HEADER TRANSPORT PROTEIN 03-FEB-99 1QAB TITLE THE STRUCTURE OF HUMAN RETINOL BINDING PROTEIN WITH ITS CARRIER TITLE 2 PROTEIN TRANSTHYRETIN REVEALS INTERACTION WITH THE CARBOXY TERMINUS TITLE 3 OF RBP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (TRANSTHYRETIN); COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: PREALBUMIN; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PROTEIN (RETINOL BINDING PROTEIN); COMPND 7 CHAIN: E, F; COMPND 8 SYNONYM: RBP SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606 KEYWDS HUMAN SERUM RETINOL BINDING PROTEIN, TRANSTHYRETIN, PREALBUMIN, KEYWDS 2 TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.M.NAYLOR,M.E.NEWCOMER REVDAT 8 27-DEC-23 1QAB 1 REMARK REVDAT 7 13-JUL-11 1QAB 1 VERSN REVDAT 6 24-FEB-09 1QAB 1 VERSN REVDAT 5 01-APR-03 1QAB 1 JRNL REVDAT 4 26-SEP-01 1QAB 3 ATOM REVDAT 3 13-APR-99 1QAB 1 JRNL REVDAT 2 09-APR-99 1QAB 1 CRYST1 REVDAT 1 16-FEB-99 1QAB 0 JRNL AUTH H.M.NAYLOR,M.E.NEWCOMER JRNL TITL THE STRUCTURE OF HUMAN RETINOL-BINDING PROTEIN (RBP) WITH JRNL TITL 2 ITS CARRIER PROTEIN TRANSTHYRETIN REVEALS AN INTERACTION JRNL TITL 3 WITH THE CARBOXY TERMINUS OF RBP. JRNL REF BIOCHEMISTRY V. 38 2647 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10052934 JRNL DOI 10.1021/BI982291I REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.4 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 10.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 11303 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) : 0.278 REMARK 3 FREE R VALUE : 0.403 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 508 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.32 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1368 REMARK 3 BIN R VALUE (WORKING SET) : 0.3250 REMARK 3 BIN FREE R VALUE : 0.4230 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 67 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 : 6412 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 51.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 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) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 28.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.910 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL 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 : NULL 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 : PROTEIN_REP.PA REMARK 3 PARAMETER FILE 2 : R REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1QAB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-99. REMARK 100 THE DEPOSITION ID IS D_1000000425. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.914 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26640 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.400 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.04000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 70.11500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 70.11500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.02000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 70.11500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 70.11500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 93.06000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 70.11500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 70.11500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 31.02000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 70.11500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 70.11500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 93.06000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 62.04000 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 10970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 125 REMARK 465 LYS A 126 REMARK 465 GLU A 127 REMARK 465 GLY B 1 REMARK 465 PRO B 2 REMARK 465 THR B 3 REMARK 465 GLY B 4 REMARK 465 THR B 5 REMARK 465 GLY B 6 REMARK 465 GLU B 7 REMARK 465 SER B 8 REMARK 465 LYS B 9 REMARK 465 GLY C 1 REMARK 465 PRO C 2 REMARK 465 THR C 3 REMARK 465 GLY C 4 REMARK 465 THR C 5 REMARK 465 GLY C 6 REMARK 465 GLU C 7 REMARK 465 SER C 8 REMARK 465 LYS C 9 REMARK 465 ASN C 124 REMARK 465 PRO C 125 REMARK 465 LYS C 126 REMARK 465 GLU C 127 REMARK 465 GLY D 1 REMARK 465 PRO D 2 REMARK 465 THR D 3 REMARK 465 GLY D 4 REMARK 465 THR D 5 REMARK 465 GLY D 6 REMARK 465 GLU D 7 REMARK 465 SER D 8 REMARK 465 LYS D 9 REMARK 465 THR D 123 REMARK 465 ASN D 124 REMARK 465 PRO D 125 REMARK 465 LYS D 126 REMARK 465 GLU D 127 REMARK 465 ASP F 175 REMARK 465 GLY F 176 REMARK 465 ARG F 177 REMARK 465 SER F 178 REMARK 465 GLU F 179 REMARK 465 ARG F 180 REMARK 465 ASN F 181 REMARK 465 LEU F 182 REMARK 465 LEU F 183 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 NZ LYS C 15 OE2 GLU C 54 1.47 REMARK 500 O LEU F 125 O ASP F 126 1.47 REMARK 500 ND1 HIS F 104 NE2 GLN F 117 1.56 REMARK 500 OD2 ASP B 18 CG ARG B 21 1.64 REMARK 500 O VAL C 65 OH TYR C 69 1.67 REMARK 500 O ASN F 66 O TRP F 67 1.73 REMARK 500 O ARG B 104 CG2 VAL B 122 1.74 REMARK 500 OD1 ASP F 103 CH2 TRP F 105 1.75 REMARK 500 CB GLN E 38 O ARG E 60 1.75 REMARK 500 O VAL E 152 OE1 GLN E 156 1.82 REMARK 500 O THR A 118 OG SER B 115 1.82 REMARK 500 O GLU F 13 N PHE F 15 1.83 REMARK 500 OD2 ASP A 18 NE ARG A 21 1.83 REMARK 500 CG PRO B 102 O THR B 123 1.84 REMARK 500 CB PRO B 102 O THR B 123 1.84 REMARK 500 OE2 GLU D 66 N ASP D 99 1.85 REMARK 500 O ASP D 99 N GLY D 101 1.86 REMARK 500 O SER F 95 N LEU F 97 1.86 REMARK 500 O LEU E 159 N LEU E 161 1.87 REMARK 500 OD1 ASP E 39 NH1 ARG E 60 1.88 REMARK 500 NZ LYS F 17 O GLY F 51 1.89 REMARK 500 O VAL D 65 OH TYR D 69 1.91 REMARK 500 OD2 ASP A 18 CD ARG A 21 1.92 REMARK 500 OD1 ASP F 103 CZ2 TRP F 105 1.93 REMARK 500 O ASP E 110 N ASP E 112 1.94 REMARK 500 O ARG E 19 CB TYR E 111 1.97 REMARK 500 OD1 ASP E 108 NE ARG E 155 1.99 REMARK 500 CE1 TYR F 90 OD2 ASP F 102 2.02 REMARK 500 NH2 ARG B 34 O GLU B 66 2.03 REMARK 500 O SER E 178 N ARG E 180 2.04 REMARK 500 NE2 GLN E 52 O PHE E 77 2.05 REMARK 500 O ASP F 48 N THR F 50 2.06 REMARK 500 CB SER C 115 OG1 THR D 119 2.07 REMARK 500 CE2 PHE F 20 CE1 PHE F 45 2.07 REMARK 500 OD2 ASP E 16 N ALA E 18 2.08 REMARK 500 O ASN E 124 N ASP E 126 2.09 REMARK 500 O TYR F 111 NE ARG F 139 2.09 REMARK 500 OE1 GLN F 52 O PHE F 77 2.09 REMARK 500 O GLU E 13 N PHE E 15 2.10 REMARK 500 CB GLN F 38 O ARG F 60 2.11 REMARK 500 OH TYR D 114 CB SER E 95 2.11 REMARK 500 C VAL E 152 NE2 GLN E 156 2.11 REMARK 500 O HIS F 104 NE2 GLN F 117 2.11 REMARK 500 O VAL E 152 NE2 GLN E 156 2.13 REMARK 500 OD1 ASP C 38 CG2 THR C 40 2.14 REMARK 500 CD1 ILE D 68 OG1 THR D 96 2.14 REMARK 500 NE2 GLN E 38 NH2 ARG E 60 2.15 REMARK 500 O CYS E 4 O CYS E 129 2.15 REMARK 500 O HIS D 56 N LEU D 58 2.15 REMARK 500 O THR F 23 NH1 ARG F 139 2.15 REMARK 500 REMARK 500 THIS ENTRY HAS 56 CLOSE CONTACTS REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O GLN E 154 OE1 GLN F 164 8455 1.44 REMARK 500 OG SER E 8 O THR F 128 8455 1.57 REMARK 500 SD MET F 27 OD1 ASP F 126 4444 1.58 REMARK 500 N CYS E 160 N CYS F 4 8455 1.74 REMARK 500 N ALA E 163 OE1 GLU F 157 8455 1.78 REMARK 500 CE2 PHE E 9 N CYS F 4 8455 1.82 REMARK 500 OE2 GLU E 157 O CYS F 160 8455 1.85 REMARK 500 O CYS E 4 OG SER F 8 8455 1.87 REMARK 500 O GLU E 158 SG CYS F 4 8455 1.87 REMARK 500 CB GLU E 157 CA LEU F 161 8455 1.88 REMARK 500 O CYS E 160 O GLU F 158 8455 1.89 REMARK 500 CD2 PHE E 9 N CYS F 4 8455 1.95 REMARK 500 O GLN E 156 N LEU F 161 8455 1.96 REMARK 500 CA GLU E 157 N LEU F 161 8455 2.02 REMARK 500 O ALA E 153 N GLN F 164 8455 2.09 REMARK 500 CB ALA E 5 CB ALA F 5 8455 2.12 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 PRO D 24 C - N - CA ANGL. DEV. = 11.3 DEGREES REMARK 500 PRO D 86 C - N - CA ANGL. DEV. = 15.2 DEGREES REMARK 500 PRO D 86 C - N - CD ANGL. DEV. = -14.2 DEGREES REMARK 500 PRO E 145 C - N - CA ANGL. DEV. = 10.1 DEGREES REMARK 500 PRO F 141 C - N - CA ANGL. DEV. = 9.3 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 PRO A 2 161.55 -49.68 REMARK 500 CYS A 10 109.20 -18.52 REMARK 500 MET A 13 111.05 -165.93 REMARK 500 ASP A 38 50.46 -119.64 REMARK 500 ASP A 39 21.83 47.24 REMARK 500 PHE A 44 -75.26 -114.90 REMARK 500 SER A 50 -158.79 -68.27 REMARK 500 THR A 59 -178.73 -170.26 REMARK 500 ASP A 74 85.50 -69.34 REMARK 500 ASN A 98 30.36 28.04 REMARK 500 SER A 100 50.75 -115.57 REMARK 500 ALA B 25 80.32 -67.20 REMARK 500 LYS B 35 124.30 -38.10 REMARK 500 ASP B 38 5.88 -64.61 REMARK 500 ASP B 39 30.51 71.72 REMARK 500 PRO B 43 135.38 -31.82 REMARK 500 ALA B 45 163.54 176.60 REMARK 500 SER B 50 -160.84 -59.85 REMARK 500 THR B 59 -172.90 167.90 REMARK 500 GLU B 62 46.83 -103.82 REMARK 500 GLN B 63 -24.20 -149.69 REMARK 500 HIS B 88 -176.20 -65.22 REMARK 500 HIS B 90 156.01 160.42 REMARK 500 SER B 100 -45.16 -12.86 REMARK 500 SER B 115 150.62 177.83 REMARK 500 VAL B 121 -142.55 -125.63 REMARK 500 VAL B 122 123.90 48.69 REMARK 500 THR B 123 -157.42 -107.26 REMARK 500 ASN B 124 53.64 -114.42 REMARK 500 PRO B 125 76.85 -53.47 REMARK 500 LYS B 126 88.48 -169.08 REMARK 500 PRO C 11 -93.06 -93.66 REMARK 500 ASN C 27 71.24 40.06 REMARK 500 ALA C 37 -39.17 -39.17 REMARK 500 ASP C 38 38.40 -92.97 REMARK 500 THR C 49 151.46 -47.77 REMARK 500 PHE C 64 92.74 -51.72 REMARK 500 PRO C 86 -157.42 -71.41 REMARK 500 PHE C 87 -14.75 -141.38 REMARK 500 ASN C 98 57.53 23.90 REMARK 500 PRO C 102 127.12 -36.10 REMARK 500 LEU D 12 51.40 34.11 REMARK 500 ASN D 27 24.23 89.83 REMARK 500 ASP D 38 26.17 -76.53 REMARK 500 PRO D 43 142.32 -30.44 REMARK 500 ALA D 45 161.92 175.16 REMARK 500 LEU D 55 89.96 -154.52 REMARK 500 HIS D 56 -120.69 -85.02 REMARK 500 HIS D 90 148.71 170.05 REMARK 500 SER D 100 -44.48 4.47 REMARK 500 REMARK 500 THIS ENTRY HAS 181 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 RTL E 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RTL F 2 DBREF 1QAB A 1 127 UNP P02766 TTHY_HUMAN 21 147 DBREF 1QAB B 1 127 UNP P02766 TTHY_HUMAN 21 147 DBREF 1QAB C 1 127 UNP P02766 TTHY_HUMAN 21 147 DBREF 1QAB D 1 127 UNP P02766 TTHY_HUMAN 21 147 DBREF 1QAB E 6 183 UNP P02753 RET4_HUMAN 24 201 DBREF 1QAB F 6 183 UNP P02753 RET4_HUMAN 24 201 SEQRES 1 A 127 GLY PRO THR GLY THR GLY GLU SER LYS CYS PRO LEU MET SEQRES 2 A 127 VAL LYS VAL LEU ASP ALA VAL ARG GLY SER PRO ALA ILE SEQRES 3 A 127 ASN VAL ALA VAL HIS VAL PHE ARG LYS ALA ALA ASP ASP SEQRES 4 A 127 THR TRP GLU PRO PHE ALA SER GLY LYS THR SER GLU SER SEQRES 5 A 127 GLY GLU LEU HIS GLY LEU THR THR GLU GLU GLN PHE VAL SEQRES 6 A 127 GLU GLY ILE TYR LYS VAL GLU ILE ASP THR LYS SER TYR SEQRES 7 A 127 TRP LYS ALA LEU GLY ILE SER PRO PHE HIS GLU HIS ALA SEQRES 8 A 127 GLU VAL VAL PHE THR ALA ASN ASP SER GLY PRO ARG ARG SEQRES 9 A 127 TYR THR ILE ALA ALA LEU LEU SER PRO TYR SER TYR SER SEQRES 10 A 127 THR THR ALA VAL VAL THR ASN PRO LYS GLU SEQRES 1 B 127 GLY PRO THR GLY THR GLY GLU SER LYS CYS PRO LEU MET SEQRES 2 B 127 VAL LYS VAL LEU ASP ALA VAL ARG GLY SER PRO ALA ILE SEQRES 3 B 127 ASN VAL ALA VAL HIS VAL PHE ARG LYS ALA ALA ASP ASP SEQRES 4 B 127 THR TRP GLU PRO PHE ALA SER GLY LYS THR SER GLU SER SEQRES 5 B 127 GLY GLU LEU HIS GLY LEU THR THR GLU GLU GLN PHE VAL SEQRES 6 B 127 GLU GLY ILE TYR LYS VAL GLU ILE ASP THR LYS SER TYR SEQRES 7 B 127 TRP LYS ALA LEU GLY ILE SER PRO PHE HIS GLU HIS ALA SEQRES 8 B 127 GLU VAL VAL PHE THR ALA ASN ASP SER GLY PRO ARG ARG SEQRES 9 B 127 TYR THR ILE ALA ALA LEU LEU SER PRO TYR SER TYR SER SEQRES 10 B 127 THR THR ALA VAL VAL THR ASN PRO LYS GLU SEQRES 1 C 127 GLY PRO THR GLY THR GLY GLU SER LYS CYS PRO LEU MET SEQRES 2 C 127 VAL LYS VAL LEU ASP ALA VAL ARG GLY SER PRO ALA ILE SEQRES 3 C 127 ASN VAL ALA VAL HIS VAL PHE ARG LYS ALA ALA ASP ASP SEQRES 4 C 127 THR TRP GLU PRO PHE ALA SER GLY LYS THR SER GLU SER SEQRES 5 C 127 GLY GLU LEU HIS GLY LEU THR THR GLU GLU GLN PHE VAL SEQRES 6 C 127 GLU GLY ILE TYR LYS VAL GLU ILE ASP THR LYS SER TYR SEQRES 7 C 127 TRP LYS ALA LEU GLY ILE SER PRO PHE HIS GLU HIS ALA SEQRES 8 C 127 GLU VAL VAL PHE THR ALA ASN ASP SER GLY PRO ARG ARG SEQRES 9 C 127 TYR THR ILE ALA ALA LEU LEU SER PRO TYR SER TYR SER SEQRES 10 C 127 THR THR ALA VAL VAL THR ASN PRO LYS GLU SEQRES 1 D 127 GLY PRO THR GLY THR GLY GLU SER LYS CYS PRO LEU MET SEQRES 2 D 127 VAL LYS VAL LEU ASP ALA VAL ARG GLY SER PRO ALA ILE SEQRES 3 D 127 ASN VAL ALA VAL HIS VAL PHE ARG LYS ALA ALA ASP ASP SEQRES 4 D 127 THR TRP GLU PRO PHE ALA SER GLY LYS THR SER GLU SER SEQRES 5 D 127 GLY GLU LEU HIS GLY LEU THR THR GLU GLU GLN PHE VAL SEQRES 6 D 127 GLU GLY ILE TYR LYS VAL GLU ILE ASP THR LYS SER TYR SEQRES 7 D 127 TRP LYS ALA LEU GLY ILE SER PRO PHE HIS GLU HIS ALA SEQRES 8 D 127 GLU VAL VAL PHE THR ALA ASN ASP SER GLY PRO ARG ARG SEQRES 9 D 127 TYR THR ILE ALA ALA LEU LEU SER PRO TYR SER TYR SER SEQRES 10 D 127 THR THR ALA VAL VAL THR ASN PRO LYS GLU SEQRES 1 E 180 CYS ALA VAL SER SER PHE ARG VAL LYS GLU ASN PHE ASP SEQRES 2 E 180 LYS ALA ARG PHE SER GLY THR TRP TYR ALA MET ALA LYS SEQRES 3 E 180 LYS ASP PRO GLU GLY LEU PHE LEU GLN ASP ASN ILE VAL SEQRES 4 E 180 ALA GLU PHE SER VAL ASP GLU THR GLY GLN MET SER ALA SEQRES 5 E 180 THR ALA LYS GLY ARG VAL ARG LEU LEU ASN ASN TRP ASP SEQRES 6 E 180 VAL CYS ALA ASP MET VAL GLY THR PHE THR ASP THR GLU SEQRES 7 E 180 ASP PRO ALA LYS PHE LYS MET LYS TYR TRP GLY VAL ALA SEQRES 8 E 180 SER PHE LEU GLN LYS GLY ASN ASP ASP HIS TRP ILE VAL SEQRES 9 E 180 ASP THR ASP TYR ASP THR TYR ALA VAL GLN TYR SER CYS SEQRES 10 E 180 ARG LEU LEU ASN LEU ASP GLY THR CYS ALA ASP SER TYR SEQRES 11 E 180 SER PHE VAL PHE SER ARG ASP PRO ASN GLY LEU PRO PRO SEQRES 12 E 180 GLU ALA GLN LYS ILE VAL ALA GLN ARG GLN GLU GLU LEU SEQRES 13 E 180 CYS LEU ALA ALA GLN TYR ARG LEU ILE VAL HIS ASN GLY SEQRES 14 E 180 TYR CYS ASP GLY ARG SER GLU ARG ASN LEU LEU SEQRES 1 F 180 CYS ALA VAL SER SER PHE ARG VAL LYS GLU ASN PHE ASP SEQRES 2 F 180 LYS ALA ARG PHE SER GLY THR TRP TYR ALA MET ALA LYS SEQRES 3 F 180 LYS ASP PRO GLU GLY LEU PHE LEU GLN ASP ASN ILE VAL SEQRES 4 F 180 ALA GLU PHE SER VAL ASP GLU THR GLY GLN MET SER ALA SEQRES 5 F 180 THR ALA LYS GLY ARG VAL ARG LEU LEU ASN ASN TRP ASP SEQRES 6 F 180 VAL CYS ALA ASP MET VAL GLY THR PHE THR ASP THR GLU SEQRES 7 F 180 ASP PRO ALA LYS PHE LYS MET LYS TYR TRP GLY VAL ALA SEQRES 8 F 180 SER PHE LEU GLN LYS GLY ASN ASP ASP HIS TRP ILE VAL SEQRES 9 F 180 ASP THR ASP TYR ASP THR TYR ALA VAL GLN TYR SER CYS SEQRES 10 F 180 ARG LEU LEU ASN LEU ASP GLY THR CYS ALA ASP SER TYR SEQRES 11 F 180 SER PHE VAL PHE SER ARG ASP PRO ASN GLY LEU PRO PRO SEQRES 12 F 180 GLU ALA GLN LYS ILE VAL ALA GLN ARG GLN GLU GLU LEU SEQRES 13 F 180 CYS LEU ALA ALA GLN TYR ARG LEU ILE VAL HIS ASN GLY SEQRES 14 F 180 TYR CYS ASP GLY ARG SER GLU ARG ASN LEU LEU HET RTL E 1 21 HET RTL F 2 21 HETNAM RTL RETINOL FORMUL 7 RTL 2(C20 H30 O) HELIX 1 1 THR A 75 LEU A 82 1 8 HELIX 2 2 LYS B 76 LYS B 80 1 5 HELIX 3 3 LYS C 76 LYS C 80 1 5 HELIX 4 4 LYS D 76 LYS D 80 1 5 HELIX 5 5 LYS E 17 ARG E 19 5 3 HELIX 6 6 ALA E 148 ILE E 151 1 4 HELIX 7 7 ALA F 18 PHE F 20 5 3 HELIX 8 8 GLN F 149 VAL F 152 1 4 HELIX 9 9 GLN F 156 CYS F 160 3 5 SHEET 1 A 3 GLU B 54 LEU B 55 0 SHEET 2 A 3 LEU B 12 LYS B 15 -1 O VAL B 14 N LEU B 55 SHEET 3 A 3 GLU B 54 LEU B 55 -1 N LEU B 55 O VAL B 14 SHEET 1 A1 3 GLU B 54 LEU B 55 0 SHEET 2 A1 3 LEU B 12 LYS B 15 -1 O VAL B 14 N LEU B 55 SHEET 3 A1 3 GLU B 54 LEU B 55 -1 N LEU B 55 O VAL B 14 SHEET 1 B 4 TRP A 41 PRO A 43 0 SHEET 2 B 4 VAL A 30 LYS A 35 -1 N ARG A 34 O GLU A 42 SHEET 3 B 4 GLY A 67 ILE A 73 -1 O ILE A 68 N LYS A 35 SHEET 4 B 4 ALA A 91 ALA A 97 -1 N ALA A 91 O ILE A 73 SHEET 1 C 4 PRO B 43 LYS B 48 0 SHEET 2 C 4 ALA B 29 ARG B 34 -1 N VAL B 30 O GLY B 47 SHEET 3 C 4 GLY B 67 ILE B 73 -1 O LYS B 70 N PHE B 33 SHEET 4 C 4 ALA B 91 ALA B 97 -1 O ALA B 91 N ILE B 73 SHEET 1 D 7 SER C 23 PRO C 24 0 SHEET 2 D 7 VAL C 14 ASP C 18 -1 N ASP C 18 O SER C 23 SHEET 3 D 7 ILE C 107 LEU C 111 1 O ILE C 107 N LYS C 15 SHEET 4 D 7 SER C 117 ALA C 120 -1 O SER C 117 N LEU C 110 SHEET 5 D 7 TYR D 116 THR D 119 -1 O TYR D 116 N THR C 118 SHEET 6 D 7 ALA D 108 LEU D 111 -1 O ALA D 108 N THR D 119 SHEET 7 D 7 LEU D 17 ASP D 18 1 O LEU D 17 N LEU D 111 SHEET 1 E 5 TRP C 41 LYS C 48 0 SHEET 2 E 5 ALA C 29 LYS C 35 -1 N VAL C 30 O GLY C 47 SHEET 3 E 5 GLY C 67 ILE C 73 -1 O ILE C 68 N LYS C 35 SHEET 4 E 5 ALA C 91 ALA C 97 -1 O ALA C 91 N ILE C 73 SHEET 5 E 5 HIS D 88 HIS D 90 -1 N GLU D 89 O VAL C 94 SHEET 1 F 2 VAL D 14 LYS D 15 0 SHEET 2 F 2 GLU D 54 LEU D 55 -1 N LEU D 55 O VAL D 14 SHEET 1 G 4 TRP D 41 GLY D 47 0 SHEET 2 G 4 VAL D 30 LYS D 35 -1 N VAL D 30 O GLY D 47 SHEET 3 G 4 GLY D 67 ILE D 73 -1 O ILE D 68 N LYS D 35 SHEET 4 G 4 VAL D 94 ALA D 97 -1 N PHE D 95 O TYR D 69 SHEET 1 H 2 LYS E 58 VAL E 61 0 SHEET 2 H 2 VAL E 69 ASP E 72 -1 O VAL E 69 N VAL E 61 SHEET 1 I 3 GLY E 75 THR E 76 0 SHEET 2 I 3 MET E 88 TYR E 90 -1 O LYS E 89 N THR E 76 SHEET 3 I 3 GLY E 100 ASP E 102 -1 O GLY E 100 N TYR E 90 SHEET 1 J 2 VAL E 116 TYR E 118 0 SHEET 2 J 2 SER E 134 VAL E 136 -1 N PHE E 135 O GLN E 117 SHEET 1 K 4 THR F 23 TYR F 25 0 SHEET 2 K 4 ASP F 39 GLU F 44 -1 N ALA F 43 O TRP F 24 SHEET 3 K 4 THR F 56 VAL F 61 -1 N THR F 56 O GLU F 44 SHEET 4 K 4 VAL F 69 ASP F 72 -1 O VAL F 69 N VAL F 61 SHEET 1 L 3 GLY F 75 PHE F 77 0 SHEET 2 L 3 LYS F 87 TYR F 90 -1 N LYS F 89 O THR F 76 SHEET 3 L 3 GLY F 100 ASP F 103 -1 N GLY F 100 O TYR F 90 SHEET 1 M 3 ASP F 108 THR F 109 0 SHEET 2 M 3 ALA F 115 GLN F 117 -1 N VAL F 116 O ASP F 108 SHEET 3 M 3 PHE F 135 PHE F 137 -1 O PHE F 135 N GLN F 117 SHEET 1 N 2 CYS F 120 LEU F 123 0 SHEET 2 N 2 ALA F 130 SER F 132 -1 N ALA F 130 O LEU F 122 SSBOND 1 CYS E 4 CYS E 160 1555 1555 2.04 SSBOND 2 CYS E 70 CYS E 174 1555 1555 2.03 SSBOND 3 CYS E 120 CYS E 129 1555 1555 2.06 SSBOND 4 CYS F 70 CYS F 174 1555 1555 2.03 SSBOND 5 CYS F 120 CYS F 129 1555 1555 2.04 SITE 1 AC1 6 GLY D 83 PHE E 36 ALA E 57 MET E 73 SITE 2 AC1 6 TYR E 90 LEU E 97 SITE 1 AC2 11 GLY B 83 LEU F 35 PHE F 36 ALA F 55 SITE 2 AC2 11 ALA F 57 MET F 73 VAL F 74 MET F 88 SITE 3 AC2 11 TYR F 90 LEU F 97 GLN F 98 CRYST1 140.230 140.230 124.080 90.00 90.00 90.00 P 41 21 2 32 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 0.007131 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007131 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008059 0.00000