HEADER IMMUNE SYSTEM/HYDROLASE 25-FEB-15 4YFC OBSLTE 16-AUG-17 4YFC 5Y32 TITLE CRYSTAL STRUCTURE OF PTP DELTA IG1-IG2 IN COMPLEX WITH IL1RAPL1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-1 RECEPTOR ACCESSORY PROTEIN-LIKE 1; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: UNP RESIDUES 19-352; COMPND 5 SYNONYM: IL1RAPL-1,X-LINKED INTERLEUKIN-1 RECEPTOR ACCESSORY PROTEIN- COMPND 6 LIKE 1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE DELTA; COMPND 10 CHAIN: A; COMPND 11 FRAGMENT: UNP RESIDUES 21-318; COMPND 12 SYNONYM: R-PTP-DELTA; COMPND 13 EC: 3.1.3.48; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: IL1RAPL1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: FREESTYLE 293-F; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 12 ORGANISM_COMMON: MOUSE; SOURCE 13 ORGANISM_TAXID: 10090; SOURCE 14 GENE: PTPRD; SOURCE 15 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 16 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM_CELL_LINE: FREESTYLE 293-F KEYWDS TRANS-SYNAPTIC, ADHESION COMPLEX, IMMUNE SYSTEM-HYDROLASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.YAMAGATA,S.FUKAI REVDAT 2 16-AUG-17 4YFC 1 OBSLTE SOURCE REMARK REVDAT 1 06-MAY-15 4YFC 0 JRNL AUTH A.YAMAGATA,T.YOSHIDA,Y.SATO,S.GOTO-ITO,T.UEMURA,A.MAEDA, JRNL AUTH 2 T.SHIROSHIMA,S.IWASAWA-OKAMOTO,H.MORI,M.MISHINA,S.FUKAI JRNL TITL MECHANISMS OF SPLICING-DEPENDENT TRANS-SYNAPTIC ADHESION BY JRNL TITL 2 PTP DELTA-IL1RAPL1/IL-1RACP FOR SYNAPTIC DIFFERENTIATION. JRNL REF NAT COMMUN V. 6 6926 2015 JRNL REFN ESSN 2041-1723 JRNL PMID 25908590 JRNL DOI 10.1038/NCOMMS7926 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.470 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 32242 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1638 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 0.0000 - 6.1801 0.99 2654 166 0.2152 0.2523 REMARK 3 2 6.1801 - 4.9072 1.00 2613 151 0.1875 0.2183 REMARK 3 3 4.9072 - 4.2874 1.00 2599 135 0.1489 0.1954 REMARK 3 4 4.2874 - 3.8956 1.00 2600 140 0.1737 0.2228 REMARK 3 5 3.8956 - 3.6165 1.00 2608 125 0.2106 0.2488 REMARK 3 6 3.6165 - 3.4034 0.99 2574 128 0.2228 0.2957 REMARK 3 7 3.4034 - 3.2330 0.99 2568 142 0.2483 0.2688 REMARK 3 8 3.2330 - 3.0923 0.99 2585 141 0.2713 0.2997 REMARK 3 9 3.0923 - 2.9733 0.98 2514 132 0.2989 0.3288 REMARK 3 10 2.9733 - 2.8707 0.98 2551 118 0.0000 0.0000 REMARK 3 11 2.8707 - 2.7809 0.97 2484 125 0.3484 0.3668 REMARK 3 12 2.7809 - 2.7014 0.87 2254 0 0.0000 0.0000 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.480 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.005 4454 REMARK 3 ANGLE : 1.409 6036 REMARK 3 CHIRALITY : 0.067 693 REMARK 3 PLANARITY : 0.005 766 REMARK 3 DIHEDRAL : 18.192 1688 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -51.1836 -10.7934 19.7762 REMARK 3 T TENSOR REMARK 3 T11: 0.1065 T22: 0.1199 REMARK 3 T33: 0.1147 T12: -0.0101 REMARK 3 T13: 0.0066 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 0.4182 L22: 0.7798 REMARK 3 L33: 0.8859 L12: -0.1703 REMARK 3 L13: 0.3502 L23: 0.0433 REMARK 3 S TENSOR REMARK 3 S11: 0.0510 S12: 0.0483 S13: 0.0059 REMARK 3 S21: 0.1688 S22: -0.0489 S23: -0.1234 REMARK 3 S31: -0.0065 S32: 0.0635 S33: -0.0216 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 4YFC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207368. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32256 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12200 REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.42900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 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: 2YD6, 4DEP, 3O4O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG4 000, 0.1 M MES, PH 6.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 81.48750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.58750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 81.48750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.58750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 ALA B 12 REMARK 465 GLN B 13 REMARK 465 PRO B 14 REMARK 465 ALA B 15 REMARK 465 ALA B 16 REMARK 465 ARG B 17 REMARK 465 ASP B 18 REMARK 465 LEU B 19 REMARK 465 LYS B 20 REMARK 465 VAL B 21 REMARK 465 VAL B 22 REMARK 465 THR B 23 REMARK 465 LYS B 24 REMARK 465 ARG B 25 REMARK 465 GLY B 26 REMARK 465 SER B 27 REMARK 465 ALA B 28 REMARK 465 ASP B 29 REMARK 465 GLY B 30 REMARK 465 LYS B 353 REMARK 465 HIS B 354 REMARK 465 HIS B 355 REMARK 465 HIS B 356 REMARK 465 HIS B 357 REMARK 465 HIS B 358 REMARK 465 HIS B 359 REMARK 465 GLU A 237 REMARK 465 VAL A 238 REMARK 465 ARG A 239 REMARK 465 ARG A 240 REMARK 465 VAL A 241 REMARK 465 PRO A 242 REMARK 465 PRO A 243 REMARK 465 ARG A 244 REMARK 465 PHE A 245 REMARK 465 SER A 246 REMARK 465 ILE A 247 REMARK 465 PRO A 248 REMARK 465 PRO A 249 REMARK 465 THR A 250 REMARK 465 ASN A 251 REMARK 465 HIS A 252 REMARK 465 GLU A 253 REMARK 465 ILE A 254 REMARK 465 MET A 255 REMARK 465 PRO A 256 REMARK 465 GLY A 257 REMARK 465 GLY A 258 REMARK 465 SER A 259 REMARK 465 VAL A 260 REMARK 465 ASN A 261 REMARK 465 ILE A 262 REMARK 465 THR A 263 REMARK 465 CYS A 264 REMARK 465 VAL A 265 REMARK 465 ALA A 266 REMARK 465 VAL A 267 REMARK 465 GLY A 268 REMARK 465 SER A 269 REMARK 465 PRO A 270 REMARK 465 MET A 271 REMARK 465 PRO A 272 REMARK 465 TYR A 273 REMARK 465 VAL A 274 REMARK 465 LYS A 275 REMARK 465 TRP A 276 REMARK 465 MET A 277 REMARK 465 LEU A 278 REMARK 465 GLY A 279 REMARK 465 ALA A 280 REMARK 465 GLU A 281 REMARK 465 ASP A 282 REMARK 465 LEU A 283 REMARK 465 THR A 284 REMARK 465 PRO A 285 REMARK 465 GLU A 286 REMARK 465 ASP A 287 REMARK 465 ASP A 288 REMARK 465 MET A 289 REMARK 465 PRO A 290 REMARK 465 ILE A 291 REMARK 465 GLY A 292 REMARK 465 ARG A 293 REMARK 465 ASN A 294 REMARK 465 VAL A 295 REMARK 465 LEU A 296 REMARK 465 GLU A 297 REMARK 465 LEU A 298 REMARK 465 ASN A 299 REMARK 465 ASP A 300 REMARK 465 VAL A 301 REMARK 465 ARG A 302 REMARK 465 GLN A 303 REMARK 465 SER A 304 REMARK 465 ALA A 305 REMARK 465 ASN A 306 REMARK 465 TYR A 307 REMARK 465 THR A 308 REMARK 465 CYS A 309 REMARK 465 VAL A 310 REMARK 465 ALA A 311 REMARK 465 MET A 312 REMARK 465 SER A 313 REMARK 465 THR A 314 REMARK 465 LEU A 315 REMARK 465 GLY A 316 REMARK 465 VAL A 317 REMARK 465 ILE A 318 REMARK 465 GLU A 319 REMARK 465 ALA A 320 REMARK 465 ILE A 321 REMARK 465 ALA A 322 REMARK 465 GLN A 323 REMARK 465 ILE A 324 REMARK 465 THR A 325 REMARK 465 LYS A 326 REMARK 465 HIS A 327 REMARK 465 HIS A 328 REMARK 465 HIS A 329 REMARK 465 HIS A 330 REMARK 465 HIS A 331 REMARK 465 HIS A 332 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 OH TYR B 64 O HOH B 501 1.94 REMARK 500 O ILE A 190 O HOH A 423 1.96 REMARK 500 OD1 ASP B 101 O HOH B 532 1.98 REMARK 500 OG SER B 333 O HOH B 521 1.99 REMARK 500 O HOH A 404 O HOH A 431 2.00 REMARK 500 O THR B 174 O HOH B 533 2.06 REMARK 500 ND2 ASN B 138 C2 NAG B 409 2.11 REMARK 500 O HOH B 512 O HOH A 409 2.11 REMARK 500 N ASN B 145 O HOH B 536 2.11 REMARK 500 OE2 GLU A 80 O HOH A 414 2.13 REMARK 500 OE1 GLN A 184 O HOH A 417 2.14 REMARK 500 O4 NAG B 404 O HOH B 518 2.18 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 B 35 -155.48 57.28 REMARK 500 TYR B 59 -74.03 -67.59 REMARK 500 ASP B 92 -153.90 -93.57 REMARK 500 SER B 94 -84.48 -96.17 REMARK 500 LYS B 98 73.09 -113.62 REMARK 500 ASN B 122 -159.12 -105.49 REMARK 500 ASN B 138 122.21 -30.06 REMARK 500 MET B 148 64.55 -153.10 REMARK 500 PRO B 173 32.04 -87.46 REMARK 500 LYS B 197 -164.74 -121.24 REMARK 500 TYR B 220 128.73 -177.61 REMARK 500 LEU B 237 109.44 -58.59 REMARK 500 LEU B 245 -79.91 -115.64 REMARK 500 SER B 250 -51.24 -120.03 REMARK 500 TRP B 299 142.86 -174.86 REMARK 500 HIS B 309 80.62 -153.03 REMARK 500 LEU B 310 75.66 51.89 REMARK 500 GLU B 325 -150.00 -90.17 REMARK 500 LEU A 141 131.21 -38.90 REMARK 500 THR A 147 -13.30 81.86 REMARK 500 SER A 189 91.93 77.17 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 435 DISTANCE = 6.41 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Mono-Saccharide NAG B 410 bound REMARK 800 to ASN B 63 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Poly-Saccharide residues NAG B REMARK 800 400 through FUL B 402 bound to ASN B 122 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Mono-Saccharide NAG B 409 bound REMARK 800 to ASN B 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Poly-Saccharide residues NAG B REMARK 800 403 through NAG B 404 bound to ASN B 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Poly-Saccharide residues NAG B REMARK 800 405 through FUL B 408 bound to ASN B 264 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YFD RELATED DB: PDB REMARK 900 RELATED ID: 4YFE RELATED DB: PDB REMARK 900 RELATED ID: 4YFG RELATED DB: PDB DBREF 4YFC B 19 352 UNP P59823 IRPL1_MOUSE 19 352 DBREF 4YFC A 28 325 UNP Q64487 PTPRD_MOUSE 21 318 SEQADV 4YFC ALA B 12 UNP P59823 EXPRESSION TAG SEQADV 4YFC GLN B 13 UNP P59823 EXPRESSION TAG SEQADV 4YFC PRO B 14 UNP P59823 EXPRESSION TAG SEQADV 4YFC ALA B 15 UNP P59823 EXPRESSION TAG SEQADV 4YFC ALA B 16 UNP P59823 EXPRESSION TAG SEQADV 4YFC ARG B 17 UNP P59823 EXPRESSION TAG SEQADV 4YFC ASP B 18 UNP P59823 EXPRESSION TAG SEQADV 4YFC LYS B 353 UNP P59823 EXPRESSION TAG SEQADV 4YFC HIS B 354 UNP P59823 EXPRESSION TAG SEQADV 4YFC HIS B 355 UNP P59823 EXPRESSION TAG SEQADV 4YFC HIS B 356 UNP P59823 EXPRESSION TAG SEQADV 4YFC HIS B 357 UNP P59823 EXPRESSION TAG SEQADV 4YFC HIS B 358 UNP P59823 EXPRESSION TAG SEQADV 4YFC HIS B 359 UNP P59823 EXPRESSION TAG SEQADV 4YFC LYS A 326 UNP Q64487 EXPRESSION TAG SEQADV 4YFC HIS A 327 UNP Q64487 EXPRESSION TAG SEQADV 4YFC HIS A 328 UNP Q64487 EXPRESSION TAG SEQADV 4YFC HIS A 329 UNP Q64487 EXPRESSION TAG SEQADV 4YFC HIS A 330 UNP Q64487 EXPRESSION TAG SEQADV 4YFC HIS A 331 UNP Q64487 EXPRESSION TAG SEQADV 4YFC HIS A 332 UNP Q64487 EXPRESSION TAG SEQRES 1 B 348 ALA GLN PRO ALA ALA ARG ASP LEU LYS VAL VAL THR LYS SEQRES 2 B 348 ARG GLY SER ALA ASP GLY CYS THR ASP TRP SER VAL ASP SEQRES 3 B 348 ILE LYS LYS TYR GLN VAL LEU VAL GLY GLU PRO VAL ARG SEQRES 4 B 348 ILE LYS CYS ALA LEU PHE TYR GLY TYR ILE ARG THR ASN SEQRES 5 B 348 TYR SER LEU ALA GLN SER ALA GLY LEU SER LEU MET TRP SEQRES 6 B 348 TYR LYS SER SER GLY PRO GLY ASP PHE GLU GLU PRO ILE SEQRES 7 B 348 ALA PHE ASP GLY SER ARG MET SER LYS GLU GLU ASP SER SEQRES 8 B 348 ILE TRP PHE ARG PRO THR LEU LEU GLN ASP SER GLY LEU SEQRES 9 B 348 TYR ALA CYS VAL ILE ARG ASN SER THR TYR CYS MET LYS SEQRES 10 B 348 VAL SER ILE SER LEU THR VAL GLY GLU ASN ASP THR GLY SEQRES 11 B 348 LEU CYS TYR ASN SER LYS MET LYS TYR PHE GLU LYS ALA SEQRES 12 B 348 GLU LEU SER LYS SER LYS GLU ILE SER CYS ARG ASP ILE SEQRES 13 B 348 GLU ASP PHE LEU LEU PRO THR ARG GLU PRO GLU ILE LEU SEQRES 14 B 348 TRP TYR LYS GLU CYS ARG THR LYS ALA TRP ARG PRO SER SEQRES 15 B 348 ILE VAL PHE LYS ARG ASP THR LEU LEU ILE LYS GLU VAL SEQRES 16 B 348 LYS GLU ASP ASP ILE GLY ASN TYR THR CYS GLU LEU LYS SEQRES 17 B 348 TYR GLY GLY PHE VAL VAL ARG ARG THR THR GLU LEU THR SEQRES 18 B 348 VAL THR ALA PRO LEU THR ASP LYS PRO PRO LYS LEU LEU SEQRES 19 B 348 TYR PRO MET GLU SER LYS LEU THR VAL GLN GLU THR GLN SEQRES 20 B 348 LEU GLY GLY SER ALA ASN LEU THR CYS ARG ALA PHE PHE SEQRES 21 B 348 GLY TYR SER GLY ASP VAL SER PRO LEU ILE TYR TRP MET SEQRES 22 B 348 LYS GLY GLU LYS PHE ILE GLU ASP LEU ASP GLU ASN ARG SEQRES 23 B 348 VAL TRP GLU SER ASP ILE ARG ILE LEU LYS GLU HIS LEU SEQRES 24 B 348 GLY GLU GLN GLU VAL SER ILE SER LEU ILE VAL ASP SER SEQRES 25 B 348 VAL GLU GLU GLY ASP LEU GLY ASN TYR SER CYS TYR VAL SEQRES 26 B 348 GLU ASN GLY ASN GLY ARG ARG HIS ALA SER VAL LEU LEU SEQRES 27 B 348 HIS LYS ARG LYS HIS HIS HIS HIS HIS HIS SEQRES 1 A 305 GLU THR PRO PRO ARG PHE THR ARG THR PRO VAL ASP GLN SEQRES 2 A 305 THR GLY VAL SER GLY GLY VAL ALA SER PHE ILE CYS GLN SEQRES 3 A 305 ALA THR GLY ASP PRO ARG PRO LYS ILE VAL TRP ASN LYS SEQRES 4 A 305 LYS GLY LYS LYS VAL SER ASN GLN ARG PHE GLU VAL ILE SEQRES 5 A 305 GLU PHE ASP ASP GLY SER GLY SER VAL LEU ARG ILE GLN SEQRES 6 A 305 PRO LEU ARG THR PRO ARG ASP GLU ALA ILE TYR GLU CYS SEQRES 7 A 305 VAL ALA SER ASN ASN VAL GLY GLU ILE SER VAL SER THR SEQRES 8 A 305 ARG LEU THR VAL LEU ARG GLU ASP GLN ILE PRO ARG GLY SEQRES 9 A 305 PHE PRO THR ILE ASP MET GLY PRO GLN LEU LYS VAL VAL SEQRES 10 A 305 GLU ARG THR ARG THR ALA THR MET LEU CYS ALA ALA SER SEQRES 11 A 305 GLY ASN PRO ASP PRO GLU ILE THR TRP PHE LYS ASP PHE SEQRES 12 A 305 LEU PRO VAL ASP THR SER ASN ASN ASN GLY ARG ILE LYS SEQRES 13 A 305 GLN LEU ARG SER GLU SER ILE GLY GLY THR PRO ILE ARG SEQRES 14 A 305 GLY ALA LEU GLN ILE GLU GLN SER GLU GLU SER ASP GLN SEQRES 15 A 305 GLY LYS TYR GLU CYS VAL ALA THR ASN SER ALA GLY THR SEQRES 16 A 305 ARG TYR SER ALA PRO ALA ASN LEU TYR VAL ARG GLU LEU SEQRES 17 A 305 ARG GLU VAL ARG ARG VAL PRO PRO ARG PHE SER ILE PRO SEQRES 18 A 305 PRO THR ASN HIS GLU ILE MET PRO GLY GLY SER VAL ASN SEQRES 19 A 305 ILE THR CYS VAL ALA VAL GLY SER PRO MET PRO TYR VAL SEQRES 20 A 305 LYS TRP MET LEU GLY ALA GLU ASP LEU THR PRO GLU ASP SEQRES 21 A 305 ASP MET PRO ILE GLY ARG ASN VAL LEU GLU LEU ASN ASP SEQRES 22 A 305 VAL ARG GLN SER ALA ASN TYR THR CYS VAL ALA MET SER SEQRES 23 A 305 THR LEU GLY VAL ILE GLU ALA ILE ALA GLN ILE THR LYS SEQRES 24 A 305 HIS HIS HIS HIS HIS HIS HET NAG B 400 14 HET NAG B 401 14 HET FUL B 402 10 HET NAG B 403 14 HET NAG B 404 14 HET NAG B 405 14 HET NAG B 406 14 HET BMA B 407 11 HET FUL B 408 10 HET NAG B 409 14 HET NAG B 410 14 HETNAM NAG N-ACETYL-D-GLUCOSAMINE HETNAM FUL BETA-L-FUCOSE HETNAM BMA BETA-D-MANNOSE HETSYN FUL 6-DEOXY-BETA-L-GALACTOSE FORMUL 3 NAG 8(C8 H15 N O6) FORMUL 3 FUL 2(C6 H12 O5) FORMUL 5 BMA C6 H12 O6 FORMUL 8 HOH *77(H2 O) HELIX 1 AA1 ALA B 54 GLY B 58 5 5 HELIX 2 AA2 ASN B 63 ALA B 70 1 8 HELIX 3 AA3 LEU B 109 SER B 113 5 5 HELIX 4 AA4 LYS B 207 ILE B 211 5 5 HELIX 5 AA5 GLU B 291 LEU B 293 5 3 HELIX 6 AA6 ARG A 124 ILE A 128 5 5 HELIX 7 AA7 GLU A 205 GLN A 209 5 5 SHEET 1 AA1 5 THR B 32 VAL B 36 0 SHEET 2 AA1 5 CYS B 126 SER B 130 1 O LYS B 128 N TRP B 34 SHEET 3 AA1 5 GLY B 114 ARG B 121 -1 N CYS B 118 O VAL B 129 SHEET 4 AA1 5 SER B 132 GLY B 136 -1 O LEU B 133 N GLY B 114 SHEET 5 AA1 5 TYR B 41 LEU B 44 1 N TYR B 41 O THR B 134 SHEET 1 AA2 5 THR B 32 VAL B 36 0 SHEET 2 AA2 5 CYS B 126 SER B 130 1 O LYS B 128 N TRP B 34 SHEET 3 AA2 5 GLY B 114 ARG B 121 -1 N CYS B 118 O VAL B 129 SHEET 4 AA2 5 SER B 73 SER B 79 -1 N SER B 79 O LEU B 115 SHEET 5 AA2 5 GLU B 87 PRO B 88 -1 O GLU B 87 N LYS B 78 SHEET 1 AA3 3 VAL B 49 LYS B 52 0 SHEET 2 AA3 3 SER B 102 PHE B 105 -1 O ILE B 103 N ILE B 51 SHEET 3 AA3 3 MET B 96 SER B 97 -1 N SER B 97 O TRP B 104 SHEET 1 AA4 4 TYR B 150 GLU B 155 0 SHEET 2 AA4 4 PHE B 223 THR B 234 1 O GLU B 230 N TYR B 150 SHEET 3 AA4 4 GLY B 212 TYR B 220 -1 N TYR B 220 O PHE B 223 SHEET 4 AA4 4 LEU B 180 LYS B 183 -1 N TYR B 182 O THR B 215 SHEET 1 AA5 3 LYS B 160 SER B 163 0 SHEET 2 AA5 3 THR B 200 ILE B 203 -1 O LEU B 201 N ILE B 162 SHEET 3 AA5 3 VAL B 195 PHE B 196 -1 N VAL B 195 O LEU B 202 SHEET 1 AA6 4 LYS B 243 TYR B 246 0 SHEET 2 AA6 4 ALA B 263 PHE B 271 -1 O ARG B 268 N TYR B 246 SHEET 3 AA6 4 GLN B 313 VAL B 321 -1 O GLN B 313 N PHE B 271 SHEET 4 AA6 4 VAL B 298 GLU B 300 -1 N TRP B 299 O ILE B 320 SHEET 1 AA7 4 LYS B 243 TYR B 246 0 SHEET 2 AA7 4 ALA B 263 PHE B 271 -1 O ARG B 268 N TYR B 246 SHEET 3 AA7 4 GLN B 313 VAL B 321 -1 O GLN B 313 N PHE B 271 SHEET 4 AA7 4 ARG B 304 GLU B 308 -1 N ARG B 304 O SER B 316 SHEET 1 AA8 5 THR B 253 THR B 257 0 SHEET 2 AA8 5 GLY B 341 LYS B 351 1 O LEU B 348 N GLN B 255 SHEET 3 AA8 5 GLY B 330 ASN B 338 -1 N TYR B 332 O VAL B 347 SHEET 4 AA8 5 LEU B 280 LYS B 285 -1 N TYR B 282 O TYR B 335 SHEET 5 AA8 5 LYS B 288 PHE B 289 -1 O LYS B 288 N LYS B 285 SHEET 1 AA9 4 THR A 29 ARG A 35 0 SHEET 2 AA9 4 ALA A 48 ASP A 57 -1 O GLN A 53 N ARG A 35 SHEET 3 AA9 4 GLY A 86 ILE A 91 -1 O LEU A 89 N PHE A 50 SHEET 4 AA9 4 PHE A 76 GLU A 80 -1 N GLU A 77 O ARG A 90 SHEET 1 AB1 5 GLN A 40 VAL A 43 0 SHEET 2 AB1 5 GLY A 112 LEU A 123 1 O THR A 121 N GLY A 42 SHEET 3 AB1 5 ALA A 101 ASN A 109 -1 N TYR A 103 O THR A 118 SHEET 4 AB1 5 LYS A 61 LYS A 66 -1 N ASN A 65 O GLU A 104 SHEET 5 AB1 5 LYS A 69 LYS A 70 -1 O LYS A 69 N LYS A 66 SHEET 1 AB2 4 THR A 134 MET A 137 0 SHEET 2 AB2 4 ALA A 150 SER A 157 -1 O ALA A 155 N MET A 137 SHEET 3 AB2 4 ILE A 195 ILE A 201 -1 O GLY A 197 N CYS A 154 SHEET 4 AB2 4 ILE A 182 ARG A 186 -1 N LYS A 183 O GLN A 200 SHEET 1 AB3 5 LYS A 142 GLU A 145 0 SHEET 2 AB3 5 ALA A 228 ARG A 233 1 O TYR A 231 N LYS A 142 SHEET 3 AB3 5 GLY A 210 ASN A 218 -1 N TYR A 212 O ALA A 228 SHEET 4 AB3 5 GLU A 163 LYS A 168 -1 N GLU A 163 O THR A 217 SHEET 5 AB3 5 LEU A 171 PRO A 172 -1 O LEU A 171 N LYS A 168 SHEET 1 AB4 4 LYS A 142 GLU A 145 0 SHEET 2 AB4 4 ALA A 228 ARG A 233 1 O TYR A 231 N LYS A 142 SHEET 3 AB4 4 GLY A 210 ASN A 218 -1 N TYR A 212 O ALA A 228 SHEET 4 AB4 4 GLY A 221 TYR A 224 -1 O ARG A 223 N ALA A 216 SSBOND 1 CYS B 31 CYS B 126 1555 1555 2.03 SSBOND 2 CYS B 53 CYS B 118 1555 1555 2.03 SSBOND 3 CYS B 143 CYS B 185 1555 1555 2.03 SSBOND 4 CYS B 164 CYS B 216 1555 1555 2.03 SSBOND 5 CYS B 267 CYS B 334 1555 1555 2.03 SSBOND 6 CYS A 52 CYS A 105 1555 1555 2.03 SSBOND 7 CYS A 154 CYS A 214 1555 1555 2.03 LINK ND2 ASN B 63 C1 NAG B 410 1555 1555 1.45 LINK ND2 ASN B 122 C1 NAG B 400 1555 1555 1.47 LINK ND2 ASN B 138 C1 NAG B 409 1555 1555 1.43 LINK ND2 ASN B 213 C1 NAG B 403 1555 1555 1.44 LINK ND2 ASN B 264 C1 NAG B 405 1555 1555 1.44 LINK O4 NAG B 400 C1 NAG B 401 1555 1555 1.44 LINK O6 NAG B 400 C1 FUL B 402 1555 1555 1.44 LINK O4 NAG B 403 C1 NAG B 404 1555 1555 1.44 LINK O4 NAG B 405 C1 NAG B 406 1555 1555 1.44 LINK O6 NAG B 405 C1 FUL B 408 1555 1555 1.43 LINK O4 NAG B 406 C1 BMA B 407 1555 1555 1.46 CISPEP 1 PRO B 82 GLY B 83 0 -2.03 CISPEP 2 ARG B 106 PRO B 107 0 -1.13 CISPEP 3 ARG B 165 ASP B 166 0 -12.45 CISPEP 4 GLU B 176 PRO B 177 0 -2.45 CISPEP 5 GLY B 221 GLY B 222 0 -0.89 CISPEP 6 TYR B 246 PRO B 247 0 -14.04 CISPEP 7 LEU B 310 GLY B 311 0 -15.06 CISPEP 8 GLU B 326 GLY B 327 0 16.96 CISPEP 9 ASP A 57 PRO A 58 0 2.20 CISPEP 10 GLN A 92 PRO A 93 0 -10.97 CISPEP 11 THR A 96 PRO A 97 0 4.32 CISPEP 12 ASN A 159 PRO A 160 0 3.68 SITE 1 AC1 3 ASN B 63 SER B 65 HOH B 509 SITE 1 AC2 8 ILE B 60 THR B 62 LEU B 72 ASN B 122 SITE 2 AC2 8 SER B 123 THR B 124 HOH B 522 HOH B 535 SITE 1 AC3 4 ASN B 138 GLY B 141 LEU B 142 CYS B 143 SITE 1 AC4 7 TYR B 144 SER B 146 LYS B 149 GLU B 184 SITE 2 AC4 7 GLY B 212 ASN B 213 HOH B 518 SITE 1 AC5 9 ARG A 146 GLU A 234 ASN B 264 THR B 266 SITE 2 AC5 9 SER B 301 ARG B 304 LEU B 306 SER B 316 SITE 3 AC5 9 SER B 318 CRYST1 162.975 81.175 91.480 90.00 91.27 90.00 C 1 2 1 4 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 0.006136 0.000000 0.000136 0.00000 SCALE2 0.000000 0.012319 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010934 0.00000