HEADER PEPTIDE BINDING PROTEIN 25-MAR-19 6R5G TITLE C-SH2 DOMAIN OF SHP-2 IN COMPLEX WITH PHOSPHO-ITSM OF PD-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 11; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN-TYROSINE PHOSPHATASE 1D,PTP-1D,PROTEIN-TYROSINE COMPND 5 PHOSPHATASE 2C,PTP-2C,SH-PTP2,SHP2,SH-PTP3; COMPND 6 EC: 3.1.3.48; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: ITSM; COMPND 10 CHAIN: B; COMPND 11 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: PTPN11, PTP2C, SHPTP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS SHP-2 C-SH2 ITSM SH2 DOMAIN PD-1 PHOSPHOTYROSINE, PEPTIDE BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.MARASCO REVDAT 4 14-JUN-23 6R5G 1 REMARK REVDAT 3 26-FEB-20 6R5G 1 JRNL REVDAT 2 19-FEB-20 6R5G 1 JRNL REVDAT 1 05-FEB-20 6R5G 0 JRNL AUTH M.MARASCO,A.BERTEOTTI,J.WEYERSHAEUSER,N.THORAUSCH, JRNL AUTH 2 J.SIKORSKA,J.KRAUSZE,H.J.BRANDT,J.KIRKPATRICK,P.RIOS, JRNL AUTH 3 W.W.SCHAMEL,M.KOHN,T.CARLOMAGNO JRNL TITL MOLECULAR MECHANISM OF SHP2 ACTIVATION BY PD-1 STIMULATION. JRNL REF SCI ADV V. 6 Y4458 2020 JRNL REFN ESSN 2375-2548 JRNL PMID 32064351 JRNL DOI 10.1126/SCIADV.AAY4458 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA, CNS REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), BRUNGER, REMARK 3 ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ARIA AND CNS WERE USED IN COMBINATION REMARK 4 REMARK 4 6R5G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1292101068. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 800 UM [U-13C; U-15N] C-SH2 REMARK 210 DOMAIN OF SHP-2, 1000 UM ITSM, REMARK 210 90% H2O/10% D2O; 800 UM [U-13C; REMARK 210 U-15N] C-SH2 DOMAIN OF SHP-2, REMARK 210 640 UM ITSM, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCACB; 3D HN(COCA)CB; 3D HCCH- REMARK 210 TOCSY; 2D 1H-13C HSQC; 3D NOESY- REMARK 210 13C HSQC; 3D 13C/15N-FILTERED REMARK 210 NOESY-13C HSQC; 2D 13C/15N- REMARK 210 FILTERED 1H-1H NOESY; 2D 13C/15N- REMARK 210 FILTERED 1H-1H TOCSY; 3D NOESY- REMARK 210 15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CCPNMR ANALYSIS, REMARK 210 NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING-MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 150 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 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 O THR B -2 H PTR B 0 1.58 REMARK 500 O LEU A 149 H VAL A 170 1.59 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 HIS A 143 78.04 -117.82 REMARK 500 1 SER A 160 -48.84 -154.11 REMARK 500 1 LYS A 164 -167.15 55.31 REMARK 500 1 THR B -2 -113.89 47.76 REMARK 500 1 GLU B -1 -35.37 70.69 REMARK 500 1 ALA B 1 146.48 57.46 REMARK 500 1 ILE B 3 73.95 55.36 REMARK 500 2 MET A 104 74.29 -104.21 REMARK 500 2 SER A 109 49.12 -74.68 REMARK 500 2 GLN B -3 -157.21 63.38 REMARK 500 2 THR B -2 -95.14 -71.08 REMARK 500 2 GLU B -1 -39.01 71.00 REMARK 500 2 PTR B 0 112.25 74.88 REMARK 500 2 ILE B 3 88.00 70.03 REMARK 500 3 SER A 109 30.19 -75.65 REMARK 500 3 THR B -2 -94.60 -137.94 REMARK 500 3 GLU B -1 -47.05 72.35 REMARK 500 3 PTR B 0 91.30 66.74 REMARK 500 3 ILE B 3 82.25 82.74 REMARK 500 4 MET A 104 -50.83 -135.97 REMARK 500 4 SER A 109 45.28 -78.54 REMARK 500 4 ASN A 161 -169.83 -163.04 REMARK 500 4 THR B -2 -109.52 53.33 REMARK 500 4 GLU B -1 -42.69 70.88 REMARK 500 4 PTR B 0 105.94 78.80 REMARK 500 4 ILE B 3 89.83 78.54 REMARK 500 5 ASN A 161 -133.44 -111.74 REMARK 500 5 LYS A 164 -161.16 -100.26 REMARK 500 5 VAL A 181 55.68 -96.83 REMARK 500 5 THR B -2 -146.99 69.04 REMARK 500 5 GLU B -1 -13.20 75.21 REMARK 500 5 PTR B 0 128.37 75.54 REMARK 500 5 ILE B 3 99.74 73.68 REMARK 500 6 SER A 109 34.65 -74.86 REMARK 500 6 SER A 160 -55.84 -168.36 REMARK 500 6 ASN A 161 -65.52 -168.07 REMARK 500 6 THR B -2 -110.57 54.13 REMARK 500 6 GLU B -1 -42.51 74.37 REMARK 500 6 PTR B 0 98.97 78.21 REMARK 500 6 ILE B 3 105.25 66.32 REMARK 500 7 PTR B 0 107.57 -46.78 REMARK 500 7 ILE B 3 120.54 68.48 REMARK 500 7 PHE B 5 71.29 48.02 REMARK 500 8 SER A 109 47.07 -71.26 REMARK 500 8 ASN A 161 62.27 -152.19 REMARK 500 8 ASP A 162 -100.01 52.55 REMARK 500 8 THR B -2 179.69 57.32 REMARK 500 8 GLU B -1 -39.25 170.57 REMARK 500 8 PTR B 0 87.97 54.63 REMARK 500 8 ILE B 3 96.84 60.06 REMARK 500 REMARK 500 THIS ENTRY HAS 65 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34384 RELATED DB: BMRB REMARK 900 C-SH2 DOMAIN OF SHP-2 IN COMPLEX WITH PHOSPHO-ITSM OF PD-1 DBREF 6R5G A 105 220 UNP Q06124 PTN11_HUMAN 105 220 DBREF 6R5G B -4 6 PDB 6R5G 6R5G -4 6 SEQADV 6R5G GLY A 102 UNP Q06124 EXPRESSION TAG SEQADV 6R5G PRO A 103 UNP Q06124 EXPRESSION TAG SEQADV 6R5G MET A 104 UNP Q06124 EXPRESSION TAG SEQRES 1 A 119 GLY PRO MET ALA ASP PRO THR SER GLU ARG TRP PHE HIS SEQRES 2 A 119 GLY HIS LEU SER GLY LYS GLU ALA GLU LYS LEU LEU THR SEQRES 3 A 119 GLU LYS GLY LYS HIS GLY SER PHE LEU VAL ARG GLU SER SEQRES 4 A 119 GLN SER HIS PRO GLY ASP PHE VAL LEU SER VAL ARG THR SEQRES 5 A 119 GLY ASP ASP LYS GLY GLU SER ASN ASP GLY LYS SER LYS SEQRES 6 A 119 VAL THR HIS VAL MET ILE ARG CYS GLN GLU LEU LYS TYR SEQRES 7 A 119 ASP VAL GLY GLY GLY GLU ARG PHE ASP SER LEU THR ASP SEQRES 8 A 119 LEU VAL GLU HIS TYR LYS LYS ASN PRO MET VAL GLU THR SEQRES 9 A 119 LEU GLY THR VAL LEU GLN LEU LYS GLN PRO LEU ASN THR SEQRES 10 A 119 THR ARG SEQRES 1 B 11 GLU GLN THR GLU PTR ALA THR ILE VAL PHE PRO HET PTR B 0 24 HETNAM PTR O-PHOSPHOTYROSINE HETSYN PTR PHOSPHONOTYROSINE FORMUL 2 PTR C9 H12 N O6 P HELIX 1 AA1 SER A 118 LYS A 129 1 12 HELIX 2 AA2 SER A 189 ASN A 200 1 12 SHEET 1 AA1 5 PHE A 113 HIS A 114 0 SHEET 2 AA1 5 SER A 134 GLU A 139 1 O VAL A 137 N HIS A 114 SHEET 3 AA1 5 PHE A 147 THR A 153 -1 O SER A 150 N LEU A 136 SHEET 4 AA1 5 LYS A 166 GLN A 175 -1 O THR A 168 N VAL A 151 SHEET 5 AA1 5 LYS A 178 ASP A 180 -1 O ASP A 180 N ARG A 173 SHEET 1 AA2 3 PHE A 113 HIS A 114 0 SHEET 2 AA2 3 SER A 134 GLU A 139 1 O VAL A 137 N HIS A 114 SHEET 3 AA2 3 GLN A 214 PRO A 215 1 O GLN A 214 N PHE A 135 SHEET 1 AA3 2 MET A 202 VAL A 203 0 SHEET 2 AA3 2 VAL A 209 LEU A 210 -1 O LEU A 210 N MET A 202 LINK C GLU B -1 N PTR B 0 1555 1555 1.33 LINK C PTR B 0 N ALA B 1 1555 1555 1.35 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 MODEL 1