HEADER IMMUNE SYSTEM 15-MAY-12 4F7E TITLE CRYSTAL STRUCTURE OF BOVINE CD1D WITH BOUND C16:0-ALPHA-GALACTOSYL TITLE 2 CERAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CD1D ANTIGEN, D POLYPEPTIDE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 129-405; COMPND 5 SYNONYM: T CELL SURFACE GLYCOPROTEIN CD1D ANTIGEN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 21-118; COMPND 11 SYNONYM: LACTOLLIN; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 GENE: CD1D; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: SF9; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PBACPHP10; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 14 ORGANISM_COMMON: BOVINE; SOURCE 15 ORGANISM_TAXID: 9913; SOURCE 16 GENE: B2M; SOURCE 17 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 18 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: SF9; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PBACPHP10 KEYWDS PROTEIN-GLYCOLIPID COMPLEX, MHC-FOLD, IG-FOLD, ANTIGEN PRESENTATION, KEYWDS 2 TCR, MEMBRANE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.WANG,D.M.ZAJONC REVDAT 3 13-SEP-23 4F7E 1 HETSYN REVDAT 2 29-JUL-20 4F7E 1 COMPND REMARK SEQADV HETNAM REVDAT 2 2 1 LINK SITE ATOM REVDAT 1 14-NOV-12 4F7E 0 JRNL AUTH J.WANG,J.GUILLAUME,N.PAUWELS,S.VAN CALENBERGH,I.VAN RHIJN, JRNL AUTH 2 D.M.ZAJONC JRNL TITL CRYSTAL STRUCTURES OF BOVINE CD1D REVEAL ALTERED JRNL TITL 2 αGALCER PRESENTATION AND A RESTRICTED A' POCKET UNABLE JRNL TITL 3 TO BIND LONG-CHAIN GLYCOLIPIDS. JRNL REF PLOS ONE V. 7 47989 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 23110152 JRNL DOI 10.1371/JOURNAL.PONE.0047989 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 20132 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) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 804 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1277 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.4010 REMARK 3 BIN FREE R VALUE SET COUNT : 55 REMARK 3 BIN FREE R VALUE : 0.3900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2947 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 97 REMARK 3 SOLVENT ATOMS : 26 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.07000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : -0.03000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.358 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.270 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.218 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.739 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3140 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4282 ; 1.400 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 367 ; 6.161 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 144 ;35.365 ;23.611 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 466 ;16.911 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;21.572 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 462 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2401 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4F7E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072548. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SIDE SCATTERING BENT CUBE-ROOT I REMARK 200 -BEAM SINGLE CRYSTAL, ASYMMETRIC REMARK 200 CUT 4.965 DEGREES REMARK 200 OPTICS : RH COATED FLAT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20240 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.19900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.900 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: PDB ENTRY 3L9R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG4000, 200 MM POTASSIUM SULFATE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 27.89250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.45850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.23950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.45850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.89250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.23950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 SER A 1 REMARK 465 PRO A 2 REMARK 465 ALA A 3 REMARK 465 PRO A 4 REMARK 465 GLN A 5 REMARK 465 THR A 6 REMARK 465 PRO A 7 REMARK 465 HIS A 279 REMARK 465 HIS A 280 REMARK 465 HIS A 281 REMARK 465 HIS A 282 REMARK 465 HIS A 283 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 86 CG CD OE1 OE2 REMARK 470 LYS A 87 CG CD CE NZ REMARK 470 ARG A 107 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 109 CG1 CG2 CD1 REMARK 470 ASP A 136 CG OD1 OD2 REMARK 470 GLN A 142 CG CD OE1 NE2 REMARK 470 LYS A 146 CG CD CE NZ REMARK 470 ARG A 171 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 224 CG CD OE1 OE2 REMARK 470 GLN A 225 CG CD OE1 NE2 REMARK 470 ASP A 270 CG OD1 OD2 REMARK 470 LYS B 19 CG CD CE NZ REMARK 470 GLU B 44 CG CD OE1 OE2 REMARK 470 LYS B 45 CG CD CE NZ REMARK 470 LYS B 57 CG CD CE NZ REMARK 470 LYS B 74 CG CD CE NZ REMARK 470 LYS B 82 CG CD CE NZ REMARK 470 GLU B 87 CG CD OE1 OE2 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 ASN A 20 -129.43 -114.62 REMARK 500 LEU A 88 11.77 -150.04 REMARK 500 GLU A 91 -179.93 -63.38 REMARK 500 PRO A 106 171.01 -54.16 REMARK 500 ARG A 107 -100.83 63.95 REMARK 500 VAL A 123 -40.64 -138.07 REMARK 500 MET A 129 -6.09 -140.28 REMARK 500 PRO A 138 150.59 -43.22 REMARK 500 HIS B 31 125.33 176.70 REMARK 500 TRP B 59 -0.62 79.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Z5L RELATED DB: PDB REMARK 900 STRUCTURE OF A HIGHLY POTENT SHORT-CHAIN GALACTOSYL CERAMIDE REMARK 900 AGONIST BOUND TO CD1D REMARK 900 RELATED ID: 1ZT4 RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF HUMAN CD1D WITH AND WITHOUT ALPHA- REMARK 900 GALACTOSYLCERAMIDE REMARK 900 RELATED ID: 4F7C RELATED DB: PDB DBREF 4F7E A 1 277 UNP A1L565 A1L565_BOVIN 129 405 DBREF 4F7E B 1 98 UNP P01888 B2MG_BOVIN 21 118 SEQADV 4F7E HIS A 278 UNP A1L565 EXPRESSION TAG SEQADV 4F7E HIS A 279 UNP A1L565 EXPRESSION TAG SEQADV 4F7E HIS A 280 UNP A1L565 EXPRESSION TAG SEQADV 4F7E HIS A 281 UNP A1L565 EXPRESSION TAG SEQADV 4F7E HIS A 282 UNP A1L565 EXPRESSION TAG SEQADV 4F7E HIS A 283 UNP A1L565 EXPRESSION TAG SEQRES 1 A 283 SER PRO ALA PRO GLN THR PRO PHE SER PHE GLN GLY LEU SEQRES 2 A 283 GLN ILE SER SER PHE ALA ASN ARG SER TRP THR ARG THR SEQRES 3 A 283 ASP GLY LEU ALA TRP LEU GLY GLU LEU GLN PRO TYR THR SEQRES 4 A 283 TRP ARG ASN GLU SER ASP THR ILE ARG PHE LEU LYS PRO SEQRES 5 A 283 TRP SER ARG GLY THR PHE SER ASP GLN GLN TRP GLU GLN SEQRES 6 A 283 LEU GLN HIS THR LEU LEU VAL TYR ARG SER SER PHE THR SEQRES 7 A 283 ARG ASP ILE TRP GLU PHE VAL GLU LYS LEU HIS VAL GLU SEQRES 8 A 283 TYR PRO LEU GLU ILE GLN ILE ALA THR GLY CYS GLU LEU SEQRES 9 A 283 LEU PRO ARG ASN ILE SER GLU SER PHE LEU ARG ALA ALA SEQRES 10 A 283 PHE GLN GLY ARG ASP VAL LEU SER PHE GLN GLY MET SER SEQRES 11 A 283 TRP VAL SER ALA PRO ASP ALA PRO PRO PHE ILE GLN GLU SEQRES 12 A 283 VAL ILE LYS VAL LEU ASN GLN ASN GLN GLY THR LYS GLU SEQRES 13 A 283 THR VAL HIS TRP LEU LEU HIS ASP ILE TRP PRO GLU LEU SEQRES 14 A 283 VAL ARG GLY VAL LEU GLN THR GLY LYS SER GLU LEU GLU SEQRES 15 A 283 LYS GLN VAL LYS PRO GLU ALA TRP LEU SER SER GLY PRO SEQRES 16 A 283 SER PRO GLY PRO GLY ARG LEU LEU LEU VAL CYS HIS VAL SEQRES 17 A 283 SER GLY PHE TYR PRO LYS PRO VAL ARG VAL MET TRP MET SEQRES 18 A 283 ARG GLY GLU GLN GLU GLU PRO GLY THR ARG GLN GLY ASP SEQRES 19 A 283 VAL MET PRO ASN ALA ASP SER THR TRP TYR LEU ARG VAL SEQRES 20 A 283 THR LEU ASP VAL ALA ALA GLY GLU VAL ALA GLY LEU SER SEQRES 21 A 283 CYS GLN VAL LYS HIS SER SER LEU GLY ASP GLN ASP ILE SEQRES 22 A 283 ILE LEU TYR TRP HIS HIS HIS HIS HIS HIS SEQRES 1 B 98 ILE GLN ARG PRO PRO LYS ILE GLN VAL TYR SER ARG HIS SEQRES 2 B 98 PRO PRO GLU ASP GLY LYS PRO ASN TYR LEU ASN CYS TYR SEQRES 3 B 98 VAL TYR GLY PHE HIS PRO PRO GLN ILE GLU ILE ASP LEU SEQRES 4 B 98 LEU LYS ASN GLY GLU LYS ILE LYS SER GLU GLN SER ASP SEQRES 5 B 98 LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU LEU SER SEQRES 6 B 98 HIS ALA GLU PHE THR PRO ASN SER LYS ASP GLN TYR SER SEQRES 7 B 98 CYS ARG VAL LYS HIS VAL THR LEU GLU GLN PRO ARG ILE SEQRES 8 B 98 VAL LYS TRP ASP ARG ASP LEU MODRES 4F7E ASN A 20 ASN GLYCOSYLATION SITE MODRES 4F7E ASN A 42 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET 0SH A 301 50 HET NAG A 304 14 HET SO4 B 101 5 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM 0SH N-[(2S,3S,4R)-1-(ALPHA-D-GALACTOPYRANOSYLOXY)-3,4- HETNAM 2 0SH DIHYDROXYOCTADECAN-2-YL]HEXADECANAMIDE HETNAM SO4 SULFATE 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 FORMUL 3 NAG 3(C8 H15 N O6) FORMUL 4 0SH C40 H79 N O9 FORMUL 6 SO4 O4 S 2- FORMUL 7 HOH *26(H2 O) HELIX 1 1 SER A 59 LYS A 87 1 29 HELIX 2 2 PHE A 140 ASN A 149 1 10 HELIX 3 3 ASN A 151 ASP A 164 1 14 HELIX 4 4 ASP A 164 GLY A 177 1 14 HELIX 5 5 GLY A 177 GLU A 182 1 6 HELIX 6 6 GLY A 254 ALA A 257 5 4 SHEET 1 A 8 ARG A 48 PHE A 49 0 SHEET 2 A 8 LEU A 35 TRP A 40 -1 N THR A 39 O ARG A 48 SHEET 3 A 8 THR A 24 LEU A 32 -1 N GLY A 28 O TRP A 40 SHEET 4 A 8 PHE A 10 PHE A 18 -1 N ILE A 15 O ASP A 27 SHEET 5 A 8 LEU A 94 LEU A 104 -1 O THR A 100 N GLY A 12 SHEET 6 A 8 SER A 110 PHE A 118 -1 O ALA A 117 N GLN A 97 SHEET 7 A 8 ARG A 121 GLN A 127 -1 O LEU A 124 N ALA A 116 SHEET 8 A 8 SER A 130 SER A 133 -1 O SER A 130 N GLN A 127 SHEET 1 B 4 GLU A 188 SER A 193 0 SHEET 2 B 4 ARG A 201 PHE A 211 -1 O HIS A 207 N TRP A 190 SHEET 3 B 4 TRP A 243 ALA A 252 -1 O TRP A 243 N GLY A 210 SHEET 4 B 4 ARG A 231 GLN A 232 -1 N ARG A 231 O THR A 248 SHEET 1 C 4 GLU A 188 SER A 193 0 SHEET 2 C 4 ARG A 201 PHE A 211 -1 O HIS A 207 N TRP A 190 SHEET 3 C 4 TRP A 243 ALA A 252 -1 O TRP A 243 N GLY A 210 SHEET 4 C 4 MET A 236 PRO A 237 -1 N MET A 236 O TYR A 244 SHEET 1 D 4 GLN A 225 GLU A 226 0 SHEET 2 D 4 VAL A 216 ARG A 222 -1 N ARG A 222 O GLN A 225 SHEET 3 D 4 LEU A 259 HIS A 265 -1 O LYS A 264 N ARG A 217 SHEET 4 D 4 ILE A 273 TYR A 276 -1 O ILE A 273 N VAL A 263 SHEET 1 E 4 LYS B 6 SER B 11 0 SHEET 2 E 4 ASN B 21 PHE B 30 -1 O TYR B 26 N GLN B 8 SHEET 3 E 4 PHE B 61 PHE B 69 -1 O ALA B 67 N LEU B 23 SHEET 4 E 4 GLU B 49 GLN B 50 -1 N GLU B 49 O HIS B 66 SHEET 1 F 4 LYS B 6 SER B 11 0 SHEET 2 F 4 ASN B 21 PHE B 30 -1 O TYR B 26 N GLN B 8 SHEET 3 F 4 PHE B 61 PHE B 69 -1 O ALA B 67 N LEU B 23 SHEET 4 F 4 SER B 54 PHE B 55 -1 N SER B 54 O TYR B 62 SHEET 1 G 4 GLU B 44 LYS B 45 0 SHEET 2 G 4 GLU B 36 LYS B 41 -1 N LYS B 41 O GLU B 44 SHEET 3 G 4 TYR B 77 LYS B 82 -1 O ARG B 80 N ASP B 38 SHEET 4 G 4 ARG B 90 LYS B 93 -1 O ARG B 90 N VAL B 81 SSBOND 1 CYS A 206 CYS A 261 1555 1555 2.05 SSBOND 2 CYS B 25 CYS B 79 1555 1555 2.06 LINK ND2 ASN A 20 C1 NAG C 1 1555 1555 1.45 LINK ND2 ASN A 42 C1 NAG A 304 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 CISPEP 1 TYR A 92 PRO A 93 0 -10.36 CISPEP 2 TYR A 212 PRO A 213 0 -5.26 CISPEP 3 HIS B 31 PRO B 32 0 5.50 CRYST1 55.785 74.479 122.917 90.00 90.00 90.00 P 21 21 21 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 0.017926 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013427 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008136 0.00000