HEADER IMMUNE SYSTEM 10-DEC-19 6V7Y TITLE HUMAN CD1D PRESENTING ALPHA-GALACTOSYLCERAMIDE IN COMPLEX WITH VHH TITLE 2 NANOBODY 1D5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTIGEN-PRESENTING GLYCOPROTEIN CD1D; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: R3G1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: NANOBODY VHH ID5; COMPND 12 CHAIN: F; COMPND 13 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: CD1D; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HI5; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PFASTBAC; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 GENE: B2M, CDABP0092, HDCMA22P; SOURCE 17 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 18 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 20 EXPRESSION_SYSTEM_CELL_LINE: HI5; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: BACMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PFASTBAC; SOURCE 23 MOL_ID: 3; SOURCE 24 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 25 ORGANISM_COMMON: LLAMA; SOURCE 26 ORGANISM_TAXID: 9844; SOURCE 27 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 28 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 29 EXPRESSION_SYSTEM_STRAIN: TG1; SOURCE 30 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 31 EXPRESSION_SYSTEM_PLASMID: PMEK219 KEYWDS LIPID, NANOBODY, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.SHAHINE,J.ROSSJOHN REVDAT 2 11-OCT-23 6V7Y 1 REMARK REVDAT 1 16-SEP-20 6V7Y 0 JRNL AUTH A.SHAHINE,J.ROSSJOHN JRNL TITL A SINGLE-DOMAIN BISPECIFIC ANTIBODY TARGETING CD1D AND THE JRNL TITL 2 NKT T-CELL RECEPTOR INDUCES A POTENT ANTITUMOR RESPONSE. JRNL REF NAT CANCER 2020 JRNL REFN ESSN 2662-1347 JRNL DOI 10.1038/S43018-020-00111-6 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 32831 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.220 REMARK 3 FREE R VALUE TEST SET COUNT : 1713 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 50 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.42 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.39 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 657 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2778 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 631 REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE : 0.3657 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.96 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 26 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3888 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 185 REMARK 3 SOLVENT ATOMS : 194 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.45220 REMARK 3 B22 (A**2) : -6.45220 REMARK 3 B33 (A**2) : 12.90430 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.360 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.264 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.218 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.252 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.215 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.899 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 4270 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 5831 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1934 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 711 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 4270 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 559 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 4844 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.14 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.13 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 3.27 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|1 - 180} REMARK 3 ORIGIN FOR THE GROUP (A): -48.7944 35.6051 26.5775 REMARK 3 T TENSOR REMARK 3 T11: 0.0505 T22: -0.0271 REMARK 3 T33: -0.2405 T12: 0.0567 REMARK 3 T13: 0.0130 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 2.5321 L22: 1.9737 REMARK 3 L33: 2.8772 L12: -0.1316 REMARK 3 L13: -0.0054 L23: 0.0564 REMARK 3 S TENSOR REMARK 3 S11: -0.1775 S12: 0.2547 S13: -0.0058 REMARK 3 S21: -0.0264 S22: 0.0659 S23: 0.0524 REMARK 3 S31: 0.0941 S32: 0.1669 S33: 0.1116 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|181 - 274} REMARK 3 ORIGIN FOR THE GROUP (A): -50.7465 34.7259 62.4897 REMARK 3 T TENSOR REMARK 3 T11: 0.1864 T22: 0.0407 REMARK 3 T33: -0.1745 T12: 0.1451 REMARK 3 T13: 0.0745 T23: 0.0968 REMARK 3 L TENSOR REMARK 3 L11: 1.4408 L22: 0.0751 REMARK 3 L33: 4.3086 L12: 0.3044 REMARK 3 L13: -0.6932 L23: -0.9414 REMARK 3 S TENSOR REMARK 3 S11: -0.0085 S12: -0.1521 S13: -0.0845 REMARK 3 S21: 0.1470 S22: 0.0348 S23: 0.1619 REMARK 3 S31: 0.0618 S32: -0.0509 S33: -0.0263 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: {B|0 - 99} REMARK 3 ORIGIN FOR THE GROUP (A): -47.4164 51.9198 49.5043 REMARK 3 T TENSOR REMARK 3 T11: 0.0645 T22: 0.0080 REMARK 3 T33: -0.1441 T12: 0.0437 REMARK 3 T13: -0.0694 T23: -0.0344 REMARK 3 L TENSOR REMARK 3 L11: 1.5305 L22: 3.1659 REMARK 3 L33: 3.9778 L12: 0.7627 REMARK 3 L13: 0.2658 L23: 1.8725 REMARK 3 S TENSOR REMARK 3 S11: -0.0657 S12: -0.1363 S13: 0.2317 REMARK 3 S21: 0.2160 S22: 0.0266 S23: 0.0198 REMARK 3 S31: -0.1612 S32: 0.0979 S33: 0.0391 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: {F|2 - 127} REMARK 3 ORIGIN FOR THE GROUP (A): -34.6487 25.0619 0.2648 REMARK 3 T TENSOR REMARK 3 T11: 0.2628 T22: 0.1574 REMARK 3 T33: -0.3040 T12: -0.0344 REMARK 3 T13: 0.1674 T23: -0.0304 REMARK 3 L TENSOR REMARK 3 L11: 2.8016 L22: -0.5896 REMARK 3 L33: 6.8843 L12: -1.6796 REMARK 3 L13: -2.4409 L23: 1.4873 REMARK 3 S TENSOR REMARK 3 S11: -0.0315 S12: 0.0598 S13: -0.0969 REMARK 3 S21: -0.1120 S22: 0.1201 S23: -0.1794 REMARK 3 S31: -0.1664 S32: 0.0608 S33: -0.0886 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6V7Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1000245858. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95372 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35426 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.340 REMARK 200 RESOLUTION RANGE LOW (A) : 63.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: 2PO6, 3P0G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULPHATE, 0.1M TRIS-HCL PH REMARK 280 7.0, 0.2M LITHIUM SULPHATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 87.02567 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 174.05133 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 174.05133 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 87.02567 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -108.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, F, 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 PRO A 194 REMARK 465 GLY A 195 REMARK 465 GLY A 220 REMARK 465 GLU A 252 REMARK 465 GLY A 275 REMARK 465 SER A 276 REMARK 465 LEU A 277 REMARK 465 VAL A 278 REMARK 465 PRO A 279 REMARK 465 ARG A 280 REMARK 465 GLY A 281 REMARK 465 SER A 282 REMARK 465 GLY A 283 REMARK 465 SER A 284 REMARK 465 ARG A 285 REMARK 465 ILE A 286 REMARK 465 ALA A 287 REMARK 465 ARG A 288 REMARK 465 LEU A 289 REMARK 465 GLU A 290 REMARK 465 GLU A 291 REMARK 465 LYS A 292 REMARK 465 VAL A 293 REMARK 465 LYS A 294 REMARK 465 THR A 295 REMARK 465 LEU A 296 REMARK 465 LYS A 297 REMARK 465 ALA A 298 REMARK 465 GLN A 299 REMARK 465 ASN A 300 REMARK 465 SER A 301 REMARK 465 GLU A 302 REMARK 465 LEU A 303 REMARK 465 ALA A 304 REMARK 465 SER A 305 REMARK 465 THR A 306 REMARK 465 ALA A 307 REMARK 465 ASN A 308 REMARK 465 MET A 309 REMARK 465 LEU A 310 REMARK 465 ARG A 311 REMARK 465 GLU A 312 REMARK 465 GLN A 313 REMARK 465 VAL A 314 REMARK 465 ALA A 315 REMARK 465 GLN A 316 REMARK 465 LEU A 317 REMARK 465 LYS A 318 REMARK 465 GLN A 319 REMARK 465 LYS A 320 REMARK 465 VAL A 321 REMARK 465 MET A 322 REMARK 465 ASN A 323 REMARK 465 HIS A 324 REMARK 465 GLY A 325 REMARK 465 SER A 326 REMARK 465 GLY A 327 REMARK 465 LEU A 328 REMARK 465 ASN A 329 REMARK 465 ASP A 330 REMARK 465 ILE A 331 REMARK 465 PHE A 332 REMARK 465 GLU A 333 REMARK 465 ALA A 334 REMARK 465 GLN A 335 REMARK 465 LYS A 336 REMARK 465 ILE A 337 REMARK 465 GLU A 338 REMARK 465 TRP A 339 REMARK 465 HIS A 340 REMARK 465 GLU A 341 REMARK 465 HIS A 342 REMARK 465 HIS A 343 REMARK 465 HIS A 344 REMARK 465 HIS A 345 REMARK 465 HIS A 346 REMARK 465 HIS A 347 REMARK 465 GLU F 1 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 80 CD OE1 OE2 REMARK 470 LYS A 83 CD CE NZ REMARK 470 ARG A 86 NE CZ NH1 NH2 REMARK 470 LYS A 118 CD CE NZ REMARK 470 GLU A 133 CG CD OE1 OE2 REMARK 470 LEU A 136 CG CD1 CD2 REMARK 470 LYS A 149 CG CD CE NZ REMARK 470 LYS A 179 CG CD CE NZ REMARK 470 LYS A 180 CG CD CE NZ REMARK 470 LYS A 185 CD CE NZ REMARK 470 LYS A 216 CD CE NZ REMARK 470 GLU A 221 CG CD OE1 OE2 REMARK 470 GLU A 223 CG CD OE1 OE2 REMARK 470 LEU A 256 CG CD1 CD2 REMARK 470 ARG A 259 CZ NH1 NH2 REMARK 470 LYS A 261 CE NZ REMARK 470 ILE B 1 CG1 CG2 CD1 REMARK 470 LYS B 19 CE NZ REMARK 470 GLU B 36 OE1 OE2 REMARK 470 LYS B 48 CG CD CE NZ REMARK 470 LYS B 58 CD CE NZ REMARK 470 LYS B 75 CG CD CE NZ REMARK 470 LYS B 94 CE NZ REMARK 470 ARG B 97 NE CZ NH1 NH2 REMARK 470 LYS F 43 CD CE NZ REMARK 470 ASP F 55 CG OD1 OD2 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 TRP A 20 CZ2 CH2 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 OG1 THR A 151 O3 AGH A 403 1.99 REMARK 500 OD1 ASP A 40 O HOH A 501 2.00 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 ARG A 86 39.52 70.71 REMARK 500 ALA A 134 127.57 -15.01 REMARK 500 GLU A 223 101.64 -169.49 REMARK 500 GLN A 225 -156.39 -120.29 REMARK 500 TRP B 60 -8.76 74.15 REMARK 500 PRO B 90 107.75 -56.72 REMARK 500 SER F 28 56.53 39.64 REMARK 500 ARG F 52 -98.80 -135.52 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 609 DISTANCE = 7.36 ANGSTROMS REMARK 525 HOH B 245 DISTANCE = 6.34 ANGSTROMS DBREF 6V7Y A 2 275 UNP P15813 CD1D_HUMAN 23 296 DBREF 6V7Y A 276 347 PDB 6V7Y 6V7Y 276 347 DBREF 6V7Y B 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 6V7Y F 1 127 PDB 6V7Y 6V7Y 1 127 SEQADV 6V7Y MET A 1 UNP P15813 INITIATING METHIONINE SEQADV 6V7Y MET B 0 UNP P61769 INITIATING METHIONINE SEQRES 1 A 347 MET GLN ARG LEU PHE PRO LEU ARG CYS LEU GLN ILE SER SEQRES 2 A 347 SER PHE ALA ASN SER SER TRP THR ARG THR ASP GLY LEU SEQRES 3 A 347 ALA TRP LEU GLY GLU LEU GLN THR HIS SER TRP SER ASN SEQRES 4 A 347 ASP SER ASP THR VAL ARG SER LEU LYS PRO TRP SER GLN SEQRES 5 A 347 GLY THR PHE SER ASP GLN GLN TRP GLU THR LEU GLN HIS SEQRES 6 A 347 ILE PHE ARG VAL TYR ARG SER SER PHE THR ARG ASP VAL SEQRES 7 A 347 LYS GLU PHE ALA LYS MET LEU ARG LEU SER TYR PRO LEU SEQRES 8 A 347 GLU LEU GLN VAL SER ALA GLY CYS GLU VAL HIS PRO GLY SEQRES 9 A 347 ASN ALA SER ASN ASN PHE PHE HIS VAL ALA PHE GLN GLY SEQRES 10 A 347 LYS ASP ILE LEU SER PHE GLN GLY THR SER TRP GLU PRO SEQRES 11 A 347 THR GLN GLU ALA PRO LEU TRP VAL ASN LEU ALA ILE GLN SEQRES 12 A 347 VAL LEU ASN GLN ASP LYS TRP THR ARG GLU THR VAL GLN SEQRES 13 A 347 TRP LEU LEU ASN GLY THR CYS PRO GLN PHE VAL SER GLY SEQRES 14 A 347 LEU LEU GLU SER GLY LYS SER GLU LEU LYS LYS GLN VAL SEQRES 15 A 347 LYS PRO LYS ALA TRP LEU SER ARG GLY PRO SER PRO GLY SEQRES 16 A 347 PRO GLY ARG LEU LEU LEU VAL CYS HIS VAL SER GLY PHE SEQRES 17 A 347 TYR PRO LYS PRO VAL TRP VAL LYS TRP MET ARG GLY GLU SEQRES 18 A 347 GLN GLU GLN GLN GLY THR GLN PRO GLY ASP ILE LEU PRO SEQRES 19 A 347 ASN ALA ASP GLU THR TRP TYR LEU ARG ALA THR LEU ASP SEQRES 20 A 347 VAL VAL ALA GLY GLU ALA ALA GLY LEU SER CYS ARG VAL SEQRES 21 A 347 LYS HIS SER SER LEU GLU GLY GLN ASP ILE VAL LEU TYR SEQRES 22 A 347 TRP GLY SER LEU VAL PRO ARG GLY SER GLY SER ARG ILE SEQRES 23 A 347 ALA ARG LEU GLU GLU LYS VAL LYS THR LEU LYS ALA GLN SEQRES 24 A 347 ASN SER GLU LEU ALA SER THR ALA ASN MET LEU ARG GLU SEQRES 25 A 347 GLN VAL ALA GLN LEU LYS GLN LYS VAL MET ASN HIS GLY SEQRES 26 A 347 SER GLY LEU ASN ASP ILE PHE GLU ALA GLN LYS ILE GLU SEQRES 27 A 347 TRP HIS GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG SEQRES 2 B 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS SEQRES 3 B 100 TYR VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP SEQRES 4 B 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SEQRES 5 B 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU SEQRES 6 B 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU SEQRES 7 B 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO SEQRES 8 B 100 LYS ILE VAL LYS TRP ASP ARG ASP MET SEQRES 1 F 127 GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 F 127 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 F 127 SER SER PHE SER SER TYR THR MET GLY TRP PHE ARG GLN SEQRES 4 F 127 ALA PRO GLY LYS GLU ARG GLU ILE VAL ALA GLY ILE ARG SEQRES 5 F 127 TRP SER ASP GLU SER PRO ILE TYR ALA ASP SER VAL LYS SEQRES 6 F 127 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 F 127 LEU TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 F 127 ALA VAL TYR TYR CYS ALA ALA ARG LEU VAL PRO PRO GLY SEQRES 9 F 127 ILE PRO ILE PRO ARG THR SER GLU SER MET ARG TYR TRP SEQRES 10 F 127 GLY LYS GLY THR LEU VAL THR VAL SER SER HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET BMA D 3 11 HET NAG A 401 14 HET SO4 A 402 5 HET AGH A 403 60 HET NAG A 404 14 HET CL A 405 1 HET CL A 406 1 HET CL A 407 1 HET CL A 408 1 HET SO4 B 101 5 HET SO4 B 102 5 HET SO4 B 103 5 HET SO4 B 104 5 HET CL B 105 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM SO4 SULFATE ION HETNAM AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]- HETNAM 2 AGH 2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE HETNAM CL CHLORIDE ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 4 NAG 6(C8 H15 N O6) FORMUL 5 BMA C6 H12 O6 FORMUL 7 SO4 5(O4 S 2-) FORMUL 8 AGH C50 H99 N O9 FORMUL 10 CL 5(CL 1-) FORMUL 19 HOH *194(H2 O) HELIX 1 AA1 MET A 1 PHE A 5 5 5 HELIX 2 AA2 SER A 56 ARG A 86 1 31 HELIX 3 AA3 PRO A 135 ASN A 146 1 12 HELIX 4 AA4 ASP A 148 GLY A 161 1 14 HELIX 5 AA5 GLY A 161 GLY A 174 1 14 HELIX 6 AA6 GLY A 174 LYS A 179 1 6 HELIX 7 AA7 HIS A 262 GLU A 266 5 5 HELIX 8 AA8 SER F 28 TYR F 32 5 5 HELIX 9 AA9 LYS F 87 THR F 91 5 5 HELIX 10 AB1 THR F 110 MET F 114 5 5 SHEET 1 AA1 8 ARG A 45 SER A 46 0 SHEET 2 AA1 8 LEU A 32 TRP A 37 -1 N SER A 36 O ARG A 45 SHEET 3 AA1 8 ARG A 22 LEU A 29 -1 N LEU A 29 O LEU A 32 SHEET 4 AA1 8 LEU A 7 PHE A 15 -1 N LEU A 10 O LEU A 26 SHEET 5 AA1 8 LEU A 91 HIS A 102 -1 O ALA A 97 N CYS A 9 SHEET 6 AA1 8 ALA A 106 PHE A 115 -1 O HIS A 112 N SER A 96 SHEET 7 AA1 8 LYS A 118 GLN A 124 -1 O ILE A 120 N VAL A 113 SHEET 8 AA1 8 SER A 127 PRO A 130 -1 O SER A 127 N GLN A 124 SHEET 1 AA2 4 LYS A 185 GLY A 191 0 SHEET 2 AA2 4 ARG A 198 PHE A 208 -1 O HIS A 204 N TRP A 187 SHEET 3 AA2 4 TRP A 240 VAL A 249 -1 O LEU A 242 N VAL A 205 SHEET 4 AA2 4 GLN A 228 PRO A 229 -1 N GLN A 228 O THR A 245 SHEET 1 AA3 4 LYS A 185 GLY A 191 0 SHEET 2 AA3 4 ARG A 198 PHE A 208 -1 O HIS A 204 N TRP A 187 SHEET 3 AA3 4 TRP A 240 VAL A 249 -1 O LEU A 242 N VAL A 205 SHEET 4 AA3 4 LEU A 233 PRO A 234 -1 N LEU A 233 O TYR A 241 SHEET 1 AA4 3 TRP A 214 MET A 218 0 SHEET 2 AA4 3 SER A 257 LYS A 261 -1 O SER A 257 N MET A 218 SHEET 3 AA4 3 ILE A 270 LEU A 272 -1 O ILE A 270 N VAL A 260 SHEET 1 AA5 4 LYS B 6 SER B 11 0 SHEET 2 AA5 4 ASN B 21 PHE B 30 -1 O SER B 28 N LYS B 6 SHEET 3 AA5 4 PHE B 62 PHE B 70 -1 O PHE B 70 N ASN B 21 SHEET 4 AA5 4 GLU B 50 HIS B 51 -1 N GLU B 50 O TYR B 67 SHEET 1 AA6 4 LYS B 6 SER B 11 0 SHEET 2 AA6 4 ASN B 21 PHE B 30 -1 O SER B 28 N LYS B 6 SHEET 3 AA6 4 PHE B 62 PHE B 70 -1 O PHE B 70 N ASN B 21 SHEET 4 AA6 4 SER B 55 PHE B 56 -1 N SER B 55 O TYR B 63 SHEET 1 AA7 4 GLU B 44 ARG B 45 0 SHEET 2 AA7 4 GLU B 36 LYS B 41 -1 N LYS B 41 O GLU B 44 SHEET 3 AA7 4 TYR B 78 ASN B 83 -1 O ARG B 81 N ASP B 38 SHEET 4 AA7 4 LYS B 91 LYS B 94 -1 O LYS B 91 N VAL B 82 SHEET 1 AA8 4 LEU F 4 SER F 7 0 SHEET 2 AA8 4 LEU F 18 ALA F 24 -1 O ALA F 23 N VAL F 5 SHEET 3 AA8 4 THR F 78 MET F 83 -1 O MET F 83 N LEU F 18 SHEET 4 AA8 4 PHE F 68 ASP F 73 -1 N THR F 69 O GLN F 82 SHEET 1 AA9 6 LEU F 11 GLN F 13 0 SHEET 2 AA9 6 THR F 121 SER F 126 1 O THR F 124 N VAL F 12 SHEET 3 AA9 6 ALA F 92 ARG F 99 -1 N TYR F 94 O THR F 121 SHEET 4 AA9 6 THR F 33 GLN F 39 -1 N THR F 33 O ARG F 99 SHEET 5 AA9 6 GLU F 46 ILE F 51 -1 O GLU F 46 N ARG F 38 SHEET 6 AA9 6 ILE F 59 TYR F 60 -1 O ILE F 59 N GLY F 50 SHEET 1 AB1 4 LEU F 11 GLN F 13 0 SHEET 2 AB1 4 THR F 121 SER F 126 1 O THR F 124 N VAL F 12 SHEET 3 AB1 4 ALA F 92 ARG F 99 -1 N TYR F 94 O THR F 121 SHEET 4 AB1 4 TYR F 116 TRP F 117 -1 O TYR F 116 N ALA F 98 SSBOND 1 CYS A 99 CYS A 163 1555 1555 2.06 SSBOND 2 CYS A 203 CYS A 258 1555 1555 2.03 SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.04 SSBOND 4 CYS F 22 CYS F 96 1555 1555 2.03 LINK ND2 ASN A 17 C1 NAG D 1 1555 1555 1.43 LINK ND2 ASN A 39 C1 NAG C 1 1555 1555 1.43 LINK ND2 ASN A 105 C1 NAG A 401 1555 1555 1.44 LINK ND2 ASN A 160 C1 NAG A 404 1555 1555 1.43 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.42 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.41 LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.44 CISPEP 1 TYR A 89 PRO A 90 0 3.63 CISPEP 2 TYR A 209 PRO A 210 0 4.31 CISPEP 3 HIS B 31 PRO B 32 0 0.28 CRYST1 73.270 73.270 261.077 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 0.013648 0.007880 0.000000 0.00000 SCALE2 0.000000 0.015760 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003830 0.00000