10 20 30 40 50 60 70 80 1JFP - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER SIGNALING PROTEIN, MEMBRANE PROTEIN 21-JUN-01 1JFP
TITLE STRUCTURE OF BOVINE RHODOPSIN (DARK ADAPTED)
CAVEAT 1JFP INCORRECT CARBON CHIRAL CENTERS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHODOPSIN; COMPND 3 CHAIN: A
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913
KEYWDS G-PROTEIN COUPLED RECEPTOR, SIGNALING PROTEIN, MEMBRANE KEYWDS 2 PROTEIN
EXPDTA SOLUTION NMR
AUTHOR P.L.YEAGLE,G.CHOI,A.D.ALBERT
REVDAT 2 24-FEB-09 1JFP 1 VERSN REVDAT 1 05-OCT-01 1JFP 0
JRNL AUTH P.L.YEAGLE,G.CHOI,A.D.ALBERT JRNL TITL STUDIES ON THE STRUCTURE OF THE G-PROTEIN-COUPLED JRNL TITL 2 RECEPTOR RHODOPSIN INCLUDING THE PUTATIVE JRNL TITL 3 G-PROTEIN BINDING SITE IN UNACTIVATED AND JRNL TITL 4 ACTIVATED FORMS. JRNL REF BIOCHEMISTRY V. 40 11932 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11570894 JRNL DOI 10.1021/BI015543F
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SYBYL 6.6 REMARK 3 AUTHORS : TRIPOS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SECONDARY STRUCTURE FROM NMR REMARK 3 STRUCTURES OF PEPTIDES ENCODING HELICES OR TURNS, AND LONG- REMARK 3 RANGE DISTANCE CONSTRAINTS FROM OTHER MEASUREMENTS ON INTACT REMARK 3 PROTEIN AMINO TERMINUS REMOVED DUE TO LACK OF LONG-RANGE REMARK 3 CONSTRAINTS
REMARK 4 REMARK 4 1JFP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUN-01. REMARK 100 THE RCSB ID CODE IS RCSB013715.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 10 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : FRAGMENTS OF RHODOPSIN REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SYBYL 6.6 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 3 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL
REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 GLY A 3 REMARK 465 THR A 4 REMARK 465 GLU A 5 REMARK 465 GLY A 6 REMARK 465 PRO A 7 REMARK 465 ASN A 8 REMARK 465 PHE A 9 REMARK 465 TYR A 10 REMARK 465 VAL A 11 REMARK 465 PRO A 12 REMARK 465 PHE A 13 REMARK 465 SER A 14 REMARK 465 ASN A 15 REMARK 465 LYS A 16 REMARK 465 THR A 17 REMARK 465 GLY A 18 REMARK 465 VAL A 19 REMARK 465 VAL A 20 REMARK 465 ARG A 21 REMARK 465 SER A 22 REMARK 465 PRO A 23 REMARK 465 PHE A 24 REMARK 465 GLU A 25 REMARK 465 ALA A 26 REMARK 465 PRO A 27 REMARK 465 GLN A 28 REMARK 465 TYR A 29 REMARK 465 TYR A 30 REMARK 465 LEU A 31 REMARK 465 ALA A 32 REMARK 465 GLU A 33 REMARK 465 PRO A 34 REMARK 465 TRP A 35 REMARK 465 GLN A 36 REMARK 465 PHE A 37 REMARK 465 SER A 38 REMARK 465 MET A 39
REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 RES CSSEQI ATOMS REMARK 470 ALA A 348 C O
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 CD2 TYR A 102 CZ PHE A 105 0.41 REMARK 500 N PRO A 53 CE2 PHE A 56 0.63 REMARK 500 N ILE A 133 CE2 TYR A 136 0.73 REMARK 500 CA PRO A 53 CD2 PHE A 56 0.81 REMARK 500 CA THR A 97 CE2 TYR A 102 0.87 REMARK 500 C PHE A 52 CZ PHE A 56 0.90 REMARK 500 NZ LYS A 339 O SER A 343 0.94 REMARK 500 O GLU A 181 SG CYS A 185 0.95 REMARK 500 N PRO A 53 CZ PHE A 56 0.96 REMARK 500 C PRO A 53 CD2 PHE A 56 1.01 REMARK 500 CE LYS A 339 CA GLN A 344 1.03 REMARK 500 CA THR A 97 CD2 TYR A 102 1.07 REMARK 500 NZ LYS A 339 C SER A 343 1.07 REMARK 500 N ILE A 133 CD2 TYR A 136 1.09 REMARK 500 CD LYS A 339 CA GLN A 344 1.10 REMARK 500 CA ILE A 133 CD2 TYR A 136 1.11 REMARK 500 O GLY A 101 CD2 PHE A 103 1.11 REMARK 500 CA PRO A 53 CG PHE A 56 1.18 REMARK 500 N THR A 97 CZ TYR A 102 1.18 REMARK 500 C SER A 98 CZ PHE A 103 1.18 REMARK 500 C THR A 97 CE2 PHE A 105 1.25 REMARK 500 CA PRO A 53 CE2 PHE A 56 1.27 REMARK 500 C THR A 97 CE2 TYR A 102 1.29 REMARK 500 CA GLU A 247 CG1 VAL A 250 1.30 REMARK 500 CB THR A 97 CE2 TYR A 102 1.30 REMARK 500 CA SER A 98 CZ PHE A 103 1.31 REMARK 500 O GLY A 101 CE2 PHE A 103 1.32 REMARK 500 N SER A 98 CE1 TYR A 102 1.32 REMARK 500 N SER A 98 CD1 TYR A 102 1.33 REMARK 500 CA ILE A 133 CE2 TYR A 136 1.33 REMARK 500 CG PHE A 313 NZ LYS A 325 1.34 REMARK 500 CD2 LEU A 72 ND2 ASN A 310 1.36 REMARK 500 C GLN A 236 OG SER A 240 1.38 REMARK 500 CG LEU A 72 ND2 ASN A 310 1.38 REMARK 500 N LEU A 99 CZ PHE A 103 1.39 REMARK 500 CE LYS A 339 N GLN A 344 1.44 REMARK 500 CG TYR A 102 CZ PHE A 105 1.44 REMARK 500 C THR A 97 CZ TYR A 102 1.45 REMARK 500 N SER A 98 CZ PHE A 103 1.45 REMARK 500 CA THR A 97 CZ PHE A 105 1.46 REMARK 500 N SER A 98 CE2 PHE A 103 1.46 REMARK 500 N THR A 97 CE1 TYR A 102 1.50 REMARK 500 CB PRO A 53 CG PHE A 56 1.50 REMARK 500 NZ LYS A 339 N GLN A 344 1.51 REMARK 500 CA THR A 97 CZ TYR A 102 1.53 REMARK 500 CG1 VAL A 139 CD GLN A 225 1.56 REMARK 500 CA PHE A 52 CZ PHE A 56 1.58 REMARK 500 CG2 VAL A 318 N ASP A 331 1.59 REMARK 500 CD2 TYR A 102 CE2 PHE A 105 1.59 REMARK 500 CD1 PHE A 313 CE LYS A 325 1.60 REMARK 500 REMARK 500 THIS ENTRY HAS 166 CLOSE CONTACTS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 253 CA MET A 253 CB 0.197 REMARK 500 LYS A 296 C THR A 297 N 0.344 REMARK 500 ILE A 307 N ILE A 307 CA 0.177 REMARK 500 ASN A 310 N ASN A 310 CA 0.198 REMARK 500 PHE A 313 CA PHE A 313 CB 0.242 REMARK 500 ASP A 331 N ASP A 331 CA 0.143 REMARK 500 LYS A 339 N LYS A 339 CA 0.132 REMARK 500 GLN A 344 N GLN A 344 CA 0.128 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 VAL A 61 CB - CA - C ANGL. DEV. = 12.9 DEGREES REMARK 500 THR A 62 CA - CB - CG2 ANGL. DEV. = 8.7 DEGREES REMARK 500 TYR A 74 CB - CG - CD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 TYR A 74 CB - CG - CD1 ANGL. DEV. = -7.3 DEGREES REMARK 500 TYR A 96 CB - CG - CD1 ANGL. DEV. = -5.3 DEGREES REMARK 500 SER A 98 N - CA - CB ANGL. DEV. = -12.7 DEGREES REMARK 500 GLU A 113 CA - C - N ANGL. DEV. = 18.5 DEGREES REMARK 500 GLU A 113 O - C - N ANGL. DEV. = -18.8 DEGREES REMARK 500 GLY A 114 C - N - CA ANGL. DEV. = -12.9 DEGREES REMARK 500 TRP A 126 CD1 - NE1 - CE2 ANGL. DEV. = -8.3 DEGREES REMARK 500 TRP A 126 CG - CD2 - CE3 ANGL. DEV. = -7.2 DEGREES REMARK 500 TRP A 126 CD2 - CE3 - CZ3 ANGL. DEV. = -14.8 DEGREES REMARK 500 TRP A 126 CE3 - CZ3 - CH2 ANGL. DEV. = -13.5 DEGREES REMARK 500 ILE A 133 CB - CA - C ANGL. DEV. = 18.8 DEGREES REMARK 500 ARG A 135 N - CA - CB ANGL. DEV. = -11.6 DEGREES REMARK 500 GLU A 134 CA - C - N ANGL. DEV. = -14.3 DEGREES REMARK 500 TYR A 136 CA - CB - CG ANGL. DEV. = 11.9 DEGREES REMARK 500 TYR A 136 CG - CD2 - CE2 ANGL. DEV. = -5.9 DEGREES REMARK 500 VAL A 137 CB - CA - C ANGL. DEV. = 12.8 DEGREES REMARK 500 CYS A 140 CB - CA - C ANGL. DEV. = -25.2 DEGREES REMARK 500 CYS A 140 N - CA - CB ANGL. DEV. = -11.4 DEGREES REMARK 500 PRO A 142 CA - N - CD ANGL. DEV. = -10.8 DEGREES REMARK 500 PRO A 142 CB - CA - C ANGL. DEV. = 31.4 DEGREES REMARK 500 PRO A 142 N - CA - CB ANGL. DEV. = -8.1 DEGREES REMARK 500 MET A 143 N - CA - CB ANGL. DEV. = -12.6 DEGREES REMARK 500 PRO A 142 CA - C - N ANGL. DEV. = -13.5 DEGREES REMARK 500 PHE A 148 CB - CG - CD2 ANGL. DEV. = 4.7 DEGREES REMARK 500 PRO A 171 CA - N - CD ANGL. DEV. = -8.8 DEGREES REMARK 500 TRP A 175 CD1 - NE1 - CE2 ANGL. DEV. = -6.3 DEGREES REMARK 500 TRP A 175 CD2 - CE2 - CZ2 ANGL. DEV. = -7.4 DEGREES REMARK 500 TRP A 175 NE1 - CE2 - CD2 ANGL. DEV. = -8.8 DEGREES REMARK 500 TRP A 175 CE2 - CD2 - CG ANGL. DEV. = -8.0 DEGREES REMARK 500 TRP A 175 CG - CD2 - CE3 ANGL. DEV. = -5.6 DEGREES REMARK 500 TYR A 178 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 TYR A 178 CB - CG - CD1 ANGL. DEV. = -9.5 DEGREES REMARK 500 TYR A 178 CG - CD1 - CE1 ANGL. DEV. = -10.0 DEGREES REMARK 500 PRO A 180 CA - N - CD ANGL. DEV. = -12.5 DEGREES REMARK 500 THR A 193 C - N - CA ANGL. DEV. = -16.1 DEGREES REMARK 500 THR A 198 CB - CA - C ANGL. DEV. = -25.5 DEGREES REMARK 500 PRO A 215 CA - N - CD ANGL. DEV. = -13.3 DEGREES REMARK 500 PRO A 215 N - CA - CB ANGL. DEV. = -9.5 DEGREES REMARK 500 PRO A 215 C - N - CA ANGL. DEV. = -10.5 DEGREES REMARK 500 LEU A 216 N - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 500 LEU A 216 C - N - CA ANGL. DEV. = 17.3 DEGREES REMARK 500 ILE A 219 C - N - CA ANGL. DEV. = 16.5 DEGREES REMARK 500 CYS A 222 CB - CA - C ANGL. DEV. = 13.8 DEGREES REMARK 500 TYR A 223 CA - CB - CG ANGL. DEV. = 13.4 DEGREES REMARK 500 TYR A 223 CB - CG - CD1 ANGL. DEV. = 3.6 DEGREES REMARK 500 THR A 229 N - CA - CB ANGL. DEV. = 12.5 DEGREES REMARK 500 GLU A 232 CB - CA - C ANGL. DEV. = 14.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 76 ANGLE DEVIATIONS. 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 45 68.27 -156.57 REMARK 500 LEU A 47 34.70 -156.61 REMARK 500 MET A 49 76.00 -153.82 REMARK 500 PRO A 53 54.25 -96.28 REMARK 500 PHE A 56 -62.29 -178.88 REMARK 500 LEU A 57 46.25 -85.10 REMARK 500 THR A 58 -50.94 -163.47 REMARK 500 LYS A 67 -177.45 48.02 REMARK 500 THR A 70 -72.49 -95.97 REMARK 500 PRO A 71 -157.20 43.86 REMARK 500 LEU A 72 36.22 -73.73 REMARK 500 LEU A 79 33.36 -86.60 REMARK 500 ALA A 82 -19.41 -156.84 REMARK 500 PHE A 91 -63.60 -105.96 REMARK 500 THR A 93 20.54 166.30 REMARK 500 LEU A 95 -3.37 -155.00 REMARK 500 THR A 97 60.08 -161.73 REMARK 500 SER A 98 26.71 162.74 REMARK 500 LEU A 99 55.80 156.67 REMARK 500 HIS A 100 75.27 64.63 REMARK 500 TYR A 102 -105.79 86.57 REMARK 500 PHE A 103 -136.67 174.94 REMARK 500 VAL A 104 -174.44 106.92 REMARK 500 PHE A 105 -35.17 156.02 REMARK 500 THR A 108 -62.50 75.74 REMARK 500 CYS A 110 -22.54 124.97 REMARK 500 PHE A 115 -68.61 -100.56 REMARK 500 THR A 118 -97.63 -72.13 REMARK 500 LEU A 119 -60.56 -16.69 REMARK 500 VAL A 130 -71.14 -82.72 REMARK 500 ILE A 133 17.35 109.39 REMARK 500 ARG A 135 -77.82 -67.47 REMARK 500 TYR A 136 -126.56 73.47 REMARK 500 VAL A 139 39.34 -67.97 REMARK 500 CYS A 140 46.66 -177.99 REMARK 500 ASN A 145 -11.32 -153.11 REMARK 500 PHE A 146 9.68 89.99 REMARK 500 ARG A 147 -63.50 -96.93 REMARK 500 ASN A 151 159.79 56.57 REMARK 500 HIS A 152 30.14 21.35 REMARK 500 ALA A 153 -25.41 -153.42 REMARK 500 PRO A 170 -99.95 -77.17 REMARK 500 PRO A 171 -81.66 47.39 REMARK 500 TYR A 178 100.33 106.28 REMARK 500 ILE A 179 36.30 71.25 REMARK 500 PRO A 180 -66.38 46.01 REMARK 500 GLU A 181 29.34 -65.95 REMARK 500 GLN A 184 -60.81 -137.40 REMARK 500 CYS A 187 88.45 -69.80 REMARK 500 ASP A 190 31.80 -151.69 REMARK 500 GLU A 197 27.10 -154.76 REMARK 500 SER A 202 66.42 -156.28 REMARK 500 TYR A 206 -45.36 -134.67 REMARK 500 MET A 207 51.71 -114.77 REMARK 500 PHE A 208 -86.59 -92.60 REMARK 500 VAL A 209 -51.62 46.61 REMARK 500 PHE A 212 30.93 -145.07 REMARK 500 ILE A 213 -72.43 -93.07 REMARK 500 PRO A 215 59.33 -155.09 REMARK 500 LEU A 216 -90.00 78.77 REMARK 500 PHE A 220 -84.17 -65.49 REMARK 500 PHE A 221 59.64 -99.14 REMARK 500 VAL A 227 -3.04 -162.07 REMARK 500 PHE A 228 45.71 -87.93 REMARK 500 THR A 229 -16.32 -144.35 REMARK 500 GLU A 232 41.24 -152.62 REMARK 500 ALA A 235 42.78 142.45 REMARK 500 GLN A 238 13.64 -162.28 REMARK 500 SER A 240 -2.83 175.17 REMARK 500 THR A 242 58.38 165.26 REMARK 500 GLN A 244 -38.73 101.72 REMARK 500 LYS A 245 -118.96 -102.25 REMARK 500 LYS A 248 -50.63 164.96 REMARK 500 VAL A 250 -40.45 -18.27 REMARK 500 ARG A 252 -5.16 -56.41 REMARK 500 MET A 253 -77.28 -1.16 REMARK 500 ILE A 259 60.47 -108.93 REMARK 500 ALA A 260 -24.42 -155.18 REMARK 500 PHE A 261 -78.51 -52.49 REMARK 500 TRP A 265 39.97 -93.84 REMARK 500 VAL A 271 47.71 -81.88 REMARK 500 ALA A 272 -38.72 -149.15 REMARK 500 TYR A 274 52.48 -102.67 REMARK 500 HIS A 278 -10.16 88.46 REMARK 500 PHE A 287 91.47 81.53 REMARK 500 MET A 288 80.83 89.95 REMARK 500 ILE A 290 -75.39 91.84 REMARK 500 PRO A 291 -19.98 -48.40 REMARK 500 ALA A 295 41.54 -97.27 REMARK 500 LYS A 296 -21.74 -142.08 REMARK 500 ASN A 302 -61.74 -91.89 REMARK 500 ILE A 307 22.77 40.58 REMARK 500 MET A 308 -23.96 -141.12 REMARK 500 MET A 309 -53.20 61.37 REMARK 500 ASN A 310 -36.16 -161.96 REMARK 500 PHE A 313 12.89 -152.49 REMARK 500 ARG A 314 82.12 -175.49 REMARK 500 CYS A 316 -119.83 178.00 REMARK 500 MET A 317 156.50 65.43 REMARK 500 VAL A 318 -158.83 142.76 REMARK 500 THR A 320 99.18 -166.58 REMARK 500 LEU A 321 -107.82 -165.74 REMARK 500 CYS A 323 14.85 56.91 REMARK 500 LYS A 325 32.86 -168.27 REMARK 500 ASN A 326 -28.65 178.24 REMARK 500 LEU A 328 -101.92 -90.01 REMARK 500 ASP A 330 111.29 -174.63 REMARK 500 ASP A 331 -155.42 -141.04 REMARK 500 ALA A 333 -159.08 -144.08 REMARK 500 SER A 334 -143.52 36.42 REMARK 500 THR A 335 -32.69 137.38 REMARK 500 THR A 336 120.04 175.00 REMARK 500 VAL A 337 -32.47 103.33 REMARK 500 LYS A 339 146.73 151.73 REMARK 500 GLU A 341 -165.52 -175.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 42 TYR A 43 121.11 REMARK 500 PHE A 45 LEU A 46 85.35 REMARK 500 LEU A 46 LEU A 47 -146.69 REMARK 500 LEU A 47 ILE A 48 127.20 REMARK 500 MET A 49 LEU A 50 74.50 REMARK 500 PHE A 52 PRO A 53 -35.61 REMARK 500 PRO A 53 ILE A 54 145.87 REMARK 500 ILE A 54 ASN A 55 148.30 REMARK 500 TYR A 60 VAL A 61 -131.15 REMARK 500 VAL A 61 THR A 62 114.72 REMARK 500 THR A 62 VAL A 63 149.87 REMARK 500 LYS A 67 LEU A 68 134.84 REMARK 500 LEU A 72 ASN A 73 125.89 REMARK 500 LEU A 79 ALA A 80 143.85 REMARK 500 ASP A 83 LEU A 84 133.37 REMARK 500 PHE A 88 GLY A 89 55.03 REMARK 500 PHE A 91 THR A 92 -143.95 REMARK 500 THR A 93 THR A 94 107.71 REMARK 500 THR A 94 LEU A 95 144.57 REMARK 500 THR A 97 SER A 98 -136.40 REMARK 500 SER A 98 LEU A 99 88.94 REMARK 500 LEU A 99 HIS A 100 -132.32 REMARK 500 HIS A 100 GLY A 101 36.74 REMARK 500 TYR A 102 PHE A 103 -56.35 REMARK 500 PHE A 103 VAL A 104 -80.11 REMARK 500 PHE A 105 GLY A 106 -80.74 REMARK 500 PRO A 107 THR A 108 145.43 REMARK 500 ALA A 117 THR A 118 149.98 REMARK 500 LEU A 131 ALA A 132 -141.37 REMARK 500 ALA A 132 ILE A 133 -49.42 REMARK 500 ILE A 133 GLU A 134 132.15 REMARK 500 GLU A 134 ARG A 135 139.56 REMARK 500 ARG A 135 TYR A 136 76.93 REMARK 500 VAL A 137 VAL A 138 77.15 REMARK 500 CYS A 140 LYS A 141 37.67 REMARK 500 LYS A 141 PRO A 142 144.17 REMARK 500 MET A 143 SER A 144 -105.50 REMARK 500 PHE A 146 ARG A 147 103.88 REMARK 500 ARG A 147 PHE A 148 -94.54 REMARK 500 PHE A 148 GLY A 149 121.13 REMARK 500 GLY A 149 GLU A 150 130.26 REMARK 500 ASN A 151 HIS A 152 67.47 REMARK 500 ALA A 153 ILE A 154 122.39 REMARK 500 ALA A 166 CYS A 167 145.45 REMARK 500 CYS A 167 ALA A 168 144.20 REMARK 500 PRO A 170 PRO A 171 145.41 REMARK 500 SER A 176 ARG A 177 148.79 REMARK 500 CYS A 185 SER A 186 -140.96 REMARK 500 SER A 186 CYS A 187 -47.69 REMARK 500 CYS A 187 GLY A 188 -144.92 REMARK 500 ILE A 189 ASP A 190 44.07 REMARK 500 ASP A 190 TYR A 191 146.67 REMARK 500 TYR A 192 THR A 193 88.95 REMARK 500 PRO A 194 HIS A 195 66.20 REMARK 500 GLU A 197 THR A 198 99.88 REMARK 500 THR A 198 ASN A 199 -138.30 REMARK 500 SER A 202 PHE A 203 106.45 REMARK 500 VAL A 204 ILE A 205 81.05 REMARK 500 MET A 207 PHE A 208 82.63 REMARK 500 VAL A 210 HIS A 211 -145.68 REMARK 500 PRO A 215 LEU A 216 -46.47 REMARK 500 ILE A 219 PHE A 220 72.32 REMARK 500 PHE A 220 PHE A 221 -111.57 REMARK 500 PHE A 221 CYS A 222 105.95 REMARK 500 CYS A 222 TYR A 223 140.55 REMARK 500 TYR A 223 GLY A 224 148.17 REMARK 500 GLY A 224 GLN A 225 148.39 REMARK 500 LEU A 226 VAL A 227 141.27 REMARK 500 VAL A 227 PHE A 228 121.29 REMARK 500 PHE A 228 THR A 229 145.70 REMARK 500 GLU A 232 ALA A 233 105.48 REMARK 500 ALA A 233 ALA A 234 141.20 REMARK 500 ALA A 235 GLN A 236 99.21 REMARK 500 GLN A 238 GLU A 239 121.19 REMARK 500 SER A 240 ALA A 241 135.75 REMARK 500 ALA A 241 THR A 242 141.77 REMARK 500 GLU A 249 VAL A 250 131.73 REMARK 500 ARG A 252 MET A 253 138.54 REMARK 500 MET A 253 VAL A 254 -149.51 REMARK 500 VAL A 258 ILE A 259 121.26 REMARK 500 ALA A 260 PHE A 261 125.60 REMARK 500 LEU A 262 ILE A 263 -144.24 REMARK 500 CYS A 264 TRP A 265 -145.66 REMARK 500 TRP A 265 LEU A 266 139.76 REMARK 500 TYR A 274 ILE A 275 99.34 REMARK 500 PHE A 276 THR A 277 127.47 REMARK 500 HIS A 278 GLN A 279 -136.86 REMARK 500 SER A 281 ASP A 282 47.89 REMARK 500 GLY A 284 PRO A 285 31.17 REMARK 500 ILE A 286 PHE A 287 -146.41 REMARK 500 PHE A 287 MET A 288 -127.67 REMARK 500 MET A 308 MET A 309 90.27 REMARK 500 MET A 309 ASN A 310 -100.56 REMARK 500 ASN A 310 LYS A 311 141.10 REMARK 500 GLN A 312 PHE A 313 144.81 REMARK 500 ARG A 314 ASN A 315 49.33 REMARK 500 CYS A 316 MET A 317 -140.78 REMARK 500 THR A 320 LEU A 321 58.59 REMARK 500 CYS A 323 GLY A 324 41.03 REMARK 500 ASN A 326 PRO A 327 -58.26 REMARK 500 PRO A 327 LEU A 328 149.31 REMARK 500 ASP A 331 GLU A 332 44.40 REMARK 500 GLU A 341 THR A 342 -62.58 REMARK 500 SER A 343 GLN A 344 -128.09 REMARK 500 GLN A 344 VAL A 345 -84.82 REMARK 500 ALA A 346 PRO A 347 -143.48 REMARK 500 PRO A 347 ALA A 348 -30.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 136 0.22 SIDE_CHAIN REMARK 500 TYR A 178 0.44 SIDE_CHAIN REMARK 500 PHE A 203 0.13 SIDE_CHAIN REMARK 500 HIS A 211 0.11 SIDE_CHAIN REMARK 500 TYR A 268 0.13 SIDE_CHAIN REMARK 500 TYR A 301 0.09 SIDE_CHAIN REMARK 500 PHE A 313 0.43 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 THR A 198 10.40 REMARK 500 VAL A 258 -11.66 REMARK 500 ILE A 290 -10.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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: (11X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 CYS A 110 115.2 ALPHA-CARBON REMARK 500 CYS A 140 88.2 ALPHA-CARBON REMARK 500 TYR A 191 133.4 ALPHA-CARBON REMARK 500 THR A 242 125.0 ALPHA-CARBON REMARK 500 THR A 335 119.1 ALPHA-CARBON 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 RET A 400
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EDS RELATED DB: PDB REMARK 900 RELATED ID: 1EDV RELATED DB: PDB REMARK 900 RELATED ID: 1EDW RELATED DB: PDB REMARK 900 RELATED ID: 1EDX RELATED DB: PDB REMARK 900 RELATED ID: 1FDF RELATED DB: PDB
DBREF 1JFP A 1 348 UNP P02699 OPSD_BOVIN 1 348
SEQRES 1 A 348 MET ASN GLY THR GLU GLY PRO ASN PHE TYR VAL PRO PHE SEQRES 2 A 348 SER ASN LYS THR GLY VAL VAL ARG SER PRO PHE GLU ALA SEQRES 3 A 348 PRO GLN TYR TYR LEU ALA GLU PRO TRP GLN PHE SER MET SEQRES 4 A 348 LEU ALA ALA TYR MET PHE LEU LEU ILE MET LEU GLY PHE SEQRES 5 A 348 PRO ILE ASN PHE LEU THR LEU TYR VAL THR VAL GLN HIS SEQRES 6 A 348 LYS LYS LEU ARG THR PRO LEU ASN TYR ILE LEU LEU ASN SEQRES 7 A 348 LEU ALA VAL ALA ASP LEU PHE MET VAL PHE GLY GLY PHE SEQRES 8 A 348 THR THR THR LEU TYR THR SER LEU HIS GLY TYR PHE VAL SEQRES 9 A 348 PHE GLY PRO THR GLY CYS ASN LEU GLU GLY PHE PHE ALA SEQRES 10 A 348 THR LEU GLY GLY GLU ILE ALA LEU TRP SER LEU VAL VAL SEQRES 11 A 348 LEU ALA ILE GLU ARG TYR VAL VAL VAL CYS LYS PRO MET SEQRES 12 A 348 SER ASN PHE ARG PHE GLY GLU ASN HIS ALA ILE MET GLY SEQRES 13 A 348 VAL ALA PHE THR TRP VAL MET ALA LEU ALA CYS ALA ALA SEQRES 14 A 348 PRO PRO LEU VAL GLY TRP SER ARG TYR ILE PRO GLU GLY SEQRES 15 A 348 MET GLN CYS SER CYS GLY ILE ASP TYR TYR THR PRO HIS SEQRES 16 A 348 GLU GLU THR ASN ASN GLU SER PHE VAL ILE TYR MET PHE SEQRES 17 A 348 VAL VAL HIS PHE ILE ILE PRO LEU ILE VAL ILE PHE PHE SEQRES 18 A 348 CYS TYR GLY GLN LEU VAL PHE THR VAL LYS GLU ALA ALA SEQRES 19 A 348 ALA GLN GLN GLN GLU SER ALA THR THR GLN LYS ALA GLU SEQRES 20 A 348 LYS GLU VAL THR ARG MET VAL ILE ILE MET VAL ILE ALA SEQRES 21 A 348 PHE LEU ILE CYS TRP LEU PRO TYR ALA GLY VAL ALA PHE SEQRES 22 A 348 TYR ILE PHE THR HIS GLN GLY SER ASP PHE GLY PRO ILE SEQRES 23 A 348 PHE MET THR ILE PRO ALA PHE PHE ALA LYS THR SER ALA SEQRES 24 A 348 VAL TYR ASN PRO VAL ILE TYR ILE MET MET ASN LYS GLN SEQRES 25 A 348 PHE ARG ASN CYS MET VAL THR THR LEU CYS CYS GLY LYS SEQRES 26 A 348 ASN PRO LEU GLY ASP ASP GLU ALA SER THR THR VAL SER SEQRES 27 A 348 LYS THR GLU THR SER GLN VAL ALA PRO ALA
HET RET A 400 48
HETNAM RET RETINAL
FORMUL 2 RET C20 H28 O
HELIX 1 1 TYR A 43 ILE A 48 1 6 HELIX 2 2 THR A 70 ASN A 73 5 4 HELIX 3 3 TYR A 74 LEU A 79 1 6 HELIX 4 4 PHE A 85 PHE A 91 1 7 HELIX 5 5 THR A 118 ALA A 132 1 15 HELIX 6 6 THR A 160 ALA A 164 5 5 HELIX 7 7 ALA A 168 SER A 176 1 9 HELIX 8 8 HIS A 195 ASN A 200 1 6 HELIX 9 9 ILE A 213 VAL A 218 1 6 HELIX 10 10 LYS A 248 VAL A 250 5 3 HELIX 11 11 THR A 251 VAL A 258 1 8 HELIX 12 12 PHE A 261 LEU A 266 1 6 HELIX 13 13 LEU A 266 THR A 277 1 12
SSBOND 1 CYS A 110 CYS A 187 1555 1555 2.05
LINK CD1 LEU A 125 C1 RET A 400 1555 1555 2.05 LINK CD2 LEU A 125 C2 RET A 400 1555 1555 1.94 LINK CD1 LEU A 125 C16 RET A 400 1555 1555 0.90 LINK CG LEU A 125 C16 RET A 400 1555 1555 1.47 LINK NZ LYS A 296 C15 RET A 400 1555 1555 1.28
CISPEP 1 ARG A 69 THR A 70 0 11.35 CISPEP 2 GLY A 106 PRO A 107 0 -22.81 CISPEP 3 CYS A 110 ASN A 111 0 -19.94 CISPEP 4 ILE A 179 PRO A 180 0 15.52 CISPEP 5 VAL A 218 ILE A 219 0 8.50 CISPEP 6 PRO A 285 ILE A 286 0 -14.50 CISPEP 7 MET A 288 THR A 289 0 11.71 CISPEP 8 TYR A 306 ILE A 307 0 5.77 CISPEP 9 VAL A 337 SER A 338 0 23.76
SITE 1 AC1 8 GLU A 113 GLY A 121 GLU A 122 LEU A 125 SITE 2 AC1 8 PHE A 208 PHE A 212 ALA A 295 LYS A 296
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000