data_1KGB # _model_server_result.job_id -K2XsX6tP7JCSo3hyBOmew _model_server_result.datetime_utc '2024-12-06 11:52:31' _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 1kgb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 1KGB # _exptl.entry_id 1KGB _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 90 _cell.angle_gamma 120 _cell.entry_id 1KGB _cell.length_a 60.987 _cell.length_b 60.987 _cell.length_c 109.131 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KGB _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 PISA,PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 1,2,3 # 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_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 30.4935 52.816291 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -30.4935 52.816291 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 216 _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 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 1.344 _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 373 n n C1 C6 RET sing 374 n n C1 C16 RET sing 375 n n C1 C17 RET sing 376 n n C2 C3 RET sing 377 n n C2 H21 RET sing 378 n n C2 H22 RET sing 379 n n C3 C4 RET sing 380 n n C3 H31 RET sing 381 n n C3 H32 RET sing 382 n n C4 C5 RET sing 383 n n C4 H41 RET sing 384 n n C4 H42 RET sing 385 n n C5 C6 RET doub 386 n n C5 C18 RET sing 387 n n C6 C7 RET sing 388 n n C7 C8 RET doub 389 e n C7 H7 RET sing 390 n n C8 C9 RET sing 391 n n C8 H8 RET sing 392 n n C9 C10 RET doub 393 e n C9 C19 RET sing 394 n n C10 C11 RET sing 395 n n C10 H10 RET sing 396 n n C11 C12 RET doub 397 e n C11 H11 RET sing 398 n n C12 C13 RET sing 399 n n C12 H12 RET sing 400 n n C13 C14 RET doub 401 e n C13 C20 RET sing 402 n n C14 C15 RET sing 403 n n C14 H14 RET sing 404 n n C15 O1 RET doub 405 n n C15 H15 RET sing 406 n n C16 H161 RET sing 407 n n C16 H162 RET sing 408 n n C16 H163 RET sing 409 n n C17 H171 RET sing 410 n n C17 H172 RET sing 411 n n C17 H173 RET sing 412 n n C18 H181 RET sing 413 n n C18 H182 RET sing 414 n n C18 H183 RET sing 415 n n C19 H191 RET sing 416 n n C19 H192 RET sing 417 n n C19 H193 RET sing 418 n n C20 H201 RET sing 419 n n C20 H202 RET sing 420 n n C20 H203 RET sing 421 n n # _atom_sites.entry_id 1KGB _atom_sites.fract_transf_matrix[1][1] 0.016397 _atom_sites.fract_transf_matrix[1][2] 0.009467 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018934 _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] 0.009163 _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 LI1 A 1 601 601 LI1 LI1 . D 3 LI1 A 1 602 602 LI1 LI1 . E 3 LI1 A 1 609 609 LI1 LI1 . F 3 LI1 A 1 610 610 LI1 LI1 . G 3 LI1 A 1 611 611 LI1 LI1 . H 3 LI1 A 1 603 603 LI1 LI1 . I 3 LI1 A 1 612 612 LI1 LI1 . J 3 LI1 A 1 613 613 LI1 LI1 . K 3 LI1 A 1 604 604 LI1 LI1 . L 3 LI1 A 1 605 605 LI1 LI1 . M 3 LI1 A 1 606 606 LI1 LI1 . N 3 LI1 A 1 607 607 LI1 LI1 . O 3 LI1 A 1 608 608 LI1 LI1 . P 4 HOH A 1 401 401 HOH HOH . P 4 HOH A 2 402 402 HOH HOH . P 4 HOH A 3 403 403 HOH HOH . P 4 HOH A 4 404 404 HOH HOH . P 4 HOH A 5 405 405 HOH HOH . P 4 HOH A 6 406 406 HOH HOH . P 4 HOH A 7 407 407 HOH HOH . P 4 HOH A 8 411 411 HOH HOH . P 4 HOH A 9 412 412 HOH HOH . P 4 HOH A 10 413 413 HOH HOH . P 4 HOH A 11 415 415 HOH HOH . P 4 HOH A 12 416 416 HOH HOH . P 4 HOH A 13 417 417 HOH HOH . P 4 HOH A 14 418 418 HOH HOH . P 4 HOH A 15 419 419 HOH HOH . P 4 HOH A 16 420 420 HOH HOH . P 4 HOH A 17 421 421 HOH HOH . P 4 HOH A 18 422 422 HOH HOH . P 4 HOH A 19 423 423 HOH HOH . P 4 HOH A 20 501 501 HOH HOH . P 4 HOH A 21 502 502 HOH HOH . P 4 HOH A 22 511 511 HOH HOH . P 4 HOH A 23 512 512 HOH HOH . P 4 HOH A 24 513 513 HOH HOH . P 4 HOH A 25 514 514 HOH HOH . P 4 HOH A 26 515 515 HOH HOH . P 4 HOH A 27 516 516 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 14.923 45.387 0.214 1 16.21 ? C1 RET 301 A 1 HETATM 2 C C2 RET . . . B 2 14.651 46.244 -1.002 1 21.74 ? C2 RET 301 A 1 HETATM 3 C C3 RET . . . B 2 14.142 47.607 -0.761 1 28.98 ? C3 RET 301 A 1 HETATM 4 C C4 RET . . . B 2 14.919 48.28 0.341 1 20.5 ? C4 RET 301 A 1 HETATM 5 C C5 RET . . . B 2 14.998 47.473 1.605 1 18.85 ? C5 RET 301 A 1 HETATM 6 C C6 RET . . . B 2 15.216 46.122 1.521 1 15.42 ? C6 RET 301 A 1 HETATM 7 C C7 RET . . . B 2 15.55 45.429 2.744 1 13.33 ? C7 RET 301 A 1 HETATM 8 C C8 RET . . . B 2 15.806 44.11 2.949 1 14.11 ? C8 RET 301 A 1 HETATM 9 C C9 RET . . . B 2 16.262 43.455 4.17 1 12.83 ? C9 RET 301 A 1 HETATM 10 C C10 RET . . . B 2 16.432 42.106 4.044 1 17.67 ? C10 RET 301 A 1 HETATM 11 C C11 RET . . . B 2 16.86 41.278 5.18 1 18.98 ? C11 RET 301 A 1 HETATM 12 C C12 RET . . . B 2 17.129 39.968 4.786 1 19.68 ? C12 RET 301 A 1 HETATM 13 C C13 RET . . . B 2 17.57 39.05 5.817 1 13.94 ? C13 RET 301 A 1 HETATM 14 C C14 RET . . . B 2 17.491 37.757 5.328 1 33.49 ? C14 RET 301 A 1 HETATM 15 C C15 RET . . . B 2 17.59 36.536 6.093 1 29.33 ? C15 RET 301 A 1 HETATM 16 C C16 RET . . . B 2 13.699 44.426 0.426 1 16.23 ? C16 RET 301 A 1 HETATM 17 C C17 RET . . . B 2 16.104 44.466 -0.296 1 16.74 ? C17 RET 301 A 1 HETATM 18 C C18 RET . . . B 2 15.169 48.255 2.875 1 17.04 ? C18 RET 301 A 1 HETATM 19 C C19 RET . . . B 2 16.529 44.122 5.463 1 21.36 ? C19 RET 301 A 1 HETATM 20 C C20 RET . . . B 2 17.948 39.4 7.171 1 14.46 ? C20 RET 301 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 20 #