data_3NSB # _model_server_result.job_id DukpJejSilyGtALTRpXJuQ _model_server_result.datetime_utc '2025-03-29 03:28:28' _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 3nsb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":300}' # _entry.id 3NSB # _exptl.entry_id 3NSB _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 3NSB _cell.length_a 60.995 _cell.length_b 60.995 _cell.length_c 109.991 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NSB _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,I,J,K,L _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 30.4975 52.82322 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 -30.4975 52.82322 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 300 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id A _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id A _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 3NSB _atom_sites.fract_transf_matrix[1][1] 0.016395 _atom_sites.fract_transf_matrix[1][2] 0.009466 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018931 _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] 0.009092 _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 1 300 300 RET RET . C 3 LI1 A 1 1000 1000 LI1 LI1 . D 3 LI1 A 1 1001 1001 LI1 LI1 . E 3 LI1 A 1 1002 1002 LI1 LI1 . F 3 LI1 A 1 1003 1003 LI1 LI1 . G 3 LI1 A 1 1004 1004 LI1 LI1 . H 3 LI1 A 1 1005 1005 LI1 LI1 . I 3 LI1 A 1 1006 1006 LI1 LI1 . J 3 LI1 A 1 1007 1007 LI1 LI1 . K 3 LI1 A 1 1008 1008 LI1 LI1 . L 4 HOH A 1 401 401 HOH HOH . L 4 HOH A 2 402 402 HOH HOH . L 4 HOH A 3 403 403 HOH HOH . L 4 HOH A 4 404 404 HOH HOH . L 4 HOH A 5 405 405 HOH HOH . L 4 HOH A 6 406 406 HOH HOH . L 4 HOH A 7 407 407 HOH HOH . L 4 HOH A 8 408 408 HOH HOH . L 4 HOH A 9 409 409 HOH HOH . L 4 HOH A 10 411 411 HOH HOH . L 4 HOH A 11 412 412 HOH HOH . L 4 HOH A 12 414 414 HOH HOH . L 4 HOH A 13 415 415 HOH HOH . L 4 HOH A 14 416 416 HOH HOH . L 4 HOH A 15 418 418 HOH HOH . L 4 HOH A 16 419 419 HOH HOH . L 4 HOH A 17 420 420 HOH HOH . L 4 HOH A 18 421 421 HOH HOH . L 4 HOH A 19 422 422 HOH HOH . L 4 HOH A 20 423 423 HOH HOH . L 4 HOH A 21 424 424 HOH HOH . L 4 HOH A 22 426 426 HOH HOH . L 4 HOH A 23 427 427 HOH HOH . L 4 HOH A 24 428 428 HOH HOH . L 4 HOH A 25 429 429 HOH HOH . L 4 HOH A 26 430 430 HOH HOH . L 4 HOH A 27 431 431 HOH HOH . L 4 HOH A 28 432 432 HOH HOH . L 4 HOH A 29 433 433 HOH HOH . L 4 HOH A 30 501 501 HOH HOH . L 4 HOH A 31 502 502 HOH HOH . L 4 HOH A 32 511 511 HOH HOH . L 4 HOH A 33 512 512 HOH HOH . L 4 HOH A 34 513 513 HOH HOH . L 4 HOH A 35 514 514 HOH HOH . L 4 HOH A 36 521 521 HOH HOH . L 4 HOH A 37 522 522 HOH HOH . L 4 HOH A 38 523 523 HOH HOH . L 4 HOH A 39 525 525 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 . A . B 2 -1.39 17.078 60.432 0.65 18.42 ? C1 RET 300 A 1 HETATM 2 C C1 RET . B . B 2 -1.043 17.417 60.346 0.35 20.02 ? C1 RET 300 A 1 HETATM 3 C C2 RET . A . B 2 -2.343 16.755 61.592 0.65 19.41 ? C2 RET 300 A 1 HETATM 4 C C2 RET . B . B 2 -1.931 17.215 61.563 0.35 22.73 ? C2 RET 300 A 1 HETATM 5 C C3 RET . A . B 2 -3.78 16.616 61.249 0.65 21.09 ? C3 RET 300 A 1 HETATM 6 C C3 RET . B . B 2 -3.372 17.182 61.287 0.35 23.4 ? C3 RET 300 A 1 HETATM 7 C C4 RET . A . B 2 -4.042 15.693 60.073 0.65 18.4 ? C4 RET 300 A 1 HETATM 8 C C4 RET . B . B 2 -3.748 16.186 60.192 0.35 23.88 ? C4 RET 300 A 1 HETATM 9 C C5 RET . A . B 2 -3.118 15.92 58.868 0.65 18.96 ? C5 RET 300 A 1 HETATM 10 C C5 RET . B . B 2 -2.868 16.246 58.936 0.35 20.77 ? C5 RET 300 A 1 HETATM 11 C C6 RET . A . B 2 -1.881 16.519 59.036 0.65 18 ? C6 RET 300 A 1 HETATM 12 C C6 RET . B . B 2 -1.598 16.764 59.027 0.35 21.63 ? C6 RET 300 A 1 HETATM 13 C C7 RET . A . B 2 -1.103 16.637 57.785 0.65 16.93 ? C7 RET 300 A 1 HETATM 14 C C7 RET . B . B 2 -0.841 16.751 57.783 0.35 17.95 ? C7 RET 300 A 1 HETATM 15 C C8 RET . A . B 2 0.169 17.073 57.567 0.65 17.37 ? C8 RET 300 A 1 HETATM 16 C C8 RET . B . B 2 0.421 17.202 57.542 0.35 18.04 ? C8 RET 300 A 1 HETATM 17 C C9 RET . A . B 2 0.955 16.918 56.354 0.65 16.57 ? C9 RET 300 A 1 HETATM 18 C C9 RET . B . B 2 1.14 17.139 56.311 0.35 19.89 ? C9 RET 300 A 1 HETATM 19 C C10 RET . A . B 2 2.161 17.562 56.421 0.65 17.95 ? C10 RET 300 A 1 HETATM 20 C C10 RET . B . B 2 2.373 17.72 56.396 0.35 20.77 ? C10 RET 300 A 1 HETATM 21 C C11 RET . A . B 2 3.192 17.391 55.37 0.65 15.63 ? C11 RET 300 A 1 HETATM 22 C C11 RET . B . B 2 3.362 17.521 55.323 0.35 23.59 ? C11 RET 300 A 1 HETATM 23 C C12 RET . A . B 2 4.409 17.961 55.696 0.65 18.29 ? C12 RET 300 A 1 HETATM 24 C C12 RET . B . B 2 4.601 18.128 55.531 0.35 25.42 ? C12 RET 300 A 1 HETATM 25 C C13 RET . A . B 2 5.49 18.051 54.712 0.65 19.62 ? C13 RET 300 A 1 HETATM 26 C C13 RET . B . B 2 5.619 18.188 54.443 0.35 26.98 ? C13 RET 300 A 1 HETATM 27 C C14 RET . A . B 2 6.545 18.709 55.28 0.65 18.55 ? C14 RET 300 A 1 HETATM 28 C C14 RET . B . B 2 6.912 18.691 54.382 0.35 25.87 ? C14 RET 300 A 1 HETATM 29 C C15 RET . A . B 2 7.777 19.25 54.721 0.65 19.98 ? C15 RET 300 A 1 HETATM 30 C C15 RET . B . B 2 7.819 19.124 55.464 0.35 27.96 ? C15 RET 300 A 1 HETATM 31 C C16 RET . A . B 2 -1.245 18.649 60.351 0.65 19.56 ? C16 RET 300 A 1 HETATM 32 C C16 RET . B . B 2 -0.913 18.977 60.144 0.35 19.73 ? C16 RET 300 A 1 HETATM 33 C C17 RET . A . B 2 -0.026 16.449 60.969 0.65 17.6 ? C17 RET 300 A 1 HETATM 34 C C17 RET . B . B 2 0.324 16.782 60.846 0.35 17.94 ? C17 RET 300 A 1 HETATM 35 C C18 RET . A . B 2 -3.778 15.379 57.637 0.65 16.11 ? C18 RET 300 A 1 HETATM 36 C C18 RET . B . B 2 -3.634 15.728 57.742 0.35 23.72 ? C18 RET 300 A 1 HETATM 37 C C19 RET . A . B 2 0.417 16.215 55.141 0.65 18.06 ? C19 RET 300 A 1 HETATM 38 C C19 RET . B . B 2 0.599 16.383 55.116 0.35 16.94 ? C19 RET 300 A 1 HETATM 39 C C20 RET . A . B 2 5.516 17.57 53.301 0.65 17.74 ? C20 RET 300 A 1 HETATM 40 C C20 RET . B . B 2 5.3 17.672 53.078 0.35 24.27 ? C20 RET 300 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 40 #