HEADER HYDROLASE 30-AUG-18 5QDX TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF PTP1B IN TITLE 2 COMPLEX WITH COMPOUND_FMOPL000484A CAVEAT 5QDX SEVERAL RESIDUES ARE NOT PROPERLY LINKED WITH SHORT C-N BOND CAVEAT 2 5QDX DISTANCE FOR CERTAIN CONFORMERS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: PROTEIN-TYROSINE PHOSPHATASE 1B,PTP-1B; COMPND 6 EC: 3.1.3.48; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PTPN1, PTP1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24B KEYWDS PANDDA, SGC - DIAMOND I04-1 FRAGMENT SCREENING, PROTEIN TYROSINE KEYWDS 2 PHOSPHATASE, PTP, PROTEIN TYROSINE PHOSPHATASE 1B, PTP1B, ENZYME, KEYWDS 3 ALLOSTERY, MULTICONFORMER, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.A.KEEDY,Z.B.HILL,J.T.BIEL,E.KANG,T.J.RETTENMAIER,J.BRANDAO-NETO, AUTHOR 2 F.VON DELFT,J.A.WELLS,J.S.FRASER REVDAT 3 06-MAR-24 5QDX 1 REMARK REVDAT 2 06-FEB-19 5QDX 1 COMPND JRNL REVDAT 1 10-OCT-18 5QDX 0 JRNL AUTH D.A.KEEDY,Z.B.HILL,J.T.BIEL,E.KANG,T.J.RETTENMAIER, JRNL AUTH 2 J.BRANDAO-NETO,N.M.PEARCE,F.VON DELFT,J.A.WELLS,J.S.FRASER JRNL TITL AN EXPANDED ALLOSTERIC NETWORK IN PTP1B BY MULTITEMPERATURE JRNL TITL 2 CRYSTALLOGRAPHY, FRAGMENT SCREENING, AND COVALENT TETHERING. JRNL REF ELIFE V. 7 2018 JRNL REFN ESSN 2050-084X JRNL PMID 29877794 JRNL DOI 10.7554/ELIFE.36307 REMARK 2 REMARK 2 RESOLUTION. 2.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 29444 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1154 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 44.0071 - 4.1221 1.00 3955 159 0.1919 0.2518 REMARK 3 2 4.1221 - 3.2721 1.00 3802 154 0.2001 0.2474 REMARK 3 3 3.2721 - 2.8586 1.00 3786 156 0.2131 0.2438 REMARK 3 4 2.8586 - 2.5973 1.00 3733 154 0.2196 0.2454 REMARK 3 5 2.5973 - 2.4111 1.00 3750 149 0.2150 0.2345 REMARK 3 6 2.4111 - 2.2690 0.86 3213 137 0.3728 0.3920 REMARK 3 7 2.2690 - 2.1554 0.85 3183 127 0.3764 0.3789 REMARK 3 8 2.1554 - 2.0615 0.77 2868 118 0.5252 0.4679 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 1.10 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.240 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.90 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 : 0.025 9006 REMARK 3 ANGLE : 2.274 12215 REMARK 3 CHIRALITY : 0.203 1276 REMARK 3 PLANARITY : 0.014 1606 REMARK 3 DIHEDRAL : 19.137 3493 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 5QDX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1001401826. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92819 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57669 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.060 REMARK 200 RESOLUTION RANGE LOW (A) : 63.016 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.16200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.44700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.260 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WELL SOLUTION: 0.3 M MAGNESIUM REMARK 280 ACETATE, 0.1 M HEPES PH 7.5, 0.1% BETA-MERCAPTOETHANOL, 13-14% REMARK 280 PEG 8000, 2% ETHANOL, VAPOR DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.48167 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 70.96333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 70.96333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.48167 REMARK 290 REMARK 290 REMARK: NULL 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL 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 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 GLY A 283 REMARK 465 ASP A 284 REMARK 465 SER A 285 REMARK 465 SER A 286 REMARK 465 VAL A 287 REMARK 465 GLN A 288 REMARK 465 ASP A 289 REMARK 465 GLN A 290 REMARK 465 TRP A 291 REMARK 465 LYS A 292 REMARK 465 GLU A 293 REMARK 465 LEU A 294 REMARK 465 SER A 295 REMARK 465 HIS A 296 REMARK 465 GLU A 297 REMARK 465 ASP A 298 REMARK 465 LEU A 299 REMARK 465 GLU A 300 REMARK 465 PRO A 301 REMARK 465 PRO A 302 REMARK 465 PRO A 303 REMARK 465 GLU A 304 REMARK 465 HIS A 305 REMARK 465 ILE A 306 REMARK 465 PRO A 307 REMARK 465 PRO A 308 REMARK 465 PRO A 309 REMARK 465 PRO A 310 REMARK 465 ARG A 311 REMARK 465 PRO A 312 REMARK 465 PRO A 313 REMARK 465 LYS A 314 REMARK 465 ARG A 315 REMARK 465 ILE A 316 REMARK 465 LEU A 317 REMARK 465 GLU A 318 REMARK 465 PRO A 319 REMARK 465 HIS A 320 REMARK 465 ASN A 321 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 HE21 GLN A 61 O HOH A 501 0.49 REMARK 500 HE21 GLN A 61 O HOH A 501 0.49 REMARK 500 NE2 GLN A 61 O HOH A 501 1.14 REMARK 500 NE2 GLN A 61 O HOH A 501 1.14 REMARK 500 HE ARG A 112 O HOH A 521 1.38 REMARK 500 HE ARG A 112 O HOH A 521 1.38 REMARK 500 HG1 THR A 164 O HOH A 505 1.38 REMARK 500 HG1 THR A 164 O HOH A 505 1.38 REMARK 500 HG SER A 80 O HOH A 517 1.42 REMARK 500 HG SER A 80 O HOH A 517 1.42 REMARK 500 O1 TRS A 402 O HOH A 502 1.49 REMARK 500 H ASP A 240 O HOH A 527 1.51 REMARK 500 H ASP A 240 O HOH A 527 1.51 REMARK 500 H ASP A 240 O HOH A 527 1.52 REMARK 500 H ASP A 240 O HOH A 527 1.52 REMARK 500 HE ARG A 112 O HOH A 521 1.52 REMARK 500 HE ARG A 112 O HOH A 521 1.52 REMARK 500 OD1 ASN A 193 O HOH A 503 1.55 REMARK 500 OD1 ASN A 193 O HOH A 503 1.55 REMARK 500 OE1 GLU A 252 HZ1 LYS A 255 1.59 REMARK 500 OE1 GLU A 252 HZ1 LYS A 255 1.59 REMARK 500 OE2 GLU A 62 O HOH A 504 1.72 REMARK 500 OE2 GLU A 62 O HOH A 504 1.72 REMARK 500 OG1 THR A 164 O HOH A 505 1.82 REMARK 500 OG1 THR A 164 O HOH A 505 1.82 REMARK 500 O HOH A 652 O HOH A 682 1.88 REMARK 500 OE2 GLU A 200 O HOH A 506 1.96 REMARK 500 OE2 GLU A 200 O HOH A 506 1.96 REMARK 500 OD1 ASN A 90 O HOH A 507 1.96 REMARK 500 OD1 ASN A 90 O HOH A 507 1.96 REMARK 500 OG SER A 242 O HOH A 508 1.98 REMARK 500 OG SER A 242 O HOH A 508 1.98 REMARK 500 O HOH A 662 O HOH A 706 1.98 REMARK 500 OD1 ASN A 90 O HOH A 507 2.09 REMARK 500 O HOH A 529 O HOH A 642 2.10 REMARK 500 O SER A 187 O HOH A 509 2.11 REMARK 500 O SER A 187 O HOH A 509 2.11 REMARK 500 OD2 ASP A 63 O HOH A 510 2.11 REMARK 500 OD2 ASP A 63 O HOH A 510 2.11 REMARK 500 O HOH A 517 O HOH A 691 2.11 REMARK 500 O LYS A 41 O HOH A 511 2.13 REMARK 500 O LYS A 41 O HOH A 511 2.13 REMARK 500 OE2 GLU A 161 O HOH A 512 2.13 REMARK 500 OE2 GLU A 161 O HOH A 512 2.13 REMARK 500 N SER A 187 O HOH A 513 2.13 REMARK 500 N SER A 187 O HOH A 513 2.13 REMARK 500 OE2 GLU A 161 O HOH A 512 2.14 REMARK 500 OE2 GLU A 161 O HOH A 512 2.14 REMARK 500 O HOH A 501 O HOH A 526 2.14 REMARK 500 O HOH A 605 O HOH A 700 2.15 REMARK 500 REMARK 500 THIS ENTRY HAS 59 CLOSE CONTACTS 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 623 O HOH A 674 4455 2.17 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 LYS A 39 C ASN A 40 N 0.172 REMARK 500 LYS A 39 C ASN A 40 N 0.172 REMARK 500 LYS A 73 C MET A 74 N 0.212 REMARK 500 LYS A 73 C MET A 74 N 0.212 REMARK 500 GLU A 76 CD GLU A 76 OE1 -0.069 REMARK 500 GLU A 76 CD GLU A 76 OE1 -0.069 REMARK 500 VAL A 92 C GLY A 93 N -0.142 REMARK 500 VAL A 92 C GLY A 93 N -0.142 REMARK 500 GLY A 117 C GLY A 117 O -0.098 REMARK 500 GLY A 117 C GLY A 117 O -0.098 REMARK 500 GLU A 129 CD GLU A 129 OE1 -0.080 REMARK 500 GLU A 129 CD GLU A 129 OE1 -0.080 REMARK 500 GLU A 129 CD GLU A 129 OE2 -0.069 REMARK 500 GLU A 129 CD GLU A 129 OE2 -0.069 REMARK 500 TRP A 179 CB TRP A 179 CG -0.246 REMARK 500 TRP A 179 CB TRP A 179 CG -0.246 REMARK 500 ASP A 181 C PHE A 182 N -0.176 REMARK 500 ASP A 181 C PHE A 182 N -0.176 REMARK 500 SER A 205 CB SER A 205 OG -0.102 REMARK 500 SER A 205 CB SER A 205 OG -0.102 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 LEU A 37 CA - CB - CG ANGL. DEV. = 13.9 DEGREES REMARK 500 LEU A 37 CA - CB - CG ANGL. DEV. = 13.9 DEGREES REMARK 500 PRO A 38 C - N - CD ANGL. DEV. = -17.0 DEGREES REMARK 500 PRO A 38 C - N - CD ANGL. DEV. = -17.0 DEGREES REMARK 500 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 CYS A 121 N - CA - CB ANGL. DEV. = 9.1 DEGREES REMARK 500 CYS A 121 N - CA - CB ANGL. DEV. = 9.1 DEGREES REMARK 500 CYS A 121 CA - CB - SG ANGL. DEV. = 7.6 DEGREES REMARK 500 CYS A 121 CA - CB - SG ANGL. DEV. = 7.6 DEGREES REMARK 500 LEU A 140 CA - CB - CG ANGL. DEV. = 14.1 DEGREES REMARK 500 LEU A 140 CA - CB - CG ANGL. DEV. = 14.1 DEGREES REMARK 500 CYS A 226 CA - CB - SG ANGL. DEV. = 8.0 DEGREES REMARK 500 LEU A 232 CB - CG - CD1 ANGL. DEV. = 11.3 DEGREES REMARK 500 LEU A 232 CB - CG - CD1 ANGL. DEV. = 11.3 DEGREES REMARK 500 LEU A 232 CB - CG - CD2 ANGL. DEV. = 11.9 DEGREES REMARK 500 LEU A 232 CB - CG - CD2 ANGL. DEV. = 11.9 DEGREES REMARK 500 ASP A 236 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASP A 236 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 257 CD - NE - CZ ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG A 257 CD - NE - CZ ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG A 257 NE - CZ - NH1 ANGL. DEV. = 8.7 DEGREES REMARK 500 ARG A 257 NE - CZ - NH1 ANGL. DEV. = 8.7 DEGREES REMARK 500 ARG A 257 NE - CZ - NH2 ANGL. DEV. = -7.8 DEGREES REMARK 500 ARG A 257 NE - CZ - NH2 ANGL. DEV. = -7.8 DEGREES REMARK 500 GLN A 262 N - CA - C ANGL. DEV. = 18.2 DEGREES REMARK 500 GLN A 262 N - CA - C ANGL. DEV. = 18.2 DEGREES REMARK 500 LYS A 279 CD - CE - NZ ANGL. DEV. = 14.3 DEGREES REMARK 500 LYS A 279 CD - CE - NZ ANGL. DEV. = 14.3 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 SER A 15 38.10 -141.09 REMARK 500 SER A 15 38.10 -141.09 REMARK 500 HIS A 60 74.86 -68.40 REMARK 500 HIS A 60 74.86 -68.40 REMARK 500 TRP A 100 -71.90 -56.98 REMARK 500 TRP A 100 -71.90 -56.98 REMARK 500 LYS A 131 71.51 -110.54 REMARK 500 LYS A 131 71.51 -110.54 REMARK 500 CYS A 215 -131.39 -129.83 REMARK 500 CYS A 215 -131.39 -129.83 REMARK 500 CYS A 215 -136.03 -140.47 REMARK 500 CYS A 215 -136.03 -140.47 REMARK 500 ILE A 219 -35.14 -134.30 REMARK 500 ILE A 219 -35.14 -134.30 REMARK 500 ILE A 261 110.95 75.35 REMARK 500 ILE A 261 110.95 75.35 REMARK 500 ILE A 261 94.96 96.55 REMARK 500 ILE A 261 94.96 96.55 REMARK 500 LYS A 279 4.08 -41.94 REMARK 500 LYS A 279 4.08 -41.94 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 GLY A 93 -10.16 REMARK 500 GLY A 93 -10.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 717 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A 718 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A 719 DISTANCE = 7.20 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue JGM A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 402 DBREF 5QDX A 1 321 UNP P18031 PTN1_HUMAN 1 321 SEQADV 5QDX SER A 32 UNP P18031 CYS 32 ENGINEERED MUTATION SEQADV 5QDX VAL A 92 UNP P18031 CYS 92 ENGINEERED MUTATION SEQRES 1 A 321 MET GLU MET GLU LYS GLU PHE GLU GLN ILE ASP LYS SER SEQRES 2 A 321 GLY SER TRP ALA ALA ILE TYR GLN ASP ILE ARG HIS GLU SEQRES 3 A 321 ALA SER ASP PHE PRO SER ARG VAL ALA LYS LEU PRO LYS SEQRES 4 A 321 ASN LYS ASN ARG ASN ARG TYR ARG ASP VAL SER PRO PHE SEQRES 5 A 321 ASP HIS SER ARG ILE LYS LEU HIS GLN GLU ASP ASN ASP SEQRES 6 A 321 TYR ILE ASN ALA SER LEU ILE LYS MET GLU GLU ALA GLN SEQRES 7 A 321 ARG SER TYR ILE LEU THR GLN GLY PRO LEU PRO ASN THR SEQRES 8 A 321 VAL GLY HIS PHE TRP GLU MET VAL TRP GLU GLN LYS SER SEQRES 9 A 321 ARG GLY VAL VAL MET LEU ASN ARG VAL MET GLU LYS GLY SEQRES 10 A 321 SER LEU LYS CYS ALA GLN TYR TRP PRO GLN LYS GLU GLU SEQRES 11 A 321 LYS GLU MET ILE PHE GLU ASP THR ASN LEU LYS LEU THR SEQRES 12 A 321 LEU ILE SER GLU ASP ILE LYS SER TYR TYR THR VAL ARG SEQRES 13 A 321 GLN LEU GLU LEU GLU ASN LEU THR THR GLN GLU THR ARG SEQRES 14 A 321 GLU ILE LEU HIS PHE HIS TYR THR THR TRP PRO ASP PHE SEQRES 15 A 321 GLY VAL PRO GLU SER PRO ALA SER PHE LEU ASN PHE LEU SEQRES 16 A 321 PHE LYS VAL ARG GLU SER GLY SER LEU SER PRO GLU HIS SEQRES 17 A 321 GLY PRO VAL VAL VAL HIS CYS SER ALA GLY ILE GLY ARG SEQRES 18 A 321 SER GLY THR PHE CYS LEU ALA ASP THR CYS LEU LEU LEU SEQRES 19 A 321 MET ASP LYS ARG LYS ASP PRO SER SER VAL ASP ILE LYS SEQRES 20 A 321 LYS VAL LEU LEU GLU MET ARG LYS PHE ARG MET GLY LEU SEQRES 21 A 321 ILE GLN THR ALA ASP GLN LEU ARG PHE SER TYR LEU ALA SEQRES 22 A 321 VAL ILE GLU GLY ALA LYS PHE ILE MET GLY ASP SER SER SEQRES 23 A 321 VAL GLN ASP GLN TRP LYS GLU LEU SER HIS GLU ASP LEU SEQRES 24 A 321 GLU PRO PRO PRO GLU HIS ILE PRO PRO PRO PRO ARG PRO SEQRES 25 A 321 PRO LYS ARG ILE LEU GLU PRO HIS ASN HET JGM A 401 64 HET TRS A 402 20 HETNAM JGM {N}-[(2~{S})-1-DIAZANYL-3-(4-HYDROXYPHENYL)-1- HETNAM 2 JGM OXIDANYLIDENE-PROPAN-2-YL]ETHANAMIDE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 JGM C11 H15 N3 O3 FORMUL 3 TRS C4 H12 N O3 1+ FORMUL 4 HOH *219(H2 O) HELIX 1 AA1 GLU A 2 GLY A 14 1 13 HELIX 2 AA2 SER A 15 ALA A 27 1 13 HELIX 3 AA3 SER A 32 LEU A 37 1 6 HELIX 4 AA4 PRO A 38 ASN A 44 5 7 HELIX 5 AA5 THR A 91 GLN A 102 1 12 HELIX 6 AA6 PRO A 188 SER A 201 1 14 HELIX 7 AA7 GLY A 220 ARG A 238 1 19 HELIX 8 AA8 ASP A 240 VAL A 244 5 5 HELIX 9 AA9 ASP A 245 ARG A 254 1 10 HELIX 10 AB1 THR A 263 MET A 282 1 20 SHEET 1 AA1 9 ARG A 56 LYS A 58 0 SHEET 2 AA1 9 TYR A 66 MET A 74 -1 O ALA A 69 N ILE A 57 SHEET 3 AA1 9 ARG A 79 THR A 84 -1 O TYR A 81 N ILE A 72 SHEET 4 AA1 9 VAL A 211 HIS A 214 1 O VAL A 211 N ILE A 82 SHEET 5 AA1 9 GLY A 106 MET A 109 1 N VAL A 108 O VAL A 212 SHEET 6 AA1 9 THR A 168 TYR A 176 1 O PHE A 174 N VAL A 107 SHEET 7 AA1 9 TYR A 153 ASN A 162 -1 N ARG A 156 O HIS A 173 SHEET 8 AA1 9 LEU A 140 ILE A 149 -1 N LYS A 141 O GLU A 161 SHEET 9 AA1 9 MET A 133 PHE A 135 -1 N PHE A 135 O LEU A 140 SHEET 1 AA2 2 MET A 114 GLU A 115 0 SHEET 2 AA2 2 SER A 118 LEU A 119 -1 O SER A 118 N GLU A 115 SITE 1 AC1 5 VAL A 184 ASP A 265 ARG A 268 PHE A 269 SITE 2 AC1 5 LEU A 272 SITE 1 AC2 5 HIS A 54 LYS A 128 GLU A 129 GLU A 130 SITE 2 AC2 5 HOH A 502 CRYST1 90.286 90.286 106.445 90.00 90.00 120.00 P 31 2 1 6 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 0.011076 0.006395 0.000000 0.00000 SCALE2 0.000000 0.012789 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009395 0.00000