data_5J7A # _model_server_result.job_id Oh2-HtBNwRVeDBfI8mLtDw _model_server_result.datetime_utc '2024-11-08 03:40:16' _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 5j7a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5J7A # _exptl.entry_id 5J7A _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 5J7A _cell.length_a 62 _cell.length_b 62 _cell.length_c 110 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5J7A _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 _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 _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 31 53.693575 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 -31 53.693575 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 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 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 1.296 _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 5J7A _atom_sites.fract_transf_matrix[1][1] 0.016129 _atom_sites.fract_transf_matrix[1][2] 0.009312 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018624 _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] 0.009091 _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 1 302 615 LI1 LI1 . D 3 LI1 A 1 303 616 LI1 LI1 . E 3 LI1 A 1 304 617 LI1 LI1 . F 3 LI1 A 1 305 618 LI1 LI1 . G 3 LI1 A 1 306 619 LI1 LI1 . H 4 HOH A 1 401 402 HOH HOH . H 4 HOH A 2 402 415 HOH HOH . H 4 HOH A 3 403 406 HOH HOH . H 4 HOH A 4 404 404 HOH HOH . H 4 HOH A 5 405 401 HOH HOH . H 4 HOH A 6 406 403 HOH HOH . H 4 HOH A 7 407 407 HOH HOH . H 4 HOH A 8 408 411 HOH HOH . H 4 HOH A 9 409 515 HOH HOH . H 4 HOH A 10 410 517 HOH HOH . H 4 HOH A 11 411 414 HOH HOH . H 4 HOH A 12 412 501 HOH HOH . H 4 HOH A 13 413 405 HOH HOH . H 4 HOH A 14 414 413 HOH HOH . H 4 HOH A 15 415 514 HOH HOH . H 4 HOH A 16 416 516 HOH HOH . H 4 HOH A 17 417 412 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 15.055 46.039 29.078 1 31.3 ? C1 RET 301 A 1 HETATM 2 C C2 RET . . . B 2 14.955 47.012 27.889 1 31.76 ? C2 RET 301 A 1 HETATM 3 C C3 RET . . . B 2 14.252 48.301 28.24 1 32.12 ? C3 RET 301 A 1 HETATM 4 C C4 RET . . . B 2 15.087 48.998 29.291 1 32.24 ? C4 RET 301 A 1 HETATM 5 C C5 RET . . . B 2 15.125 48.108 30.522 1 31.78 ? C5 RET 301 A 1 HETATM 6 C C6 RET . . . B 2 15.298 46.76 30.422 1 31.3 ? C6 RET 301 A 1 HETATM 7 C C7 RET . . . B 2 15.741 46.042 31.665 1 31.06 ? C7 RET 301 A 1 HETATM 8 C C8 RET . . . B 2 15.991 44.731 31.813 1 30.44 ? C8 RET 301 A 1 HETATM 9 C C9 RET . . . B 2 16.43 44.108 33.087 1 30.44 ? C9 RET 301 A 1 HETATM 10 C C10 RET . . . B 2 16.623 42.777 33.025 1 30.14 ? C10 RET 301 A 1 HETATM 11 C C11 RET . . . B 2 17.068 41.942 34.145 1 30.37 ? C11 RET 301 A 1 HETATM 12 C C12 RET . . . B 2 17.211 40.636 33.908 1 30.18 ? C12 RET 301 A 1 HETATM 13 C C13 RET . . . B 2 17.636 39.643 34.919 1 30.49 ? C13 RET 301 A 1 HETATM 14 C C14 RET . . . B 2 17.73 38.365 34.476 1 30.35 ? C14 RET 301 A 1 HETATM 15 C C15 RET . . . B 2 17.628 37.202 35.342 1 30.48 ? C15 RET 301 A 1 HETATM 16 C C16 RET . . . B 2 13.76 45.226 29.21 1 31.01 ? C16 RET 301 A 1 HETATM 17 C C17 RET . . . B 2 16.248 45.139 28.707 1 31.43 ? C17 RET 301 A 1 HETATM 18 C C18 RET . . . B 2 14.999 48.831 31.838 1 31.97 ? C18 RET 301 A 1 HETATM 19 C C19 RET . . . B 2 16.669 44.846 34.386 1 30.88 ? C19 RET 301 A 1 HETATM 20 C C20 RET . . . B 2 17.954 40.061 36.331 1 31.04 ? C20 RET 301 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 20 #