ARG ASP ILE GLU GLN VAL PRO GLN SEQRES 9 C 117 GLN PRO THR TYR VAL GLN ALA HIS HIS HIS HIS HIS HIS SEQRES 1 B 5 ACE PTR 02K ASN PRA SEQRES 1 D 5 ACE PTR 02K ASN PRA HET ACE B 1 3 HET PTR B 2 16 HET 02K B 3 9 HET PRA B 5 10 HET ACE D 1 3 HET PTR D 2 16 HET 02K D 3 9 HET PRA D 5 10 HET GOL C 201 6 HET CA C 202 1 HET CL C 203 1 HET GOL D 101 6 HETNAM ACE ACETYL GROUP HETNAM PTR O-PHOSPHOTYROSINE HETNAM 02K 1-AMINOCYCLOHEXANECARBOXYLIC ACID HETNAM PRA 3-PHENYLPROPYLAMINE HETNAM GOL GLYCEROL HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION HETSYN PTR PHOSPHONOTYROSINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL 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 PRA 2(C9 H13 N) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 6 CA CA 2+ FORMUL 7 CL CL 1- FORMUL 9 HOH *147(H2 O) HELIX 1 AA1 PRO A 66 GLN A 77 1 12 HELIX 2 AA2 SER A 127 HIS A 135 1 9 HELIX 3 AA3 PRO C 66 LYS C 76 1 11 HELIX 4 AA4 SER C 127 HIS C 135 1 9 SHEET 1 AA1 5 TYR A 118 PHE A 119 0 SHEET 2 AA1 5 ASP A 104 ARG A 112 -1 N LEU A 111 O PHE A 119 SHEET 3 AA1 5 PHE A 95 PHE A 101 -1 N VAL A 99 O GLN A 106 SHEET 4 AA1 5 ALA A 82 GLU A 87 -1 N ALA A 82 O LYS A 100 SHEET 5 AA1 5 ARG A 149 ASP A 150 1 O ARG A 149 N PHE A 83 SHEET 1 AA2 5 PHE C 61 GLY C 63 0 SHEET 2 AA2 5 ALA C 82 GLU C 87 1 O ILE C 85 N PHE C 62 SHEET 3 AA2 5 PHE C 95 PHE C 101 -1 O SER C 96 N ARG C 86 SHEET 4 AA2 5 ASP C 104 ARG C 112 -1 O GLN C 106 N VAL C 99 SHEET 5 AA2 5 TYR C 118 PHE C 119 -1 O PHE C 119 N LEU C 111 SHEET 1 AA3 3 PHE C 61 GLY C 63 0 SHEET 2 AA3 3 ALA C 82 GLU C 87 1 O ILE C 85 N PHE C 62 SHEET 3 AA3 3 ARG C 149 ASP C 150 1 O ARG C 149 N PHE C 83 LINK C ACE B 1 N PTR B 2 1555 1555 1.32 LINK C PTR B 2 N 02K B 3 1555 1555 1.31 LINK C 02K B 3 N ASN B 4 1555 1555 1.37 LINK C ASN B 4 N PRA B 5 1555 1555 1.36 LINK C ACE D 1 N PTR D 2 1555 1555 1.34 LINK C PTR D 2 N 02K D 3 1555 1555 1.32 LINK C 02K D 3 N ASN D 4 1555 1555 1.34 LINK C ASN D 4 N PRA D 5 1555 1555 1.33 LINK OE1 GLU A 152 CA CA C 202 1555 4455 2.69 LINK OE2 GLU A 152 CA CA C 202 1555 4455 1.94 LINK OE1 GLU C 152 CA CA C 202 1555 1555 2.91 SITE 1 AC1 8 SER A 75 LYS A 76 GLN A 77 ARG A 78 SITE 2 AC1 8 LEU C 120 TRP C 121 ARG C 142 ASN D 4 SITE 1 AC2 4 HIS A 79 GLU A 152 HIS C 79 GLU C 152 SITE 1 AC3 6 ASN A 103 TRP C 121 ARG C 142 HOH C 310 SITE 2 AC3 6 HOH C 356 ASN D 4 SITE 1 AC4 3 ARG C 67 ACE D 1 PTR D 2 SITE 1 AC5 5 LEU A 111 ASN A 143 PTR B 2 02K B 3 SITE 2 AC5 5 ASN B 4 SITE 1 AC6 5 SER A 75 LEU C 111 PTR D 2 02K D 3 SITE 2 AC6 5 ASN D 4 SITE 1 AC7 14 ARG A 67 ARG A 86 SER A 96 HIS A 107 SITE 2 AC7 14 PHE A 108 LYS A 109 ARG A 142 HOH A 216 SITE 3 AC7 14 HOH A 220 02K B 3 ASN B 4 PRA B 5 SITE 4 AC7 14 HOH B 102 HOH B 104 SITE 1 AC8 16 ARG A 67 ARG A 86 SER A 96 HIS A 107 SITE 2 AC8 16 PHE A 108 LYS A 109 TRP A 121 ARG A 142 SITE 3 AC8 16 HOH A 216 ACE B 1 ASN B 4 PRA B 5 SITE 4 AC8 16 HOH B 101 HOH B 102 HOH B 103 HOH B 104 SITE 1 AC9 11 HIS A 107 PHE A 108 LYS A 109 LEU A 120 SITE 2 AC9 11 TRP A 121 HOH A 243 ACE B 1 PTR B 2 SITE 3 AC9 11 PRA B 5 HOH B 101 HOH B 103 SITE 1 AD1 13 ARG C 67 ARG C 86 SER C 88 SER C 90 SITE 2 AD1 13 SER C 96 HIS C 107 PHE C 108 LYS C 109 SITE 3 AD1 13 02K D 3 ASN D 4 PRA D 5 GOL D 101 SITE 4 AD1 13 HOH D 201 SITE 1 AD2 16 ASN A 103 HOH A 215 HOH A 252 ARG C 67 SITE 2 AD2 16 ARG C 86 SER C 88 SER C 90 SER C 96 SITE 3 AD2 16 HIS C 107 PHE C 108 LYS C 109 ACE D 1 SITE 4 AD2 16 ASN D 4 PRA D 5 GOL D 101 HOH D 201 SITE 1 AD3 12 SER A 75 ASN A 103 HOH A 215 HOH A 252 SITE 2 AD3 12 HIS C 107 PHE C 108 LYS C 109 LEU C 120 SITE 3 AD3 12 GOL C 201 CL C 203 PTR D 2 PRA D 5 CRYST1 36.010 62.977 90.889 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 0.027770 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015879 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011002 0.00000