HEADER IMMUNE SYSTEM 26-MAY-05 1ZT4 TITLE THE CRYSTAL STRUCTURE OF HUMAN CD1D WITH AND WITHOUT ALPHA- TITLE 2 GALACTOSYLCERAMIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-CELL SURFACE GLYCOPROTEIN CD1D; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: CD1D HEAVY CHAIN; COMPND 5 SYNONYM: CD1D ANTIGEN, R3G1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 9 CHAIN: B, D; COMPND 10 SYNONYM: HDCMA22P; COMPND 11 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: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HMS174; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET23D; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: B2M; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: HMS174; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET23D KEYWDS HUMAN CD1D, CD1, MHC CLASS I, EMPTY BINDING GROOVE, GLYCOLIPID, KEYWDS 2 ALPHA-GALACTOSYLCERAMIDE, ALPHA-GALCER, STRUCTURAL PROTEOMICS IN KEYWDS 3 EUROPE, SPINE, STRUCTURAL GENOMICS, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.KOCH,V.S.STRONGE,D.SHEPHERD,S.D.GADOLA,B.MATHEW,G.RITTER, AUTHOR 2 A.R.FERSHT,G.S.BESRA,R.R.SCHMIDT,E.Y.JONES,V.CERUNDOLO,STRUCTURAL AUTHOR 3 PROTEOMICS IN EUROPE (SPINE) REVDAT 8 20-NOV-24 1ZT4 1 REMARK REVDAT 7 23-AUG-23 1ZT4 1 REMARK REVDAT 6 17-JUN-20 1ZT4 1 REMARK SEQADV SEQRES REVDAT 5 24-JUL-19 1ZT4 1 REMARK REVDAT 4 13-JUL-11 1ZT4 1 VERSN REVDAT 3 24-FEB-09 1ZT4 1 VERSN REVDAT 2 09-AUG-05 1ZT4 1 JRNL REVDAT 1 19-JUL-05 1ZT4 0 JRNL AUTH M.KOCH,V.S.STRONGE,D.SHEPHERD,S.D.GADOLA,B.MATHEW,G.RITTER, JRNL AUTH 2 A.R.FERSHT,G.S.BESRA,R.R.SCHMIDT,E.Y.JONES,V.CERUNDOLO JRNL TITL THE CRYSTAL STRUCTURE OF HUMAN CD1D WITH AND WITHOUT JRNL TITL 2 ALPHA-GALACTOSYLCERAMIDE JRNL REF NAT.IMMUNOL. V. 6 819 2005 JRNL REFN ISSN 1529-2908 JRNL PMID 16007090 JRNL DOI 10.1038/NI1225 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 17432 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 SET) : 0.234 REMARK 3 FREE R VALUE : 0.326 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 867 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.14 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3250 REMARK 3 BIN FREE R VALUE : 0.4010 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 96 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6015 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 18 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.60600 REMARK 3 B22 (A**2) : -0.14500 REMARK 3 B33 (A**2) : 0.75000 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.650 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 80.00 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : AGL_NEW_CNS.PAR REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZT4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000033087. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9340 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17523 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.18400 REMARK 200 R SYM (I) : 0.18400 REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.20 REMARK 200 R MERGE FOR SHELL (I) : 0.94000 REMARK 200 R SYM FOR SHELL (I) : 0.94000 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1CD1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, POTASSIUM FLUORIDE, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.0K 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 25.23500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 88.03500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 88.03500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.23500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.15000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS HEAVY CHAIN FROM CD1D PLUS BETA- REMARK 300 MICROGLOBULIN, CHAINS A AND B (LIGAND BOUND MOLECULE) OR CHAINS C REMARK 300 AND D (NON-LIGAND OR EMPTY MOLECULE). 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: 4780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: 2500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 10170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 ALA A 1 REMARK 465 GLU A 2 REMARK 465 VAL A 3 REMARK 465 PRO A 4 REMARK 465 GLN A 5 REMARK 465 GLY A 278 REMARK 465 GLY A 279 REMARK 465 SER A 280 REMARK 465 TYR A 281 REMARK 465 ALA C 1 REMARK 465 GLU C 2 REMARK 465 VAL C 3 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 LYS A 152 CG CD CE NZ REMARK 470 ARG A 193 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 219 CG CD CE NZ REMARK 470 ARG A 222 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 228 CG CD OE1 NE2 REMARK 470 LYS B 75 CG CD CE NZ REMARK 470 MET B 99 CG SD CE REMARK 470 LYS C 152 CG CD CE NZ REMARK 470 ARG C 193 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 219 CG CD CE NZ REMARK 470 ARG C 222 CG CD NE CZ NH1 NH2 REMARK 470 GLN C 228 CG CD OE1 NE2 REMARK 470 TYR C 281 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS D 75 CG CD CE NZ REMARK 470 MET D 99 CG SD CE 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 OG SER C 41 OD1 ASP C 43 2.08 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 TYR A 92 N - CA - C ANGL. DEV. = 18.6 DEGREES REMARK 500 PRO A 93 C - N - CA ANGL. DEV. = -15.9 DEGREES REMARK 500 PRO A 93 C - N - CD ANGL. DEV. = 14.1 DEGREES REMARK 500 GLU A 136 N - CA - C ANGL. DEV. = -20.1 DEGREES REMARK 500 ALA A 137 N - CA - C ANGL. DEV. = -18.3 DEGREES REMARK 500 PRO C 195 C - N - CA ANGL. DEV. = 10.9 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 PHE A 8 50.26 -119.62 REMARK 500 LEU A 29 146.97 -173.64 REMARK 500 SER A 54 8.74 -69.18 REMARK 500 ASP A 60 -9.36 -51.66 REMARK 500 MET A 87 -73.50 -49.83 REMARK 500 ARG A 89 79.42 39.37 REMARK 500 SER A 91 156.16 -41.96 REMARK 500 PRO A 106 101.87 -36.71 REMARK 500 ASN A 108 -102.85 -80.75 REMARK 500 PHE A 114 101.47 -160.91 REMARK 500 ILE A 123 -30.44 -144.39 REMARK 500 GLN A 135 -85.76 -28.83 REMARK 500 ALA A 137 97.34 175.63 REMARK 500 PRO A 138 148.14 -32.31 REMARK 500 ASN A 149 -7.94 -57.11 REMARK 500 ASP A 151 92.92 -64.34 REMARK 500 LYS A 178 -62.84 -29.66 REMARK 500 LYS A 183 138.56 -33.30 REMARK 500 SER A 192 167.39 176.15 REMARK 500 PRO A 199 174.08 -58.53 REMARK 500 LEU A 202 -158.06 -97.85 REMARK 500 TYR A 212 -79.41 -99.17 REMARK 500 TRP A 220 38.43 -86.63 REMARK 500 MET A 221 75.70 -64.54 REMARK 500 ARG A 222 -78.89 -34.81 REMARK 500 GLU A 226 138.86 -14.50 REMARK 500 GLN A 227 -167.62 -123.88 REMARK 500 ALA A 239 6.64 -53.34 REMARK 500 GLU A 241 -18.10 87.55 REMARK 500 SER A 266 -39.98 -31.28 REMARK 500 GLU A 269 -91.99 -58.96 REMARK 500 ILE B 1 47.10 -77.05 REMARK 500 ASN B 17 119.19 -36.53 REMARK 500 HIS B 31 135.98 173.97 REMARK 500 PRO B 32 -179.02 -67.18 REMARK 500 ASP B 59 10.07 -68.19 REMARK 500 GLU B 74 -36.26 -36.35 REMARK 500 PRO B 90 100.07 -59.02 REMARK 500 ARG B 97 -6.75 -49.89 REMARK 500 GLN C 5 -6.32 -148.34 REMARK 500 ARG C 6 56.77 -115.50 REMARK 500 LEU C 29 147.30 -176.57 REMARK 500 PRO C 106 103.22 -35.83 REMARK 500 ASN C 108 -94.96 -79.24 REMARK 500 ASP C 122 153.55 -49.76 REMARK 500 ILE C 123 -28.37 -144.75 REMARK 500 THR C 129 -10.81 -155.43 REMARK 500 ALA C 137 136.75 -19.68 REMARK 500 LYS C 183 147.25 -35.47 REMARK 500 PRO C 197 -134.31 -113.54 REMARK 500 REMARK 500 THIS ENTRY HAS 72 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AGH A 282 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: CD1D_CELL_SURFACE_ANTIGEN RELATED DB: TARGETDB DBREF 1ZT4 A 1 281 UNP P15813 CD1D_HUMAN 19 300 DBREF 1ZT4 C 1 281 UNP P15813 CD1D_HUMAN 19 300 DBREF 1ZT4 B 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 1ZT4 D 1 99 UNP P61769 B2MG_HUMAN 21 119 SEQADV 1ZT4 MET B 0 UNP P61769 INITIATING METHIONINE SEQADV 1ZT4 MET D 0 UNP P61769 INITIATING METHIONINE SEQRES 1 A 281 ALA GLU VAL PRO GLN ARG LEU PHE PRO LEU ARG CYS LEU SEQRES 2 A 281 GLN ILE SER SER PHE ALA ASN SER SER TRP THR ARG THR SEQRES 3 A 281 ASP GLY LEU ALA TRP LEU GLY GLU LEU GLN THR HIS SER SEQRES 4 A 281 TRP SER ASN ASP SER ASP THR VAL ARG SER LEU LYS PRO SEQRES 5 A 281 TRP SER GLN GLY THR PHE SER ASP GLN GLN TRP GLU THR SEQRES 6 A 281 LEU GLN HIS ILE PHE ARG VAL TYR ARG SER SER PHE THR SEQRES 7 A 281 ARG ASP VAL LYS GLU PHE ALA LYS MET LEU ARG LEU SER SEQRES 8 A 281 TYR PRO LEU GLU LEU GLN VAL SER ALA GLY CYS GLU VAL SEQRES 9 A 281 HIS PRO GLY ASN ALA SER ASN ASN PHE PHE HIS VAL ALA SEQRES 10 A 281 PHE GLN GLY LYS ASP ILE LEU SER PHE GLN GLY THR SER SEQRES 11 A 281 TRP GLU PRO THR GLN GLU ALA PRO LEU TRP VAL ASN LEU SEQRES 12 A 281 ALA ILE GLN VAL LEU ASN GLN ASP LYS TRP THR ARG GLU SEQRES 13 A 281 THR VAL GLN TRP LEU LEU ASN GLY THR CYS PRO GLN PHE SEQRES 14 A 281 VAL SER GLY LEU LEU GLU SER GLY LYS SER GLU LEU LYS SEQRES 15 A 281 LYS GLN VAL LYS PRO LYS ALA TRP LEU SER ARG GLY PRO SEQRES 16 A 281 SER PRO GLY PRO GLY ARG LEU LEU LEU VAL CYS HIS VAL SEQRES 17 A 281 SER GLY PHE TYR PRO LYS PRO VAL TRP VAL LYS TRP MET SEQRES 18 A 281 ARG GLY GLU GLN GLU GLN GLN GLY THR GLN PRO GLY ASP SEQRES 19 A 281 ILE LEU PRO ASN ALA ASP GLU THR TRP TYR LEU ARG ALA SEQRES 20 A 281 THR LEU ASP VAL VAL ALA GLY GLU ALA ALA GLY LEU SER SEQRES 21 A 281 CYS ARG VAL LYS HIS SER SER LEU GLU GLY GLN ASP ILE SEQRES 22 A 281 VAL LEU TYR TRP GLY GLY SER TYR 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 C 281 ALA GLU VAL PRO GLN ARG LEU PHE PRO LEU ARG CYS LEU SEQRES 2 C 281 GLN ILE SER SER PHE ALA ASN SER SER TRP THR ARG THR SEQRES 3 C 281 ASP GLY LEU ALA TRP LEU GLY GLU LEU GLN THR HIS SER SEQRES 4 C 281 TRP SER ASN ASP SER ASP THR VAL ARG SER LEU LYS PRO SEQRES 5 C 281 TRP SER GLN GLY THR PHE SER ASP GLN GLN TRP GLU THR SEQRES 6 C 281 LEU GLN HIS ILE PHE ARG VAL TYR ARG SER SER PHE THR SEQRES 7 C 281 ARG ASP VAL LYS GLU PHE ALA LYS MET LEU ARG LEU SER SEQRES 8 C 281 TYR PRO LEU GLU LEU GLN VAL SER ALA GLY CYS GLU VAL SEQRES 9 C 281 HIS PRO GLY ASN ALA SER ASN ASN PHE PHE HIS VAL ALA SEQRES 10 C 281 PHE GLN GLY LYS ASP ILE LEU SER PHE GLN GLY THR SER SEQRES 11 C 281 TRP GLU PRO THR GLN GLU ALA PRO LEU TRP VAL ASN LEU SEQRES 12 C 281 ALA ILE GLN VAL LEU ASN GLN ASP LYS TRP THR ARG GLU SEQRES 13 C 281 THR VAL GLN TRP LEU LEU ASN GLY THR CYS PRO GLN PHE SEQRES 14 C 281 VAL SER GLY LEU LEU GLU SER GLY LYS SER GLU LEU LYS SEQRES 15 C 281 LYS GLN VAL LYS PRO LYS ALA TRP LEU SER ARG GLY PRO SEQRES 16 C 281 SER PRO GLY PRO GLY ARG LEU LEU LEU VAL CYS HIS VAL SEQRES 17 C 281 SER GLY PHE TYR PRO LYS PRO VAL TRP VAL LYS TRP MET SEQRES 18 C 281 ARG GLY GLU GLN GLU GLN GLN GLY THR GLN PRO GLY ASP SEQRES 19 C 281 ILE LEU PRO ASN ALA ASP GLU THR TRP TYR LEU ARG ALA SEQRES 20 C 281 THR LEU ASP VAL VAL ALA GLY GLU ALA ALA GLY LEU SER SEQRES 21 C 281 CYS ARG VAL LYS HIS SER SER LEU GLU GLY GLN ASP ILE SEQRES 22 C 281 VAL LEU TYR TRP GLY GLY SER TYR SEQRES 1 D 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG SEQRES 2 D 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS SEQRES 3 D 100 TYR VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP SEQRES 4 D 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SEQRES 5 D 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU SEQRES 6 D 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU SEQRES 7 D 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO SEQRES 8 D 100 LYS ILE VAL LYS TRP ASP ARG ASP MET HET AGH A 282 60 HETNAM AGH N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]- HETNAM 2 AGH 2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE FORMUL 5 AGH C50 H99 N O9 FORMUL 6 HOH *18(H2 O) HELIX 1 1 SER A 59 LEU A 88 1 30 HELIX 2 2 LEU A 139 ASN A 149 1 11 HELIX 3 3 TRP A 153 GLY A 164 1 12 HELIX 4 4 GLY A 164 LYS A 182 1 19 HELIX 5 5 SER C 59 LEU C 88 1 30 HELIX 6 6 PRO C 138 ASP C 151 1 14 HELIX 7 7 ASP C 151 GLY C 164 1 14 HELIX 8 8 GLY C 164 LYS C 183 1 20 SHEET 1 A 8 ARG A 48 SER A 49 0 SHEET 2 A 8 LEU A 35 TRP A 40 -1 N SER A 39 O ARG A 48 SHEET 3 A 8 TRP A 23 LEU A 32 -1 N GLY A 28 O TRP A 40 SHEET 4 A 8 LEU A 10 ASN A 20 -1 N ARG A 11 O TRP A 31 SHEET 5 A 8 LEU A 94 VAL A 104 -1 O LEU A 94 N PHE A 18 SHEET 6 A 8 SER A 110 PHE A 118 -1 O ALA A 117 N GLN A 97 SHEET 7 A 8 LYS A 121 GLN A 127 -1 O LYS A 121 N PHE A 118 SHEET 8 A 8 SER A 130 PRO A 133 -1 O GLU A 132 N SER A 125 SHEET 1 B 4 LYS A 188 GLY A 194 0 SHEET 2 B 4 LEU A 203 PHE A 211 -1 O LEU A 203 N GLY A 194 SHEET 3 B 4 TRP A 243 ASP A 250 -1 O ALA A 247 N CYS A 206 SHEET 4 B 4 GLN A 231 PRO A 232 -1 N GLN A 231 O THR A 248 SHEET 1 C 4 LYS A 188 GLY A 194 0 SHEET 2 C 4 LEU A 203 PHE A 211 -1 O LEU A 203 N GLY A 194 SHEET 3 C 4 TRP A 243 ASP A 250 -1 O ALA A 247 N CYS A 206 SHEET 4 C 4 LEU A 236 PRO A 237 -1 N LEU A 236 O TYR A 244 SHEET 1 D 3 TRP A 217 LYS A 219 0 SHEET 2 D 3 SER A 260 LYS A 264 -1 O ARG A 262 N LYS A 219 SHEET 3 D 3 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 ASN B 24 N TYR B 10 SHEET 3 E 4 PHE B 62 PHE B 70 -1 O PHE B 70 N ASN B 21 SHEET 4 E 4 GLU B 50 HIS B 51 -1 N GLU B 50 O TYR B 67 SHEET 1 F 4 LYS B 6 SER B 11 0 SHEET 2 F 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 F 4 PHE B 62 PHE B 70 -1 O PHE B 70 N ASN B 21 SHEET 4 F 4 SER B 55 PHE B 56 -1 N SER B 55 O TYR B 63 SHEET 1 G 4 GLU B 44 ARG 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 78 ASN B 83 -1 O ALA B 79 N LEU B 40 SHEET 4 G 4 ILE B 92 LYS B 94 -1 O VAL B 93 N CYS B 80 SHEET 1 H 8 ARG C 48 SER C 49 0 SHEET 2 H 8 LEU C 35 TRP C 40 -1 N SER C 39 O ARG C 48 SHEET 3 H 8 THR C 24 LEU C 32 -1 N GLY C 28 O TRP C 40 SHEET 4 H 8 LEU C 10 PHE C 18 -1 N LEU C 13 O LEU C 29 SHEET 5 H 8 LEU C 94 VAL C 104 -1 O LEU C 94 N PHE C 18 SHEET 6 H 8 SER C 110 PHE C 118 -1 O ALA C 117 N GLN C 97 SHEET 7 H 8 LYS C 121 GLN C 127 -1 O LYS C 121 N PHE C 118 SHEET 8 H 8 SER C 130 PRO C 133 -1 O GLU C 132 N SER C 125 SHEET 1 I 4 LYS C 188 GLY C 194 0 SHEET 2 I 4 LEU C 203 PHE C 211 -1 O VAL C 205 N SER C 192 SHEET 3 I 4 TRP C 243 LEU C 249 -1 O ALA C 247 N CYS C 206 SHEET 4 I 4 GLN C 231 PRO C 237 -1 N GLN C 231 O THR C 248 SHEET 1 J 3 TRP C 217 LYS C 219 0 SHEET 2 J 3 SER C 260 LYS C 264 -1 O LYS C 264 N TRP C 217 SHEET 3 J 3 LEU C 275 TYR C 276 -1 O LEU C 275 N CYS C 261 SHEET 1 K 2 MET C 221 ARG C 222 0 SHEET 2 K 2 GLN C 225 GLU C 226 -1 O GLN C 225 N ARG C 222 SHEET 1 L 4 LYS D 6 SER D 11 0 SHEET 2 L 4 ASN D 21 PHE D 30 -1 O ASN D 24 N TYR D 10 SHEET 3 L 4 PHE D 62 PHE D 70 -1 O PHE D 70 N ASN D 21 SHEET 4 L 4 GLU D 50 HIS D 51 -1 N GLU D 50 O TYR D 67 SHEET 1 M 4 LYS D 6 SER D 11 0 SHEET 2 M 4 ASN D 21 PHE D 30 -1 O ASN D 24 N TYR D 10 SHEET 3 M 4 PHE D 62 PHE D 70 -1 O PHE D 70 N ASN D 21 SHEET 4 M 4 SER D 55 PHE D 56 -1 N SER D 55 O TYR D 63 SHEET 1 N 4 GLU D 44 ARG D 45 0 SHEET 2 N 4 GLU D 36 LYS D 41 -1 N LYS D 41 O GLU D 44 SHEET 3 N 4 TYR D 78 ASN D 83 -1 O ALA D 79 N LEU D 40 SHEET 4 N 4 ILE D 92 LYS D 94 -1 O VAL D 93 N CYS D 80 SSBOND 1 CYS A 102 CYS A 166 1555 1555 2.04 SSBOND 2 CYS A 206 CYS A 261 1555 1555 2.03 SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.03 SSBOND 4 CYS C 102 CYS C 166 1555 1555 2.04 SSBOND 5 CYS C 206 CYS C 261 1555 1555 2.03 SSBOND 6 CYS D 25 CYS D 80 1555 1555 2.03 CISPEP 1 HIS B 31 PRO B 32 0 0.50 CISPEP 2 TYR C 92 PRO C 93 0 -0.24 CISPEP 3 HIS D 31 PRO D 32 0 0.28 SITE 1 AC1 16 CYS A 12 GLN A 14 LEU A 66 TYR A 73 SITE 2 AC1 16 SER A 76 PHE A 77 ASP A 80 PHE A 84 SITE 3 AC1 16 LEU A 90 VAL A 116 PHE A 118 ASP A 151 SITE 4 AC1 16 TRP A 153 THR A 154 PHE A 169 GLN C 127 CRYST1 50.470 94.300 176.070 90.00 90.00 90.00 P 21 21 21 8 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 0.019814 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010604 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005680 0.00000 CONECT 800 1314 CONECT 1314 800 CONECT 1609 2025 CONECT 2025 1609 CONECT 2373 2832 CONECT 2832 2373 CONECT 3808 4322 CONECT 4322 3808 CONECT 4617 5033 CONECT 5033 4617 CONECT 5400 5859 CONECT 5859 5400 CONECT 6020 6021 6040 CONECT 6021 6020 6022 6052 CONECT 6022 6021 6023 6026 CONECT 6023 6022 6024 6039 CONECT 6024 6023 6025 CONECT 6025 6024 6038 CONECT 6026 6022 CONECT 6027 6028 CONECT 6028 6027 6029 CONECT 6029 6028 6030 CONECT 6030 6029 6031 CONECT 6031 6030 6032 CONECT 6032 6031 6033 CONECT 6033 6032 6034 CONECT 6034 6033 6035 CONECT 6035 6034 6036 CONECT 6036 6035 6037 CONECT 6037 6036 6038 CONECT 6038 6025 6037 CONECT 6039 6023 CONECT 6040 6020 6041 CONECT 6041 6040 6042 6050 CONECT 6042 6041 6043 CONECT 6043 6042 6044 6046 CONECT 6044 6043 6045 CONECT 6045 6044 CONECT 6046 6043 6047 6048 CONECT 6047 6046 CONECT 6048 6046 6049 6050 CONECT 6049 6048 CONECT 6050 6041 6048 6051 CONECT 6051 6050 CONECT 6052 6021 6053 CONECT 6053 6052 6054 6055 CONECT 6054 6053 CONECT 6055 6053 6056 CONECT 6056 6055 6057 CONECT 6057 6056 6058 CONECT 6058 6057 6059 CONECT 6059 6058 6060 CONECT 6060 6059 6061 CONECT 6061 6060 6062 CONECT 6062 6061 6063 CONECT 6063 6062 6064 CONECT 6064 6063 6065 CONECT 6065 6064 6066 CONECT 6066 6065 6067 CONECT 6067 6066 6068 CONECT 6068 6067 6069 CONECT 6069 6068 6070 CONECT 6070 6069 6071 CONECT 6071 6070 6072 CONECT 6072 6071 6073 CONECT 6073 6072 6074 CONECT 6074 6073 6075 CONECT 6075 6074 6076 CONECT 6076 6075 6077 CONECT 6077 6076 6078 CONECT 6078 6077 6079 CONECT 6079 6078 MASTER 396 0 1 8 60 0 4 6 6093 4 72 60 END