HEADER HYDROLASE 29-AUG-23 8U0H TITLE CRYSTAL STRUCTURE OF PTPN2 WITH A PROTAC COMPND MOL_ID: 1; COMPND 2 MOLECULE: PTPN2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-314; COMPND 5 SYNONYM: MER TYROSINE KINASE DOMAIN, TYROSINE-PROTEIN PHOSPHATASE COMPND 6 NON-RECEPTOR TYPE 2,T-CELL PROTEIN-TYROSINE PHOSPHATASE,TCPTP; COMPND 7 EC: 3.1.3.48; COMPND 8 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: PTPN2, PTPT; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9 KEYWDS PROTEIN TYROSINE PHOSPHATASE, DEGRADER, PROTAC, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.JAIN,K.LONGENECKER,W.QIU REVDAT 1 04-SEP-24 8U0H 0 JRNL AUTH Q.HAO,M.K.RATHINASWAMY,K.L.KLINGE,M.BRATKOWSKI,A.MAFI, JRNL AUTH 2 C.K.BAUMGARTNER,K.M.HAMEL,G.K.VEITS,R.JAIN,C.CATALANO, JRNL AUTH 3 M.FITZGERALD,A.W.HIRD,E.PARK,H.U.VORA,J.A.HENDERSON, JRNL AUTH 4 K.LONGENECKER,C.W.HUTCHINS,W.QIU,G.SCAPIN,Q.SUN,V.S.STOLL, JRNL AUTH 5 C.SUN,P.LI,D.EATON,D.STOKOE,S.L.FISHER,C.G.NASVESCHUK, JRNL AUTH 6 M.PADDOCK,M.E.KORT JRNL TITL MECHANISTIC INSIGHTS INTO A HETEROBIFUNCTIONAL JRNL TITL 2 DEGRADER-INDUCED PTPN2/N1 COMPLEX. JRNL REF COMMUN CHEM V. 7 183 2024 JRNL REFN ESSN 2399-3669 JRNL PMID 39152201 JRNL DOI 10.1038/S42004-024-01263-7 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 55485 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2780 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 38.5900 - 5.2300 0.99 2811 130 0.1685 0.2042 REMARK 3 2 5.2300 - 4.1600 1.00 2698 132 0.1376 0.1252 REMARK 3 3 4.1600 - 3.6300 1.00 2668 158 0.1445 0.1552 REMARK 3 4 3.6300 - 3.3000 1.00 2663 129 0.1533 0.1813 REMARK 3 5 3.3000 - 3.0600 1.00 2645 117 0.1730 0.1842 REMARK 3 6 3.0600 - 2.8800 1.00 2656 122 0.1858 0.2140 REMARK 3 7 2.8800 - 2.7400 1.00 2591 169 0.1834 0.1850 REMARK 3 8 2.7400 - 2.6200 1.00 2683 126 0.1887 0.2242 REMARK 3 9 2.6200 - 2.5200 1.00 2620 139 0.1813 0.2218 REMARK 3 10 2.5200 - 2.4300 1.00 2584 153 0.1936 0.2414 REMARK 3 11 2.4300 - 2.3600 1.00 2617 138 0.1964 0.2208 REMARK 3 12 2.3500 - 2.2900 1.00 2642 130 0.1864 0.2016 REMARK 3 13 2.2900 - 2.2300 1.00 2596 151 0.1931 0.2194 REMARK 3 14 2.2300 - 2.1700 1.00 2586 145 0.1932 0.2057 REMARK 3 15 2.1700 - 2.1200 1.00 2616 148 0.1931 0.2053 REMARK 3 16 2.1200 - 2.0800 1.00 2593 158 0.2018 0.2597 REMARK 3 17 2.0800 - 2.0400 1.00 2576 146 0.2140 0.2502 REMARK 3 18 2.0400 - 2.0000 1.00 2606 146 0.2264 0.2437 REMARK 3 19 2.0000 - 1.9600 1.00 2653 116 0.2449 0.2854 REMARK 3 20 1.9600 - 1.9300 1.00 2601 127 0.2780 0.3271 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.218 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.352 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.018 4881 REMARK 3 ANGLE : 1.719 6643 REMARK 3 CHIRALITY : 0.116 702 REMARK 3 PLANARITY : 0.011 936 REMARK 3 DIHEDRAL : 14.773 1902 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8U0H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1000276978. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 365575 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 38.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.06263 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.68970 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.49M SODIUM PHOSPHATE MONOBASIC REMARK 280 MONOHYDRATE, 0.91M POTASSIUM PHOSPHATE DIBASIC, PH 6.9, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.10500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 75.10500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 38.59000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 63.25500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.59000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 63.25500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 75.10500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.59000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 63.25500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 75.10500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.59000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 63.25500 REMARK 290 SMTRY3 8 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: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NA NA A 803 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1065 LIES ON A SPECIAL POSITION. REMARK 375 HOH B1007 LIES ON A SPECIAL POSITION. 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 MET A -1 REMARK 465 ALA A 0 REMARK 465 LYS A 280 REMARK 465 GLY A 281 REMARK 465 ASP A 282 REMARK 465 SER A 283 REMARK 465 SER A 284 REMARK 465 ILE A 285 REMARK 465 GLN A 286 REMARK 465 LYS A 287 REMARK 465 ARG A 288 REMARK 465 TRP A 289 REMARK 465 LYS A 290 REMARK 465 GLU A 291 REMARK 465 LEU A 292 REMARK 465 SER A 293 REMARK 465 LYS A 294 REMARK 465 GLU A 295 REMARK 465 ASP A 296 REMARK 465 LEU A 297 REMARK 465 SER A 298 REMARK 465 PRO A 299 REMARK 465 ALA A 300 REMARK 465 PHE A 301 REMARK 465 ASP A 302 REMARK 465 HIS A 303 REMARK 465 SER A 304 REMARK 465 PRO A 305 REMARK 465 ASN A 306 REMARK 465 LYS A 307 REMARK 465 ILE A 308 REMARK 465 MET A 309 REMARK 465 THR A 310 REMARK 465 GLU A 311 REMARK 465 LYS A 312 REMARK 465 TYR A 313 REMARK 465 ASN A 314 REMARK 465 HIS A 315 REMARK 465 HIS A 316 REMARK 465 HIS A 317 REMARK 465 HIS A 318 REMARK 465 HIS A 319 REMARK 465 HIS A 320 REMARK 465 HIS A 321 REMARK 465 HIS A 322 REMARK 465 MET B -1 REMARK 465 ALA B 0 REMARK 465 MET B 1 REMARK 465 ILE B 279 REMARK 465 LYS B 280 REMARK 465 GLY B 281 REMARK 465 ASP B 282 REMARK 465 SER B 283 REMARK 465 SER B 284 REMARK 465 ILE B 285 REMARK 465 GLN B 286 REMARK 465 LYS B 287 REMARK 465 ARG B 288 REMARK 465 TRP B 289 REMARK 465 LYS B 290 REMARK 465 GLU B 291 REMARK 465 LEU B 292 REMARK 465 SER B 293 REMARK 465 LYS B 294 REMARK 465 GLU B 295 REMARK 465 ASP B 296 REMARK 465 LEU B 297 REMARK 465 SER B 298 REMARK 465 PRO B 299 REMARK 465 ALA B 300 REMARK 465 PHE B 301 REMARK 465 ASP B 302 REMARK 465 HIS B 303 REMARK 465 SER B 304 REMARK 465 PRO B 305 REMARK 465 ASN B 306 REMARK 465 LYS B 307 REMARK 465 ILE B 308 REMARK 465 MET B 309 REMARK 465 THR B 310 REMARK 465 GLU B 311 REMARK 465 LYS B 312 REMARK 465 TYR B 313 REMARK 465 ASN B 314 REMARK 465 HIS B 315 REMARK 465 HIS B 316 REMARK 465 HIS B 317 REMARK 465 HIS B 318 REMARK 465 HIS B 319 REMARK 465 HIS B 320 REMARK 465 HIS B 321 REMARK 465 HIS B 322 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 O HOH A 1041 O HOH A 1077 2.03 REMARK 500 O HOH B 1049 O HOH B 1059 2.03 REMARK 500 O HOH A 1093 O HOH B 1071 2.04 REMARK 500 O HOH B 1045 O HOH B 1052 2.19 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 O HOH A 1019 O HOH A 1019 3655 2.14 REMARK 500 O HOH A 1011 O HOH A 1101 4555 2.18 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 GLN A 19 C PRO A 20 N 0.153 REMARK 500 PRO A 128 N PRO A 128 CA 0.201 REMARK 500 PRO B 2 N PRO B 2 CA 0.214 REMARK 500 GLN B 19 C PRO B 20 N 0.119 REMARK 500 PRO B 20 N PRO B 20 CA 0.207 REMARK 500 TYR B 32 C PRO B 33 N 0.147 REMARK 500 SER B 52 C PRO B 53 N 0.142 REMARK 500 GLY B 88 C PRO B 89 N 0.141 REMARK 500 PRO B 91 N PRO B 91 CA 0.216 REMARK 500 PRO B 128 N PRO B 128 CA 0.208 REMARK 500 ASN B 206 C PRO B 207 N 0.152 REMARK 500 PRO B 211 N PRO B 211 CA 0.210 REMARK 500 PRO B 262 N PRO B 262 CA 0.208 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 PRO A 20 C - N - CA ANGL. DEV. = 9.5 DEGREES REMARK 500 PRO A 128 C - N - CA ANGL. DEV. = 16.0 DEGREES REMARK 500 ASP A 240 CB - CA - C ANGL. DEV. = 14.8 DEGREES REMARK 500 PRO B 2 CA - N - CD ANGL. DEV. = -10.6 DEGREES REMARK 500 PRO B 20 C - N - CA ANGL. DEV. = 17.4 DEGREES REMARK 500 PRO B 20 CA - N - CD ANGL. DEV. = -8.9 DEGREES REMARK 500 PRO B 33 C - N - CA ANGL. DEV. = 11.0 DEGREES REMARK 500 PRO B 53 C - N - CA ANGL. DEV. = 10.4 DEGREES REMARK 500 PRO B 89 C - N - CA ANGL. DEV. = 11.2 DEGREES REMARK 500 PRO B 91 C - N - CA ANGL. DEV. = 15.6 DEGREES REMARK 500 PRO B 128 C - N - CA ANGL. DEV. = 15.9 DEGREES REMARK 500 PRO B 207 C - N - CA ANGL. DEV. = 13.9 DEGREES REMARK 500 PRO B 207 C - N - CD ANGL. DEV. = -13.4 DEGREES REMARK 500 PRO B 211 C - N - CA ANGL. DEV. = 16.1 DEGREES REMARK 500 PRO B 211 CA - N - CD ANGL. DEV. = -9.3 DEGREES REMARK 500 PRO B 262 C - N - CA ANGL. DEV. = 16.1 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 CYS A 123 141.01 -170.64 REMARK 500 ASP A 130 -158.15 -121.68 REMARK 500 SER A 202 2.51 -67.29 REMARK 500 CYS A 216 -132.18 -131.19 REMARK 500 ILE A 220 -37.08 -133.75 REMARK 500 ILE A 259 115.75 81.06 REMARK 500 HIS B 34 51.91 -140.12 REMARK 500 ASP B 130 -158.83 -119.11 REMARK 500 SER B 188 151.40 80.28 REMARK 500 CYS B 216 -134.69 -135.01 REMARK 500 ILE B 220 -32.79 -130.00 REMARK 500 ILE B 259 114.51 74.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP A 55 -10.01 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 NA A 803 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1083 O REMARK 620 2 HOH A1083 O 80.0 REMARK 620 N 1 DBREF 8U0H A 1 314 UNP P17706 PTN2_HUMAN 1 314 DBREF 8U0H B 1 314 UNP P17706 PTN2_HUMAN 1 314 SEQADV 8U0H MET A -1 UNP P17706 EXPRESSION TAG SEQADV 8U0H ALA A 0 UNP P17706 EXPRESSION TAG SEQADV 8U0H HIS A 315 UNP P17706 EXPRESSION TAG SEQADV 8U0H HIS A 316 UNP P17706 EXPRESSION TAG SEQADV 8U0H HIS A 317 UNP P17706 EXPRESSION TAG SEQADV 8U0H HIS A 318 UNP P17706 EXPRESSION TAG SEQADV 8U0H HIS A 319 UNP P17706 EXPRESSION TAG SEQADV 8U0H HIS A 320 UNP P17706 EXPRESSION TAG SEQADV 8U0H HIS A 321 UNP P17706 EXPRESSION TAG SEQADV 8U0H HIS A 322 UNP P17706 EXPRESSION TAG SEQADV 8U0H MET B -1 UNP P17706 EXPRESSION TAG SEQADV 8U0H ALA B 0 UNP P17706 EXPRESSION TAG SEQADV 8U0H HIS B 315 UNP P17706 EXPRESSION TAG SEQADV 8U0H HIS B 316 UNP P17706 EXPRESSION TAG SEQADV 8U0H HIS B 317 UNP P17706 EXPRESSION TAG SEQADV 8U0H HIS B 318 UNP P17706 EXPRESSION TAG SEQADV 8U0H HIS B 319 UNP P17706 EXPRESSION TAG SEQADV 8U0H HIS B 320 UNP P17706 EXPRESSION TAG SEQADV 8U0H HIS B 321 UNP P17706 EXPRESSION TAG SEQADV 8U0H HIS B 322 UNP P17706 EXPRESSION TAG SEQRES 1 A 324 MET ALA MET PRO THR THR ILE GLU ARG GLU PHE GLU GLU SEQRES 2 A 324 LEU ASP THR GLN ARG ARG TRP GLN PRO LEU TYR LEU GLU SEQRES 3 A 324 ILE ARG ASN GLU SER HIS ASP TYR PRO HIS ARG VAL ALA SEQRES 4 A 324 LYS PHE PRO GLU ASN ARG ASN ARG ASN ARG TYR ARG ASP SEQRES 5 A 324 VAL SER PRO TYR ASP HIS SER ARG VAL LYS LEU GLN ASN SEQRES 6 A 324 ALA GLU ASN ASP TYR ILE ASN ALA SER LEU VAL ASP ILE SEQRES 7 A 324 GLU GLU ALA GLN ARG SER TYR ILE LEU THR GLN GLY PRO SEQRES 8 A 324 LEU PRO ASN THR CYS CYS HIS PHE TRP LEU MET VAL TRP SEQRES 9 A 324 GLN GLN LYS THR LYS ALA VAL VAL MET LEU ASN ARG ILE SEQRES 10 A 324 VAL GLU LYS GLU SER VAL LYS CYS ALA GLN TYR TRP PRO SEQRES 11 A 324 THR ASP ASP GLN GLU MET LEU PHE LYS GLU THR GLY PHE SEQRES 12 A 324 SER VAL LYS LEU LEU SER GLU ASP VAL LYS SER TYR TYR SEQRES 13 A 324 THR VAL HIS LEU LEU GLN LEU GLU ASN ILE ASN SER GLY SEQRES 14 A 324 GLU THR ARG THR ILE SER HIS PHE HIS TYR THR THR TRP SEQRES 15 A 324 PRO ASP PHE GLY VAL PRO GLU SER PRO ALA SER PHE LEU SEQRES 16 A 324 ASN PHE LEU PHE LYS VAL ARG GLU SER GLY SER LEU ASN SEQRES 17 A 324 PRO ASP HIS GLY PRO ALA VAL ILE HIS CYS SER ALA GLY SEQRES 18 A 324 ILE GLY ARG SER GLY THR PHE SER LEU VAL ASP THR CYS SEQRES 19 A 324 LEU VAL LEU MET GLU LYS GLY ASP ASP ILE ASN ILE LYS SEQRES 20 A 324 GLN VAL LEU LEU ASN MET ARG LYS TYR ARG MET GLY LEU SEQRES 21 A 324 ILE GLN THR PRO ASP GLN LEU ARG PHE SER TYR MET ALA SEQRES 22 A 324 ILE ILE GLU GLY ALA LYS CYS ILE LYS GLY ASP SER SER SEQRES 23 A 324 ILE GLN LYS ARG TRP LYS GLU LEU SER LYS GLU ASP LEU SEQRES 24 A 324 SER PRO ALA PHE ASP HIS SER PRO ASN LYS ILE MET THR SEQRES 25 A 324 GLU LYS TYR ASN HIS HIS HIS HIS HIS HIS HIS HIS SEQRES 1 B 324 MET ALA MET PRO THR THR ILE GLU ARG GLU PHE GLU GLU SEQRES 2 B 324 LEU ASP THR GLN ARG ARG TRP GLN PRO LEU TYR LEU GLU SEQRES 3 B 324 ILE ARG ASN GLU SER HIS ASP TYR PRO HIS ARG VAL ALA SEQRES 4 B 324 LYS PHE PRO GLU ASN ARG ASN ARG ASN ARG TYR ARG ASP SEQRES 5 B 324 VAL SER PRO TYR ASP HIS SER ARG VAL LYS LEU GLN ASN SEQRES 6 B 324 ALA GLU ASN ASP TYR ILE ASN ALA SER LEU VAL ASP ILE SEQRES 7 B 324 GLU GLU ALA GLN ARG SER TYR ILE LEU THR GLN GLY PRO SEQRES 8 B 324 LEU PRO ASN THR CYS CYS HIS PHE TRP LEU MET VAL TRP SEQRES 9 B 324 GLN GLN LYS THR LYS ALA VAL VAL MET LEU ASN ARG ILE SEQRES 10 B 324 VAL GLU LYS GLU SER VAL LYS CYS ALA GLN TYR TRP PRO SEQRES 11 B 324 THR ASP ASP GLN GLU MET LEU PHE LYS GLU THR GLY PHE SEQRES 12 B 324 SER VAL LYS LEU LEU SER GLU ASP VAL LYS SER TYR TYR SEQRES 13 B 324 THR VAL HIS LEU LEU GLN LEU GLU ASN ILE ASN SER GLY SEQRES 14 B 324 GLU THR ARG THR ILE SER HIS PHE HIS TYR THR THR TRP SEQRES 15 B 324 PRO ASP PHE GLY VAL PRO GLU SER PRO ALA SER PHE LEU SEQRES 16 B 324 ASN PHE LEU PHE LYS VAL ARG GLU SER GLY SER LEU ASN SEQRES 17 B 324 PRO ASP HIS GLY PRO ALA VAL ILE HIS CYS SER ALA GLY SEQRES 18 B 324 ILE GLY ARG SER GLY THR PHE SER LEU VAL ASP THR CYS SEQRES 19 B 324 LEU VAL LEU MET GLU LYS GLY ASP ASP ILE ASN ILE LYS SEQRES 20 B 324 GLN VAL LEU LEU ASN MET ARG LYS TYR ARG MET GLY LEU SEQRES 21 B 324 ILE GLN THR PRO ASP GLN LEU ARG PHE SER TYR MET ALA SEQRES 22 B 324 ILE ILE GLU GLY ALA LYS CYS ILE LYS GLY ASP SER SER SEQRES 23 B 324 ILE GLN LYS ARG TRP LYS GLU LEU SER LYS GLU ASP LEU SEQRES 24 B 324 SER PRO ALA PHE ASP HIS SER PRO ASN LYS ILE MET THR SEQRES 25 B 324 GLU LYS TYR ASN HIS HIS HIS HIS HIS HIS HIS HIS HET UB0 A 801 67 HET ACT A 802 4 HET NA A 803 1 HET UB0 B 801 67 HET ACT B 802 4 HETNAM UB0 (5P)-3-(CARBOXYMETHOXY)-4-CHLORO-5-(3-{[(4S)-1-({3-[2- HETNAM 2 UB0 (4-{3-[(3R)-2,6-DIOXOPIPERIDIN-3-YL]-2-OXO-2,3- HETNAM 3 UB0 DIHYDRO-1,3-BENZOXAZOL-6-YL}PIPERIDIN-1-YL) HETNAM 4 UB0 ACETAMIDO]PHENYL}METHANESULFONYL)-2,2- HETNAM 5 UB0 DIMETHYLPIPERIDIN-4-YL]AMINO}PHENYL)THIOPHENE-2- HETNAM 6 UB0 CARBOXYLIC ACID HETNAM ACT ACETATE ION HETNAM NA SODIUM ION FORMUL 3 UB0 2(C46 H49 CL N6 O12 S2) FORMUL 4 ACT 2(C2 H3 O2 1-) FORMUL 5 NA NA 1+ FORMUL 8 HOH *385(H2 O) HELIX 1 AA1 THR A 3 ARG A 16 1 14 HELIX 2 AA2 ARG A 17 SER A 29 1 13 HELIX 3 AA3 ARG A 35 ASN A 46 5 12 HELIX 4 AA4 THR A 93 GLN A 104 1 12 HELIX 5 AA5 SER A 188 SER A 202 1 15 HELIX 6 AA6 GLY A 221 LYS A 238 1 18 HELIX 7 AA7 ASN A 243 LYS A 253 1 11 HELIX 8 AA8 THR A 261 ILE A 279 1 19 HELIX 9 AA9 THR B 3 ARG B 16 1 14 HELIX 10 AB1 ARG B 17 SER B 29 1 13 HELIX 11 AB2 ARG B 35 ASN B 46 5 12 HELIX 12 AB3 GLU B 77 GLN B 80 5 4 HELIX 13 AB4 THR B 93 GLN B 104 1 12 HELIX 14 AB5 GLU B 187 SER B 202 1 16 HELIX 15 AB6 GLY B 221 LYS B 238 1 18 HELIX 16 AB7 ASN B 243 LYS B 253 1 11 HELIX 17 AB8 THR B 261 CYS B 278 1 18 SHEET 1 AA1 9 ARG A 58 LYS A 60 0 SHEET 2 AA1 9 TYR A 68 ILE A 76 -1 O ALA A 71 N VAL A 59 SHEET 3 AA1 9 ARG A 81 THR A 86 -1 O TYR A 83 N VAL A 74 SHEET 4 AA1 9 ALA A 212 HIS A 215 1 O ILE A 214 N ILE A 84 SHEET 5 AA1 9 ALA A 108 MET A 111 1 N VAL A 110 O VAL A 213 SHEET 6 AA1 9 THR A 169 TYR A 177 1 O PHE A 175 N MET A 111 SHEET 7 AA1 9 TYR A 154 ASN A 163 -1 N THR A 155 O HIS A 176 SHEET 8 AA1 9 PHE A 141 VAL A 150 -1 N LYS A 144 O GLN A 160 SHEET 9 AA1 9 MET A 134 PHE A 136 -1 N PHE A 136 O PHE A 141 SHEET 1 AA2 2 VAL A 116 GLU A 117 0 SHEET 2 AA2 2 SER A 120 VAL A 121 -1 O SER A 120 N GLU A 117 SHEET 1 AA3 9 ARG B 58 LYS B 60 0 SHEET 2 AA3 9 TYR B 68 ILE B 76 -1 O ALA B 71 N VAL B 59 SHEET 3 AA3 9 ARG B 81 THR B 86 -1 O TYR B 83 N VAL B 74 SHEET 4 AA3 9 ALA B 212 HIS B 215 1 O ILE B 214 N ILE B 84 SHEET 5 AA3 9 ALA B 108 MET B 111 1 N VAL B 110 O VAL B 213 SHEET 6 AA3 9 THR B 169 TYR B 177 1 O TYR B 177 N MET B 111 SHEET 7 AA3 9 TYR B 154 ASN B 163 -1 N THR B 155 O HIS B 176 SHEET 8 AA3 9 PHE B 141 VAL B 150 -1 N LEU B 146 O LEU B 158 SHEET 9 AA3 9 MET B 134 PHE B 136 -1 N PHE B 136 O PHE B 141 SHEET 1 AA4 2 VAL B 116 GLU B 117 0 SHEET 2 AA4 2 SER B 120 VAL B 121 -1 O SER B 120 N GLU B 117 LINK NA NA A 803 O HOH A1083 1555 1555 3.11 LINK NA NA A 803 O HOH A1083 1555 4555 3.11 CRYST1 77.180 126.510 150.210 90.00 90.00 90.00 C 2 2 21 16 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 0.012957 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007905 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006657 0.00000