data_6JYD # _model_server_result.job_id 3y6tXk7vs-m0PAYjCEIgpQ _model_server_result.datetime_utc '2024-11-23 02:18:29' _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 6jyd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 6JYD # _exptl.entry_id 6JYD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 2 _entity.src_method syn _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 110.03 _cell.angle_gamma 90 _cell.entry_id 6JYD _cell.length_a 102.783 _cell.length_b 49.285 _cell.length_c 69.334 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JYD _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 PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_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 _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 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 NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 251 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 235 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _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 301 _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 1.351 _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 330 n n C1 C6 RET sing 331 n n C1 C16 RET sing 332 n n C1 C17 RET sing 333 n n C2 C3 RET sing 334 n n C2 H21 RET sing 335 n n C2 H22 RET sing 336 n n C3 C4 RET sing 337 n n C3 H31 RET sing 338 n n C3 H32 RET sing 339 n n C4 C5 RET sing 340 n n C4 H41 RET sing 341 n n C4 H42 RET sing 342 n n C5 C6 RET doub 343 n n C5 C18 RET sing 344 n n C6 C7 RET sing 345 n n C7 C8 RET doub 346 e n C7 H7 RET sing 347 n n C8 C9 RET sing 348 n n C8 H8 RET sing 349 n n C9 C10 RET doub 350 e n C9 C19 RET sing 351 n n C10 C11 RET sing 352 n n C10 H10 RET sing 353 n n C11 C12 RET doub 354 e n C11 H11 RET sing 355 n n C12 C13 RET sing 356 n n C12 H12 RET sing 357 n n C13 C14 RET doub 358 e n C13 C20 RET sing 359 n n C14 C15 RET sing 360 n n C14 H14 RET sing 361 n n C15 O1 RET doub 362 n n C15 H15 RET sing 363 n n C16 H161 RET sing 364 n n C16 H162 RET sing 365 n n C16 H163 RET sing 366 n n C17 H171 RET sing 367 n n C17 H172 RET sing 368 n n C17 H173 RET sing 369 n n C18 H181 RET sing 370 n n C18 H182 RET sing 371 n n C18 H183 RET sing 372 n n C19 H191 RET sing 373 n n C19 H192 RET sing 374 n n C19 H193 RET sing 375 n n C20 H201 RET sing 376 n n C20 H202 RET sing 377 n n C20 H203 RET sing 378 n n # _atom_sites.entry_id 6JYD _atom_sites.fract_transf_matrix[1][1] 0.009729 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003547 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02029 _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] 0.015351 _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 RET A 1 301 301 RET RET . C 3 CL A 1 302 1 CL CL . D 3 CL A 1 303 2 CL CL . E 4 OLA A 1 304 1 OLA OLA . F 4 OLA A 1 305 2 OLA OLA . G 4 OLA A 1 306 3 OLA OLA . H 4 OLA A 1 307 4 OLA OLA . I 4 OLA A 1 308 5 OLA OLA . J 4 OLA A 1 309 6 OLA OLA . K 4 OLA A 1 310 7 OLA OLA . L 4 OLA A 1 311 8 OLA OLA . M 4 OLA A 1 312 9 OLA OLA . N 4 OLA A 1 313 10 OLA OLA . O 4 OLA A 1 314 11 OLA OLA . P 5 HOH A 1 401 1 HOH HOH . P 5 HOH A 2 402 43 HOH HOH . P 5 HOH A 3 403 21 HOH HOH . P 5 HOH A 4 404 5 HOH HOH . P 5 HOH A 5 405 47 HOH HOH . P 5 HOH A 6 406 4 HOH HOH . P 5 HOH A 7 407 75 HOH HOH . P 5 HOH A 8 408 29 HOH HOH . P 5 HOH A 9 409 27 HOH HOH . P 5 HOH A 10 410 57 HOH HOH . P 5 HOH A 11 411 23 HOH HOH . P 5 HOH A 12 412 31 HOH HOH . P 5 HOH A 13 413 42 HOH HOH . P 5 HOH A 14 414 24 HOH HOH . P 5 HOH A 15 415 37 HOH HOH . P 5 HOH A 16 416 59 HOH HOH . P 5 HOH A 17 417 79 HOH HOH . P 5 HOH A 18 418 69 HOH HOH . P 5 HOH A 19 419 26 HOH HOH . P 5 HOH A 20 420 7 HOH HOH . P 5 HOH A 21 421 13 HOH HOH . P 5 HOH A 22 422 20 HOH HOH . P 5 HOH A 23 423 32 HOH HOH . P 5 HOH A 24 424 76 HOH HOH . P 5 HOH A 25 425 60 HOH HOH . P 5 HOH A 26 426 14 HOH HOH . P 5 HOH A 27 427 9 HOH HOH . P 5 HOH A 28 428 34 HOH HOH . P 5 HOH A 29 429 63 HOH HOH . P 5 HOH A 30 430 25 HOH HOH . P 5 HOH A 31 431 74 HOH HOH . P 5 HOH A 32 432 36 HOH HOH . P 5 HOH A 33 433 78 HOH HOH . P 5 HOH A 34 434 55 HOH HOH . P 5 HOH A 35 435 10 HOH HOH . P 5 HOH A 36 436 46 HOH HOH . P 5 HOH A 37 437 6 HOH HOH . P 5 HOH A 38 438 22 HOH HOH . P 5 HOH A 39 439 19 HOH HOH . P 5 HOH A 40 440 3 HOH HOH . P 5 HOH A 41 441 52 HOH HOH . P 5 HOH A 42 442 12 HOH HOH . P 5 HOH A 43 443 28 HOH HOH . P 5 HOH A 44 444 2 HOH HOH . P 5 HOH A 45 445 40 HOH HOH . P 5 HOH A 46 446 41 HOH HOH . P 5 HOH A 47 447 62 HOH HOH . P 5 HOH A 48 448 61 HOH HOH . P 5 HOH A 49 449 18 HOH HOH . P 5 HOH A 50 450 65 HOH HOH . P 5 HOH A 51 451 70 HOH HOH . P 5 HOH A 52 452 39 HOH HOH . P 5 HOH A 53 453 16 HOH HOH . P 5 HOH A 54 454 87 HOH HOH . P 5 HOH A 55 455 72 HOH HOH . P 5 HOH A 56 456 44 HOH HOH . P 5 HOH A 57 457 68 HOH HOH . P 5 HOH A 58 458 45 HOH HOH . P 5 HOH A 59 459 49 HOH HOH . P 5 HOH A 60 460 67 HOH HOH . P 5 HOH A 61 461 15 HOH HOH . P 5 HOH A 62 462 33 HOH HOH . P 5 HOH A 63 463 77 HOH HOH . P 5 HOH A 64 464 17 HOH HOH . P 5 HOH A 65 465 11 HOH HOH . P 5 HOH A 66 466 50 HOH HOH . P 5 HOH A 67 467 85 HOH HOH . P 5 HOH A 68 468 66 HOH HOH . P 5 HOH A 69 469 8 HOH HOH . P 5 HOH A 70 470 30 HOH HOH . P 5 HOH A 71 471 56 HOH HOH . P 5 HOH A 72 472 53 HOH HOH . P 5 HOH A 73 473 64 HOH HOH . P 5 HOH A 74 474 84 HOH HOH . P 5 HOH A 75 475 88 HOH HOH . P 5 HOH A 76 476 35 HOH HOH . P 5 HOH A 77 477 73 HOH HOH . P 5 HOH A 78 478 58 HOH HOH . P 5 HOH A 79 479 48 HOH HOH . P 5 HOH A 80 480 80 HOH HOH . P 5 HOH A 81 481 83 HOH HOH . P 5 HOH A 82 482 54 HOH HOH . P 5 HOH A 83 483 51 HOH HOH . P 5 HOH A 84 484 38 HOH HOH . P 5 HOH A 85 485 82 HOH HOH . P 5 HOH A 86 486 71 HOH HOH . P 5 HOH A 87 487 86 HOH HOH . P 5 HOH A 88 488 81 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 . . . B 2 -20.363 -15.482 5.229 1 26.54 ? C1 RET 301 A 1 HETATM 2 C C2 RET . . . B 2 -21.082 -14.5 6.144 1 19.74 ? C2 RET 301 A 1 HETATM 3 C C3 RET . . . B 2 -22.588 -14.683 6.072 1 16.53 ? C3 RET 301 A 1 HETATM 4 C C4 RET . . . B 2 -23.063 -14.294 4.683 1 19.7 ? C4 RET 301 A 1 HETATM 5 C C5 RET . . . B 2 -22.185 -14.894 3.606 1 20.72 ? C5 RET 301 A 1 HETATM 6 C C6 RET . . . B 2 -21.018 -15.517 3.846 1 18.11 ? C6 RET 301 A 1 HETATM 7 C C7 RET . . . B 2 -20.426 -16.245 2.685 1 21.19 ? C7 RET 301 A 1 HETATM 8 C C8 RET . . . B 2 -19.537 -17.237 2.796 1 17.3 ? C8 RET 301 A 1 HETATM 9 C C9 RET . . . B 2 -18.959 -17.989 1.67 1 22.93 ? C9 RET 301 A 1 HETATM 10 C C10 RET . . . B 2 -17.875 -18.737 1.922 1 20.39 ? C10 RET 301 A 1 HETATM 11 C C11 RET . . . B 2 -17.207 -19.566 0.924 1 21.29 ? C11 RET 301 A 1 HETATM 12 C C12 RET . . . B 2 -16.284 -20.403 1.392 1 17.35 ? C12 RET 301 A 1 HETATM 13 C C13 RET . . . B 2 -15.52 -21.338 0.552 1 25.72 ? C13 RET 301 A 1 HETATM 14 C C14 RET . . . B 2 -14.603 -22.117 1.145 1 23.11 ? C14 RET 301 A 1 HETATM 15 C C15 RET . . . B 2 -13.817 -23.076 0.379 1 25.23 ? C15 RET 301 A 1 HETATM 16 C C16 RET . . . B 2 -18.902 -15.038 5.154 1 20.03 ? C16 RET 301 A 1 HETATM 17 C C17 RET . . . B 2 -20.447 -16.859 5.886 1 16.89 ? C17 RET 301 A 1 HETATM 18 C C18 RET . . . B 2 -22.691 -14.785 2.194 1 18.87 ? C18 RET 301 A 1 HETATM 19 C C19 RET . . . B 2 -19.591 -17.946 0.308 1 16.22 ? C19 RET 301 A 1 HETATM 20 C C20 RET . . . B 2 -15.788 -21.442 -0.924 1 23.99 ? C20 RET 301 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #