data_9F9E # _model_server_result.job_id iq2PBX7dM46_KcluBb6VtQ _model_server_result.datetime_utc '2025-01-22 16:47:48' _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 9f9e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":316}' # _entry.id 9F9E # _exptl.entry_id 9F9E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description RETINAL _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 90 _cell.angle_gamma 120 _cell.entry_id 9F9E _cell.length_a 62.95 _cell.length_b 62.95 _cell.length_c 111.7 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9F9E _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id Q _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 NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 212 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 216 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id Q _struct_conn.ptnr2_label_atom_id C15 _struct_conn.ptnr2_label_comp_id RET _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id RET _struct_conn.ptnr2_auth_seq_id 316 _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 1.341 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C20 H28 O' _chem_comp.formula_weight 284.436 _chem_comp.id RET _chem_comp.mon_nstd_flag . _chem_comp.name RETINAL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C1 C2 RET sing 437 n n C1 C6 RET sing 438 n n C1 C16 RET sing 439 n n C1 C17 RET sing 440 n n C2 C3 RET sing 441 n n C2 H21 RET sing 442 n n C2 H22 RET sing 443 n n C3 C4 RET sing 444 n n C3 H31 RET sing 445 n n C3 H32 RET sing 446 n n C4 C5 RET sing 447 n n C4 H41 RET sing 448 n n C4 H42 RET sing 449 n n C5 C6 RET doub 450 n n C5 C18 RET sing 451 n n C6 C7 RET sing 452 n n C7 C8 RET doub 453 e n C7 H7 RET sing 454 n n C8 C9 RET sing 455 n n C8 H8 RET sing 456 n n C9 C10 RET doub 457 e n C9 C19 RET sing 458 n n C10 C11 RET sing 459 n n C10 H10 RET sing 460 n n C11 C12 RET doub 461 e n C11 H11 RET sing 462 n n C12 C13 RET sing 463 n n C12 H12 RET sing 464 n n C13 C14 RET doub 465 e n C13 C20 RET sing 466 n n C14 C15 RET sing 467 n n C14 H14 RET sing 468 n n C15 O1 RET doub 469 n n C15 H15 RET sing 470 n n C16 H161 RET sing 471 n n C16 H162 RET sing 472 n n C16 H163 RET sing 473 n n C17 H171 RET sing 474 n n C17 H172 RET sing 475 n n C17 H173 RET sing 476 n n C18 H181 RET sing 477 n n C18 H182 RET sing 478 n n C18 H183 RET sing 479 n n C19 H191 RET sing 480 n n C19 H192 RET sing 481 n n C19 H193 RET sing 482 n n C20 H201 RET sing 483 n n C20 H202 RET sing 484 n n C20 H203 RET sing 485 n n # _atom_sites.entry_id 9F9E _atom_sites.fract_transf_matrix[1][1] 0.015886 _atom_sites.fract_transf_matrix[1][2] 0.009172 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018343 _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] 0.008953 _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 LI1 A 1 301 302 LI1 LI1 . C 2 LI1 A 1 302 303 LI1 LI1 . D 2 LI1 A 1 303 305 LI1 LI1 . E 2 LI1 A 1 304 306 LI1 LI1 . F 2 LI1 A 1 305 307 LI1 LI1 . G 2 LI1 A 1 306 308 LI1 LI1 . H 3 OLC A 1 307 309 OLC OLC . I 3 OLC A 1 308 310 OLC OLC . J 3 OLC A 1 309 311 OLC OLC . K 3 OLC A 1 310 312 OLC OLC . L 2 LI1 A 1 311 313 LI1 LI1 . M 2 LI1 A 1 312 314 LI1 LI1 . N 2 LI1 A 1 313 315 LI1 LI1 . O 2 LI1 A 1 314 316 LI1 LI1 . P 2 LI1 A 1 315 317 LI1 LI1 . Q 4 RET A 1 316 216 RET LYR . R 5 HOH A 1 401 431 HOH HOH . R 5 HOH A 2 402 457 HOH HOH . R 5 HOH A 3 403 442 HOH HOH . R 5 HOH A 4 404 433 HOH HOH . R 5 HOH A 5 405 425 HOH HOH . R 5 HOH A 6 406 403 HOH HOH . R 5 HOH A 7 407 413 HOH HOH . R 5 HOH A 8 408 434 HOH HOH . R 5 HOH A 9 409 432 HOH HOH . R 5 HOH A 10 410 450 HOH HOH . R 5 HOH A 11 411 409 HOH HOH . R 5 HOH A 12 412 475 HOH HOH . R 5 HOH A 13 413 411 HOH HOH . R 5 HOH A 14 414 421 HOH HOH . R 5 HOH A 15 415 439 HOH HOH . R 5 HOH A 16 416 410 HOH HOH . R 5 HOH A 17 417 400 HOH HOH . R 5 HOH A 18 418 480 HOH HOH . R 5 HOH A 19 419 407 HOH HOH . R 5 HOH A 20 420 420 HOH HOH . R 5 HOH A 21 421 477 HOH HOH . R 5 HOH A 22 422 414 HOH HOH . R 5 HOH A 23 423 456 HOH HOH . R 5 HOH A 24 424 469 HOH HOH . R 5 HOH A 25 425 441 HOH HOH . R 5 HOH A 26 426 451 HOH HOH . R 5 HOH A 27 427 402 HOH HOH . R 5 HOH A 28 428 423 HOH HOH . R 5 HOH A 29 429 430 HOH HOH . R 5 HOH A 30 430 478 HOH HOH . R 5 HOH A 31 431 404 HOH HOH . R 5 HOH A 32 432 415 HOH HOH . R 5 HOH A 33 433 418 HOH HOH . R 5 HOH A 34 434 416 HOH HOH . R 5 HOH A 35 435 412 HOH HOH . R 5 HOH A 36 436 427 HOH HOH . R 5 HOH A 37 437 401 HOH HOH . R 5 HOH A 38 438 422 HOH HOH . R 5 HOH A 39 439 467 HOH HOH . R 5 HOH A 40 440 417 HOH HOH . R 5 HOH A 41 441 419 HOH HOH . R 5 HOH A 42 442 436 HOH HOH . R 5 HOH A 43 443 426 HOH HOH . R 5 HOH A 44 444 476 HOH HOH . R 5 HOH A 45 445 464 HOH HOH . R 5 HOH A 46 446 440 HOH HOH . R 5 HOH A 47 447 429 HOH HOH . R 5 HOH A 48 448 428 HOH HOH . R 5 HOH A 49 449 470 HOH HOH . R 5 HOH A 50 450 438 HOH HOH . R 5 HOH A 51 451 481 HOH HOH . R 5 HOH A 52 452 446 HOH HOH . R 5 HOH A 53 453 424 HOH HOH . R 5 HOH A 54 454 466 HOH HOH . R 5 HOH A 55 455 444 HOH HOH . R 5 HOH A 56 456 479 HOH HOH . R 5 HOH A 57 457 462 HOH HOH . R 5 HOH A 58 458 459 HOH HOH . R 5 HOH A 59 459 455 HOH HOH . R 5 HOH A 60 460 448 HOH HOH . R 5 HOH A 61 461 445 HOH HOH . R 5 HOH A 62 462 443 HOH HOH . R 5 HOH A 63 463 449 HOH HOH . R 5 HOH A 64 464 454 HOH HOH . R 5 HOH A 65 465 472 HOH HOH . R 5 HOH A 66 466 447 HOH HOH . R 5 HOH A 67 467 463 HOH HOH . R 5 HOH A 68 468 465 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 C1 RET . . . Q 4 15.04 46.671 29.606 1 12.09 ? C1 RET 316 A 1 HETATM 2 C C2 RET . . . Q 4 14.598 47.631 28.487 1 16.72 ? C2 RET 316 A 1 HETATM 3 C C3 RET . . . Q 4 15.309 48.975 28.517 1 26.57 ? C3 RET 316 A 1 HETATM 4 C C4 RET . . . Q 4 15.063 49.674 29.837 1 11.07 ? C4 RET 316 A 1 HETATM 5 C C5 RET . . . Q 4 15.159 48.759 31.027 1 8.98 ? C5 RET 316 A 1 HETATM 6 C C6 RET . . . Q 4 15.343 47.433 30.902 1 9.74 ? C6 RET 316 A 1 HETATM 7 C C7 RET . . . Q 4 15.959 46.667 31.995 1 13.44 ? C7 RET 316 A 1 HETATM 8 C C8 RET . . . Q 4 15.861 45.382 32.347 1 15.36 ? C8 RET 316 A 1 HETATM 9 C C9 RET . . . Q 4 16.451 44.768 33.526 1 7.76 ? C9 RET 316 A 1 HETATM 10 C C10 RET . . . Q 4 16.644 43.426 33.559 1 12.09 ? C10 RET 316 A 1 HETATM 11 C C11 RET . . . Q 4 17.412 42.698 34.522 1 17.01 ? C11 RET 316 A 1 HETATM 12 C C12 RET . . . Q 4 17.548 41.364 34.625 1 13.48 ? C12 RET 316 A 1 HETATM 13 C C13 RET . . . Q 4 18.411 40.677 35.577 1 21.7 ? C13 RET 316 A 1 HETATM 14 C C14 RET . . . Q 4 18.672 39.357 35.416 1 26.7 ? C14 RET 316 A 1 HETATM 15 C C15 RET . . . Q 4 17.86 38.185 35.155 1 24.15 ? C15 RET 316 A 1 HETATM 16 C C16 RET . . . Q 4 16.282 45.906 29.133 1 20.94 ? C16 RET 316 A 1 HETATM 17 C C17 RET . . . Q 4 13.891 45.679 29.82 1 11.68 ? C17 RET 316 A 1 HETATM 18 C C18 RET . . . Q 4 15.206 49.503 32.332 1 11.18 ? C18 RET 316 A 1 HETATM 19 C C19 RET . . . Q 4 17.031 45.681 34.571 1 10.32 ? C19 RET 316 A 1 HETATM 20 C C20 RET . . . Q 4 19.268 41.534 36.464 1 19.87 ? C20 RET 316 A 1 HETATM 21 H H21 RET . . . Q 4 14.752 47.221 27.612 1 20.07 ? H21 RET 316 A 1 HETATM 22 H H22 RET . . . Q 4 13.634 47.792 28.545 1 20.07 ? H22 RET 316 A 1 HETATM 23 H H31 RET . . . Q 4 14.997 49.539 27.781 1 31.89 ? H31 RET 316 A 1 HETATM 24 H H32 RET . . . Q 4 16.271 48.851 28.384 1 31.89 ? H32 RET 316 A 1 HETATM 25 H H41 RET . . . Q 4 14.174 50.084 29.83 1 13.28 ? H41 RET 316 A 1 HETATM 26 H H42 RET . . . Q 4 15.71 50.4 29.949 1 13.28 ? H42 RET 316 A 1 HETATM 27 H H7 RET . . . Q 4 16.77 47.119 32.304 1 16.13 ? H7 RET 316 A 1 HETATM 28 H H8 RET . . . Q 4 15.7 44.758 31.61 1 18.43 ? H8 RET 316 A 1 HETATM 29 H H10 RET . . . Q 4 16.222 42.887 32.859 1 14.5 ? H10 RET 316 A 1 HETATM 30 H H11 RET . . . Q 4 18.161 43.2 34.903 1 20.41 ? H11 RET 316 A 1 HETATM 31 H H12 RET . . . Q 4 17.029 40.802 34.015 1 16.17 ? H12 RET 316 A 1 HETATM 32 H H14 RET . . . Q 4 19.609 39.083 35.482 1 32.04 ? H14 RET 316 A 1 HETATM 33 H H15 RET . . . Q 4 16.903 38.294 34.978 1 28.98 ? H15 RET 316 A 1 HETATM 34 H H161 RET . . . Q 4 16.149 45.502 28.251 1 25.13 ? H161 RET 316 A 1 HETATM 35 H H162 RET . . . Q 4 17.066 46.488 29.065 1 25.13 ? H162 RET 316 A 1 HETATM 36 H H163 RET . . . Q 4 16.519 45.18 29.746 1 25.13 ? H163 RET 316 A 1 HETATM 37 H H171 RET . . . Q 4 13.308 45.973 30.55 1 14.02 ? H171 RET 316 A 1 HETATM 38 H H172 RET . . . Q 4 14.234 44.791 30.046 1 14.02 ? H172 RET 316 A 1 HETATM 39 H H173 RET . . . Q 4 13.345 45.597 29.012 1 14.02 ? H173 RET 316 A 1 HETATM 40 H H181 RET . . . Q 4 14.841 50.41 32.282 1 13.42 ? H181 RET 316 A 1 HETATM 41 H H182 RET . . . Q 4 16.11 49.616 32.689 1 13.42 ? H182 RET 316 A 1 HETATM 42 H H183 RET . . . Q 4 14.704 49.07 33.052 1 13.42 ? H183 RET 316 A 1 HETATM 43 H H191 RET . . . Q 4 17.959 45.902 34.351 1 12.39 ? H191 RET 316 A 1 HETATM 44 H H192 RET . . . Q 4 16.515 46.512 34.62 1 12.39 ? H192 RET 316 A 1 HETATM 45 H H193 RET . . . Q 4 17.012 45.249 35.449 1 12.39 ? H193 RET 316 A 1 HETATM 46 H H201 RET . . . Q 4 18.743 42.244 36.887 1 23.84 ? H201 RET 316 A 1 HETATM 47 H H202 RET . . . Q 4 19.68 41.006 37.178 1 23.84 ? H202 RET 316 A 1 HETATM 48 H H203 RET . . . Q 4 19.989 41.961 35.958 1 23.84 ? H203 RET 316 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 48 #