PDB Short entry for 1ZT4 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 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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