data_5L8M # _model_server_result.job_id YnqDeHQ6wifRbTRBAFeIUg _model_server_result.datetime_utc '2024-11-07 23:37:56' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5l8m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5L8M # _exptl.entry_id 5L8M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 585.67 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 92.6 _cell.angle_gamma 90 _cell.entry_id 5L8M _cell.length_a 94.1 _cell.length_b 54.8 _cell.length_c 69.9 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5L8M _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D 1 1 A,B,C,D 1 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 38 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 24 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id CBA _struct_conn.ptnr2_label_comp_id LBV _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id LBV _struct_conn.ptnr2_auth_seq_id 401 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 1.611 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C33 H37 N4 O6 1' _chem_comp.formula_weight 585.67 _chem_comp.id LBV _chem_comp.mon_nstd_flag . _chem_comp.name '3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '2(R),3(E)- PHYTOCHROMOBILIN' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1A N_A LBV sing 179 n n C1A C2A LBV sing 180 n n C1B C2B LBV doub 181 n y C1B CHB LBV sing 182 n n O1B CGB LBV doub 183 n n C1C CHC LBV doub 184 z n C1D CHD LBV doub 185 z n C2A CMA LBV sing 186 n n C2A C3A LBV sing 187 n n C2B CMB LBV sing 188 n n C2C C1C LBV sing 189 n n O2C CGC LBV doub 190 n n C2D C1D LBV sing 191 n n C2D CMD LBV sing 192 n n C3A CAA LBV doub 193 e n C3B C2B LBV sing 194 n y C3B CAB LBV sing 195 n n C3C C2C LBV doub 196 n n C3C C4C LBV sing 197 n n C3D C2D LBV doub 198 n n C4A C3A LBV sing 199 n n C4A CHB LBV doub 200 z n C4B C3B LBV doub 201 n y C4B N_B LBV sing 202 n y C4C N_C LBV doub 203 n n C4D C3D LBV sing 204 n n C4D N_D LBV sing 205 n n CAA CBA LBV sing 206 n n CAC C2C LBV sing 207 n n CAC CBC LBV sing 208 n n CAD C3D LBV sing 209 n n CBB CAB LBV sing 210 n n CBB CGB LBV sing 211 n n CBD CAD LBV doub 212 n n CGB O2B LBV sing 213 n n CGC O1C LBV sing 214 n n CGC CBC LBV sing 215 n n CHC C4B LBV sing 216 n n CHD C4C LBV sing 217 n n CMC C3C LBV sing 218 n n N_A C4A LBV sing 219 n n O_A C1A LBV doub 220 n n N_B C1B LBV sing 221 n y N_C C1C LBV sing 222 n n N_D C1D LBV sing 223 n n O_D C4D LBV doub 224 n n O1C HO1C LBV sing 225 n n C2A H2A LBV sing 226 n n O2B HO2B LBV sing 227 n n CAA HAA1 LBV sing 228 n n CAB HAB1 LBV sing 229 n n CAB HAB2 LBV sing 230 n n CAC HAC1 LBV sing 231 n n CAC HAC2 LBV sing 232 n n CAD HAD1 LBV sing 233 n n CBA HBA1 LBV sing 234 n n CBA HBA2 LBV sing 235 n n CBA HBA3 LBV sing 236 n n CBB HBB1 LBV sing 237 n n CBB HBB2 LBV sing 238 n n CBC HBC1 LBV sing 239 n n CBC HBC2 LBV sing 240 n n CBD HBD1 LBV sing 241 n n CBD HBD2 LBV sing 242 n n CHB HHB1 LBV sing 243 n n CHC HHC1 LBV sing 244 n n CHD HHD1 LBV sing 245 n n CMA HMA1 LBV sing 246 n n CMA HMA2 LBV sing 247 n n CMA HMA3 LBV sing 248 n n CMB HMB1 LBV sing 249 n n CMB HMB2 LBV sing 250 n n CMB HMB3 LBV sing 251 n n CMC HMC1 LBV sing 252 n n CMC HMC2 LBV sing 253 n n CMC HMC3 LBV sing 254 n n CMD HMD1 LBV sing 255 n n CMD HMD2 LBV sing 256 n n CMD HMD3 LBV sing 257 n n N_A HAD LBV sing 258 n n N_B HAE LBV sing 259 n n N_C HAF LBV sing 260 n n N_D HAG LBV sing 261 n n # _atom_sites.entry_id 5L8M _atom_sites.fract_transf_matrix[1][1] 0.010627 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000483 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018248 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.014321 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 LBV A 1 401 405 LBV LBV . C 3 ACT A 1 402 1 ACT ACT . D 4 HOH A 1 501 168 HOH HOH . D 4 HOH A 2 502 149 HOH HOH . D 4 HOH A 3 503 156 HOH HOH . D 4 HOH A 4 504 47 HOH HOH . D 4 HOH A 5 505 147 HOH HOH . D 4 HOH A 6 506 179 HOH HOH . D 4 HOH A 7 507 188 HOH HOH . D 4 HOH A 8 508 142 HOH HOH . D 4 HOH A 9 509 218 HOH HOH . D 4 HOH A 10 510 49 HOH HOH . D 4 HOH A 11 511 197 HOH HOH . D 4 HOH A 12 512 219 HOH HOH . D 4 HOH A 13 513 112 HOH HOH . D 4 HOH A 14 514 62 HOH HOH . D 4 HOH A 15 515 136 HOH HOH . D 4 HOH A 16 516 199 HOH HOH . D 4 HOH A 17 517 148 HOH HOH . D 4 HOH A 18 518 141 HOH HOH . D 4 HOH A 19 519 93 HOH HOH . D 4 HOH A 20 520 169 HOH HOH . D 4 HOH A 21 521 35 HOH HOH . D 4 HOH A 22 522 270 HOH HOH . D 4 HOH A 23 523 85 HOH HOH . D 4 HOH A 24 524 269 HOH HOH . D 4 HOH A 25 525 252 HOH HOH . D 4 HOH A 26 526 145 HOH HOH . D 4 HOH A 27 527 174 HOH HOH . D 4 HOH A 28 528 95 HOH HOH . D 4 HOH A 29 529 129 HOH HOH . D 4 HOH A 30 530 6 HOH HOH . D 4 HOH A 31 531 143 HOH HOH . D 4 HOH A 32 532 8 HOH HOH . D 4 HOH A 33 533 144 HOH HOH . D 4 HOH A 34 534 58 HOH HOH . D 4 HOH A 35 535 12 HOH HOH . D 4 HOH A 36 536 61 HOH HOH . D 4 HOH A 37 537 66 HOH HOH . D 4 HOH A 38 538 25 HOH HOH . D 4 HOH A 39 539 21 HOH HOH . D 4 HOH A 40 540 150 HOH HOH . D 4 HOH A 41 541 163 HOH HOH . D 4 HOH A 42 542 30 HOH HOH . D 4 HOH A 43 543 236 HOH HOH . D 4 HOH A 44 544 181 HOH HOH . D 4 HOH A 45 545 59 HOH HOH . D 4 HOH A 46 546 137 HOH HOH . D 4 HOH A 47 547 82 HOH HOH . D 4 HOH A 48 548 164 HOH HOH . D 4 HOH A 49 549 64 HOH HOH . D 4 HOH A 50 550 75 HOH HOH . D 4 HOH A 51 551 31 HOH HOH . D 4 HOH A 52 552 131 HOH HOH . D 4 HOH A 53 553 146 HOH HOH . D 4 HOH A 54 554 26 HOH HOH . D 4 HOH A 55 555 29 HOH HOH . D 4 HOH A 56 556 221 HOH HOH . D 4 HOH A 57 557 152 HOH HOH . D 4 HOH A 58 558 194 HOH HOH . D 4 HOH A 59 559 193 HOH HOH . D 4 HOH A 60 560 56 HOH HOH . D 4 HOH A 61 561 160 HOH HOH . D 4 HOH A 62 562 134 HOH HOH . D 4 HOH A 63 563 140 HOH HOH . D 4 HOH A 64 564 36 HOH HOH . D 4 HOH A 65 565 3 HOH HOH . D 4 HOH A 66 566 248 HOH HOH . D 4 HOH A 67 567 267 HOH HOH . D 4 HOH A 68 568 27 HOH HOH . D 4 HOH A 69 569 86 HOH HOH . D 4 HOH A 70 570 247 HOH HOH . D 4 HOH A 71 571 130 HOH HOH . D 4 HOH A 72 572 57 HOH HOH . D 4 HOH A 73 573 227 HOH HOH . D 4 HOH A 74 574 51 HOH HOH . D 4 HOH A 75 575 186 HOH HOH . D 4 HOH A 76 576 200 HOH HOH . D 4 HOH A 77 577 139 HOH HOH . D 4 HOH A 78 578 151 HOH HOH . D 4 HOH A 79 579 63 HOH HOH . D 4 HOH A 80 580 138 HOH HOH . D 4 HOH A 81 581 220 HOH HOH . D 4 HOH A 82 582 244 HOH HOH . D 4 HOH A 83 583 268 HOH HOH . D 4 HOH A 84 584 70 HOH HOH . D 4 HOH A 85 585 16 HOH HOH . D 4 HOH A 86 586 135 HOH HOH . D 4 HOH A 87 587 191 HOH HOH . D 4 HOH A 88 588 120 HOH HOH . D 4 HOH A 89 589 97 HOH HOH . D 4 HOH A 90 590 183 HOH HOH . D 4 HOH A 91 591 154 HOH HOH . D 4 HOH A 92 592 245 HOH HOH . D 4 HOH A 93 593 155 HOH HOH . D 4 HOH A 94 594 11 HOH HOH . D 4 HOH A 95 595 109 HOH HOH . D 4 HOH A 96 596 239 HOH HOH . D 4 HOH A 97 597 260 HOH HOH . D 4 HOH A 98 598 258 HOH HOH . D 4 HOH A 99 599 94 HOH HOH . D 4 HOH A 100 600 40 HOH HOH . D 4 HOH A 101 601 52 HOH HOH . D 4 HOH A 102 602 111 HOH HOH . D 4 HOH A 103 603 242 HOH HOH . D 4 HOH A 104 604 241 HOH HOH . D 4 HOH A 105 605 53 HOH HOH . D 4 HOH A 106 606 196 HOH HOH . D 4 HOH A 107 607 190 HOH HOH . D 4 HOH A 108 608 118 HOH HOH . D 4 HOH A 109 609 84 HOH HOH . D 4 HOH A 110 610 273 HOH HOH . D 4 HOH A 111 611 170 HOH HOH . D 4 HOH A 112 612 228 HOH HOH . D 4 HOH A 113 613 246 HOH HOH . D 4 HOH A 114 614 271 HOH HOH . D 4 HOH A 115 615 213 HOH HOH . D 4 HOH A 116 616 226 HOH HOH . D 4 HOH A 117 617 272 HOH HOH . D 4 HOH A 118 618 104 HOH HOH . D 4 HOH A 119 619 132 HOH HOH . D 4 HOH A 120 620 133 HOH HOH . D 4 HOH A 121 621 110 HOH HOH . D 4 HOH A 122 622 45 HOH HOH . D 4 HOH A 123 623 162 HOH HOH . D 4 HOH A 124 624 153 HOH HOH . D 4 HOH A 125 625 178 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1A LBV . . . B 2 -7.51 16.599 3.853 1 34.01 ? C1A LBV 401 A 1 HETATM 2 C C1B LBV . . . B 2 -7.942 18.775 7.778 1 27.15 ? C1B LBV 401 A 1 HETATM 3 O O1B LBV . . . B 2 -8.81 24.053 11.338 1 25.83 ? O1B LBV 401 A 1 HETATM 4 C C1C LBV . . . B 2 -12.499 19.117 7.919 1 24.95 ? C1C LBV 401 A 1 HETATM 5 O O1C LBV . . . B 2 -15.159 22.826 7.278 1 24.39 ? O1C LBV 401 A 1 HETATM 6 C C1D LBV . . . B 2 -14.903 17.136 4.342 1 27.53 ? C1D LBV 401 A 1 HETATM 7 C C2A LBV . . . B 2 -6.023 16.22 3.926 1 35.21 ? C2A LBV 401 A 1 HETATM 8 C C2B LBV . . . B 2 -7.767 19.527 8.944 1 27.02 ? C2B LBV 401 A 1 HETATM 9 O O2B LBV . . . B 2 -10.583 23.049 12.147 1 26.59 ? O2B LBV 401 A 1 HETATM 10 C C2C LBV . . . B 2 -13.837 19.34 8.223 1 24.35 ? C2C LBV 401 A 1 HETATM 11 O O2C LBV . . . B 2 -16.573 21.883 8.631 1 24.97 ? O2C LBV 401 A 1 HETATM 12 C C2D LBV . . . B 2 -15.202 16.083 3.475 1 29.15 ? C2D LBV 401 A 1 HETATM 13 C C3A LBV . . . B 2 -5.68 16.802 5.237 1 35.24 ? C3A LBV 401 A 1 HETATM 14 C C3B LBV . . . B 2 -9.027 19.888 9.371 1 26.17 ? C3B LBV 401 A 1 HETATM 15 C C3C LBV . . . B 2 -14.616 18.644 7.29 1 24.81 ? C3C LBV 401 A 1 HETATM 16 C C3D LBV . . . B 2 -16.27 16.505 2.709 1 29.22 ? C3D LBV 401 A 1 HETATM 17 C C4A LBV . . . B 2 -6.801 17.435 5.873 1 31.73 ? C4A LBV 401 A 1 HETATM 18 C C4B LBV . . . B 2 -9.952 19.39 8.475 1 25.66 ? C4B LBV 401 A 1 HETATM 19 C C4C LBV . . . B 2 -13.697 18.033 6.431 1 24.91 ? C4C LBV 401 A 1 HETATM 20 C C4D LBV . . . B 2 -16.573 17.808 3.133 1 28.42 ? C4D LBV 401 A 1 HETATM 21 C CAA LBV . . . B 2 -4.378 17.175 5.548 1 38.24 ? CAA LBV 401 A 1 HETATM 22 C CAB LBV . . . B 2 -9.334 20.731 10.559 1 26.31 ? CAB LBV 401 A 1 HETATM 23 C CAC LBV . . . B 2 -14.326 20.187 9.377 1 25.3 ? CAC LBV 401 A 1 HETATM 24 C CAD LBV . . . B 2 -16.925 15.679 1.636 1 30.22 ? CAD LBV 401 A 1 HETATM 25 C CBA LBV . . . B 2 -3.185 16.327 5.222 1 41.32 ? CBA LBV 401 A 1 HETATM 26 C CBB LBV . . . B 2 -9.642 22.158 10.166 1 26.03 ? CBB LBV 401 A 1 HETATM 27 C CBC LBV . . . B 2 -14.295 21.674 9.169 1 24.29 ? CBC LBV 401 A 1 HETATM 28 C CBD LBV . . . B 2 -18.169 15.996 1.145 1 32.16 ? CBD LBV 401 A 1 HETATM 29 C CGB LBV . . . B 2 -9.679 23.147 11.278 1 25.54 ? CGB LBV 401 A 1 HETATM 30 C CGC LBV . . . B 2 -15.399 22.166 8.313 1 24.75 ? CGC LBV 401 A 1 HETATM 31 C CHB LBV . . . B 2 -6.749 18.184 7.044 1 28.74 ? CHB LBV 401 A 1 HETATM 32 C CHC LBV . . . B 2 -11.433 19.664 8.653 1 25.99 ? CHC LBV 401 A 1 HETATM 33 C CHD LBV . . . B 2 -13.869 17.099 5.249 1 25.87 ? CHD LBV 401 A 1 HETATM 34 C CMA LBV . . . B 2 -5.371 16.93 2.786 1 35.39 ? CMA LBV 401 A 1 HETATM 35 C CMB LBV . . . B 2 -6.484 19.868 9.631 1 26.96 ? CMB LBV 401 A 1 HETATM 36 C CMC LBV . . . B 2 -16.107 18.601 7.256 1 25.16 ? CMC LBV 401 A 1 HETATM 37 C CMD LBV . . . B 2 -14.521 14.754 3.404 1 29.98 ? CMD LBV 401 A 1 HETATM 38 N N_A LBV . . . B 2 -7.919 17.33 5.058 1 33.21 ? N_A LBV 401 A 1 HETATM 39 O O_A LBV . . . B 2 -8.283 16.364 2.944 1 36.88 ? O_A LBV 401 A 1 HETATM 40 N N_B LBV . . . B 2 -9.284 18.716 7.517 1 26.65 ? N_B LBV 401 A 1 HETATM 41 N N_C LBV . . . B 2 -12.456 18.326 6.834 1 24.96 ? N_C LBV 401 A 1 HETATM 42 N N_D LBV . . . B 2 -15.73 18.157 4.113 1 28.39 ? N_D LBV 401 A 1 HETATM 43 O O_D LBV . . . B 2 -17.428 18.548 2.705 1 28.71 ? O_D LBV 401 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 236 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 43 #