PDB Short entry for 1BAD HEADER PHOTORECEPTOR 30-JUL-92 1BAD TITLE AN ENERGY-BASED APPROACH TO PACKING THE 7-HELIX BUNDLE OF TITLE 2 BACTERIORHODOPSIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIORHODOPSIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS PHOTORECEPTOR EXPDTA THEORETICAL MODEL AUTHOR K.C.CHOU,L.CARLACCI,G.M.MAGGIORA,L.A.PARODI,M.W.SCHULZ REVDAT 2 01-APR-03 1BAD 1 JRNL REVDAT 1 31-JAN-94 1BAD 0 JRNL AUTH K.C.CHOU,L.CARLACCI,G.M.MAGGIORA,L.A.PARODI, JRNL AUTH 2 M.W.SCHULZ JRNL TITL AN ENERGY-BASED APPROACH TO PACKING THE 7-HELIX JRNL TITL 2 BUNDLE OF BACTERIORHODOPSIN. JRNL REF PROTEIN SCI. V. 1 810 1992 JRNL REFN ASTM PRCIEI US ISSN 0961-8368 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.CARLACCI,M.W.SCHULZ,K.-C.CHOU REMARK 1 TITL GEOMETRIC AND ENERGY PARAMETERS IN LYSINE-RETINAL REMARK 1 TITL 2 CHROMOPHORES REMARK 1 REF PROTEIN ENG. V. 4 885 1991 REMARK 1 REFN ASTM PRENE9 UK ISSN 0269-2139 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.HENDERSON,J.M.BALDWIN,T.A.CESKA,F.ZEMLIN, REMARK 1 AUTH 2 E.BECKMANN,K.H.DOWNING REMARK 1 TITL MODEL FOR THE STRUCTURE OF BACTERIORHODOPSIN BASED REMARK 1 TITL 2 ON HIGH-RESOLUTION ELECTRON CRYO-MICROSCOPY REMARK 1 REF J.MOL.BIOL. V. 213 899 1990 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 3 REMARK 1 AUTH K.-C.CHOU,G.NEMETHY,H.A.SCHERAGA REMARK 1 TITL ENERGETIC APPROACH TO THE PACKING OF REMARK 1 TITL 2 ALPHA-HELICES. 2. GENERAL TREATMENT OF REMARK 1 TITL 3 NONEQUIVALENT AND NONREGULAR HELICES REMARK 1 REF J.AM.CHEM.SOC. V. 106 3161 1984 REMARK 1 REFN ASTM JACSAT US ISSN 0002-7863 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BAD COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 THIS STRUCTURE WAS GENERATED WITH RESIDUE 111 SPECIFIED AS REMARK 5 ILE. GENE SEQUENCING HAS SHOWN THAT THIS RESIDUE SHOULD BE REMARK 5 LEU. THIS HAS BEEN CORRECTED IN THIS ENTRY BY RENAMING REMARK 5 RESIDUE 111 AS LEU AND REMOVING THE SIDE CHAIN ATOMS BEYOND REMARK 5 CB. REMARK 6 REMARK 6 PCA IS PYRROLIDONE CARBOXYLIC ACID. REMARK 7 REMARK 7 RET 216 IN HELIX G IS THE 13-CIS RETINAL-LYSINE WITH REMARK 7 UNPROTONATED SCHIFF BASE (PROTEIN ENGINEERING, VOL. 4, REMARK 7 PP. 885-889, 1991). REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS. 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 PCA A 1 REMARK 465 ALA A 2 REMARK 465 GLN A 3 REMARK 465 ILE A 4 REMARK 465 THR A 5 REMARK 465 GLY A 6 REMARK 465 ARG A 7 REMARK 465 PRO A 8 REMARK 465 GLY A 33 REMARK 465 VAL A 34 REMARK 465 SER A 35 REMARK 465 ASP A 36 REMARK 465 PRO A 37 REMARK 465 GLY A 63 REMARK 465 TYR A 64 REMARK 465 GLY A 65 REMARK 465 LEU A 66 REMARK 465 THR A 67 REMARK 465 MET A 68 REMARK 465 VAL A 69 REMARK 465 PRO A 70 REMARK 465 PHE A 71 REMARK 465 GLY A 72 REMARK 465 GLY A 73 REMARK 465 VAL A 101 REMARK 465 ASP A 102 REMARK 465 ALA A 103 REMARK 465 ASP A 104 REMARK 465 GLN A 105 REMARK 465 THR A 128 REMARK 465 LYS A 129 REMARK 465 VAL A 130 REMARK 465 TYR A 131 REMARK 465 SER A 132 REMARK 465 TYR A 133 REMARK 465 ARG A 134 REMARK 465 PHE A 135 REMARK 465 VAL A 136 REMARK 465 SER A 158 REMARK 465 LYS A 159 REMARK 465 ALA A 160 REMARK 465 GLU A 161 REMARK 465 SER A 162 REMARK 465 MET A 163 REMARK 465 ARG A 164 REMARK 465 PRO A 165 REMARK 465 GLY A 192 REMARK 465 SER A 193 REMARK 465 GLU A 194 REMARK 465 GLY A 195 REMARK 465 ALA A 196 REMARK 465 GLY A 197 REMARK 465 ILE A 198 REMARK 465 VAL A 199 REMARK 465 PRO A 200 REMARK 465 LEU A 201 REMARK 465 SER A 226 REMARK 465 ARG A 227 REMARK 465 ALA A 228 REMARK 465 ILE A 229 REMARK 465 PHE A 230 REMARK 465 GLY A 231 REMARK 465 GLU A 232 REMARK 465 ALA A 233 REMARK 465 GLU A 234 REMARK 465 ALA A 235 REMARK 465 PRO A 236 REMARK 465 GLU A 237 REMARK 465 PRO A 238 REMARK 465 SER A 239 REMARK 465 ALA A 240 REMARK 465 GLY A 241 REMARK 465 ASP A 242 REMARK 465 GLY A 243 REMARK 465 ALA A 244 REMARK 465 ALA A 245 REMARK 465 ALA A 246 REMARK 465 THR A 247 REMARK 465 SER A 248 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 LEU A 111 CG CD1 CD2 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 VAL A 49 PRO A 50 -125.01 REMARK 500 THR A 90 PRO A 91 -149.03 DBREF 1BAD A 2 248 UNP P02945 BACR_HALHA 15 261 SEQRES 1 A 248 PCA ALA GLN ILE THR GLY ARG PRO GLU TRP ILE TRP LEU SEQRES 2 A 248 ALA LEU GLY THR ALA LEU MET GLY LEU GLY THR LEU TYR SEQRES 3 A 248 PHE LEU VAL LYS GLY MET GLY VAL SER ASP PRO ASP ALA SEQRES 4 A 248 LYS LYS PHE TYR ALA ILE THR THR LEU VAL PRO ALA ILE SEQRES 5 A 248 ALA PHE THR MET TYR LEU SER MET LEU LEU GLY TYR GLY SEQRES 6 A 248 LEU THR MET VAL PRO PHE GLY GLY GLU GLN ASN PRO ILE SEQRES 7 A 248 TYR TRP ALA ARG TYR ALA ASP TRP LEU PHE THR THR PRO SEQRES 8 A 248 LEU LEU LEU LEU ASP LEU ALA LEU LEU VAL ASP ALA ASP SEQRES 9 A 248 GLN GLY THR ILE LEU ALA LEU VAL GLY ALA ASP GLY ILE SEQRES 10 A 248 MET ILE GLY THR GLY LEU VAL GLY ALA LEU THR LYS VAL SEQRES 11 A 248 TYR SER TYR ARG PHE VAL TRP TRP ALA ILE SER THR ALA SEQRES 12 A 248 ALA MET LEU TYR ILE LEU TYR VAL LEU PHE PHE GLY PHE SEQRES 13 A 248 THR SER LYS ALA GLU SER MET ARG PRO GLU VAL ALA SER SEQRES 14 A 248 THR PHE LYS VAL LEU ARG ASN VAL THR VAL VAL LEU TRP SEQRES 15 A 248 SER ALA TYR PRO VAL VAL TRP LEU ILE GLY SER GLU GLY SEQRES 16 A 248 ALA GLY ILE VAL PRO LEU ASN ILE GLU THR LEU LEU PHE SEQRES 17 A 248 MET VAL LEU ASP VAL SER ALA LYS VAL GLY PHE GLY LEU SEQRES 18 A 248 ILE LEU LEU ARG SER ARG ALA ILE PHE GLY GLU ALA GLU SEQRES 19 A 248 ALA PRO GLU PRO SER ALA GLY ASP GLY ALA ALA ALA THR SEQRES 20 A 248 SER FTNOTE 1 VAL 49 - PRO 50 OMEGA = 234.99 PEPTIDE BOND DEVIATES FTNOTE 1 SIGNIFICANTLY FROM TRANS CONFORMATION FTNOTE 2 THR 90 - PRO 91 OMEGA = 210.97 PEPTIDE BOND DEVIATES FTNOTE 2 SIGNIFICANTLY FROM TRANS CONFORMATION HET RET 216 20 HETNAM RET RETINAL FORMUL 2 RET C20 H28 O HELIX 1 A GLU A 9 MET A 32 1 24 HELIX 2 B ASP A 38 LEU A 62 1 25 HELIX 3 C GLU A 74 LEU A 100 1 27 HELIX 4 D GLY A 106 LEU A 127 1 22 HELIX 5 E TRP A 137 THR A 157 1 21 HELIX 6 F GLU A 166 ILE A 191 1 26 HELIX 7 G ASN A 202 ARG A 225 1 24 LINK NZ LYS A 216 C15 RET 216 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