data_5B6V # _model_server_result.job_id cYcIw0cefefmmFoGOZGI6w _model_server_result.datetime_utc '2024-11-23 01:39:14' _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 5b6v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":300}' # _entry.id 5B6V # _exptl.entry_id 5B6V _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 5B6V _cell.length_a 62.5 _cell.length_b 62.5 _cell.length_c 112 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5B6V _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,M,N,O,P,Q,R _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_455 -y-1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -62.5 0 0 3 'crystal symmetry operation' 3_445 -x+y-1,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -31.25 -54.126588 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 ? _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 1.311 _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 571 n n C1 C6 RET sing 572 n n C1 C16 RET sing 573 n n C1 C17 RET sing 574 n n C2 C3 RET sing 575 n n C2 H21 RET sing 576 n n C2 H22 RET sing 577 n n C3 C4 RET sing 578 n n C3 H31 RET sing 579 n n C3 H32 RET sing 580 n n C4 C5 RET sing 581 n n C4 H41 RET sing 582 n n C4 H42 RET sing 583 n n C5 C6 RET doub 584 n n C5 C18 RET sing 585 n n C6 C7 RET sing 586 n n C7 C8 RET doub 587 e n C7 H7 RET sing 588 n n C8 C9 RET sing 589 n n C8 H8 RET sing 590 n n C9 C10 RET doub 591 e n C9 C19 RET sing 592 n n C10 C11 RET sing 593 n n C10 H10 RET sing 594 n n C11 C12 RET doub 595 e n C11 H11 RET sing 596 n n C12 C13 RET sing 597 n n C12 H12 RET sing 598 n n C13 C14 RET doub 599 e n C13 C20 RET sing 600 n n C14 C15 RET sing 601 n n C14 H14 RET sing 602 n n C15 O1 RET doub 603 n n C15 H15 RET sing 604 n n C16 H161 RET sing 605 n n C16 H162 RET sing 606 n n C16 H163 RET sing 607 n n C17 H171 RET sing 608 n n C17 H172 RET sing 609 n n C17 H173 RET sing 610 n n C18 H181 RET sing 611 n n C18 H182 RET sing 612 n n C18 H183 RET sing 613 n n C19 H191 RET sing 614 n n C19 H192 RET sing 615 n n C19 H193 RET sing 616 n n C20 H201 RET sing 617 n n C20 H202 RET sing 618 n n C20 H203 RET sing 619 n n # _atom_sites.entry_id 5B6V _atom_sites.fract_transf_matrix[1][1] 0.016 _atom_sites.fract_transf_matrix[1][2] 0.009238 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018475 _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] 0.008929 _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 L2P A 1 600 600 L2P L2P . D 4 TRD A 1 601 601 TRD TRD . E 5 D10 A 1 602 602 D10 D10 . F 6 HP6 A 1 603 603 HP6 HP6 . G 7 OCT A 1 604 604 OCT OCT . H 7 OCT A 1 605 605 OCT OCT . I 8 MYS A 1 606 606 MYS MYS . J 9 UND A 1 607 607 UND UND . K 3 L2P A 1 608 608 L2P L2P . L 3 L2P A 1 609 609 L2P L2P . M 8 MYS A 1 610 610 MYS MYS . N 10 DD9 A 1 611 611 DD9 DD9 . O 11 C14 A 1 612 612 C14 C14 . P 7 OCT A 1 613 613 OCT OCT . Q 9 UND A 1 614 614 UND UND . R 12 HOH A 1 400 400 HOH HOH . R 12 HOH A 2 401 401 HOH HOH . R 12 HOH A 3 402 402 HOH HOH . R 12 HOH A 4 403 403 HOH HOH . R 12 HOH A 5 404 404 HOH HOH . R 12 HOH A 6 405 405 HOH HOH . R 12 HOH A 7 406 406 HOH HOH . R 12 HOH A 8 407 407 HOH HOH . R 12 HOH A 9 408 408 HOH HOH . R 12 HOH A 10 414 414 HOH HOH . R 12 HOH A 11 425 425 HOH HOH . R 12 HOH A 12 424 424 HOH HOH . R 12 HOH A 13 433 433 HOH HOH . R 12 HOH A 14 438 438 HOH HOH . R 12 HOH A 15 441 441 HOH HOH . R 12 HOH A 16 442 442 HOH HOH . R 12 HOH A 17 443 443 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 -16.178 -7.753 -5.371 1 40.72 ? C1 RET 300 A 1 HETATM 2 C C2 RET . . . B 2 -16.572 -6.849 -6.541 1 43.85 ? C2 RET 300 A 1 HETATM 3 C C3 RET . . . B 2 -15.937 -5.483 -6.475 1 55.04 ? C3 RET 300 A 1 HETATM 4 C C4 RET . . . B 2 -16.466 -4.823 -5.221 1 39.07 ? C4 RET 300 A 1 HETATM 5 C C5 RET . . . B 2 -16.024 -5.634 -4.027 1 39.42 ? C5 RET 300 A 1 HETATM 6 C C6 RET . . . B 2 -15.868 -6.976 -4.087 1 35.11 ? C6 RET 300 A 1 HETATM 7 C C7 RET . . . B 2 -15.404 -7.672 -2.848 1 38.49 ? C7 RET 300 A 1 HETATM 8 C C8 RET . . . B 2 -15.205 -8.988 -2.748 1 35.63 ? C8 RET 300 A 1 HETATM 9 C C9 RET . . . B 2 -14.736 -9.658 -1.507 1 37.77 ? C9 RET 300 A 1 HETATM 10 C C10 RET . . . B 2 -14.577 -10.989 -1.59 1 34.99 ? C10 RET 300 A 1 HETATM 11 C C11 RET . . . B 2 -14.124 -11.835 -0.485 1 37.8 ? C11 RET 300 A 1 HETATM 12 C C12 RET . . . B 2 -14.043 -13.134 -0.767 1 35.66 ? C12 RET 300 A 1 HETATM 13 C C13 RET . . . B 2 -13.62 -14.163 0.205 1 37.58 ? C13 RET 300 A 1 HETATM 14 C C14 RET . . . B 2 -13.625 -15.419 -0.278 1 40.23 ? C14 RET 300 A 1 HETATM 15 C C15 RET . . . B 2 -13.276 -16.631 0.453 1 40.03 ? C15 RET 300 A 1 HETATM 16 C C16 RET . . . B 2 -17.355 -8.704 -5.13 1 42.4 ? C16 RET 300 A 1 HETATM 17 C C17 RET . . . B 2 -14.926 -8.503 -5.823 1 39.6 ? C17 RET 300 A 1 HETATM 18 C C18 RET . . . B 2 -15.761 -4.852 -2.772 1 39.76 ? C18 RET 300 A 1 HETATM 19 C C19 RET . . . B 2 -14.451 -8.942 -0.212 1 34.73 ? C19 RET 300 A 1 HETATM 20 C C20 RET . . . B 2 -13.235 -13.794 1.611 1 38.07 ? C20 RET 300 A 1 HETATM 21 H H21 RET . . . B 2 -17.645 -6.651 -6.502 1 52.62 ? H21 RET 300 A 1 HETATM 22 H H22 RET . . . B 2 -16.617 -7.44 -7.458 1 52.62 ? H22 RET 300 A 1 HETATM 23 H H31 RET . . . B 2 -16.439 -4.814 -7.177 1 66.04 ? H31 RET 300 A 1 HETATM 24 H H32 RET . . . B 2 -14.85 -5.585 -6.497 1 66.04 ? H32 RET 300 A 1 HETATM 25 H H41 RET . . . B 2 -17.552 -4.934 -5.181 1 46.89 ? H41 RET 300 A 1 HETATM 26 H H42 RET . . . B 2 -16.146 -3.779 -5.197 1 46.89 ? H42 RET 300 A 1 HETATM 27 H H7 RET . . . B 2 -15.217 -7.069 -1.975 1 46.19 ? H7 RET 300 A 1 HETATM 28 H H8 RET . . . B 2 -15.395 -9.598 -3.615 1 42.76 ? H8 RET 300 A 1 HETATM 29 H H10 RET . . . B 2 -14.797 -11.465 -2.531 1 41.98 ? H10 RET 300 A 1 HETATM 30 H H11 RET . . . B 2 -13.519 -11.416 0.301 1 45.36 ? H11 RET 300 A 1 HETATM 31 H H12 RET . . . B 2 -14.301 -13.453 -1.763 1 42.79 ? H12 RET 300 A 1 HETATM 32 H H14 RET . . . B 2 -13.916 -15.541 -1.308 1 48.27 ? H14 RET 300 A 1 HETATM 33 H H15 RET . . . B 2 -13.087 -16.585 1.512 1 48.03 ? H15 RET 300 A 1 HETATM 34 H H161 RET . . . B 2 -17.345 -9.03 -4.123 1 50.88 ? H161 RET 300 A 1 HETATM 35 H H162 RET . . . B 2 -18.264 -8.198 -5.328 1 50.88 ? H162 RET 300 A 1 HETATM 36 H H163 RET . . . B 2 -17.27 -9.541 -5.773 1 50.88 ? H163 RET 300 A 1 HETATM 37 H H171 RET . . . B 2 -15.076 -9.544 -5.703 1 47.52 ? H171 RET 300 A 1 HETATM 38 H H172 RET . . . B 2 -14.099 -8.195 -5.237 1 47.52 ? H172 RET 300 A 1 HETATM 39 H H173 RET . . . B 2 -14.735 -8.289 -6.842 1 47.52 ? H173 RET 300 A 1 HETATM 40 H H181 RET . . . B 2 -15.928 -3.823 -2.956 1 47.72 ? H181 RET 300 A 1 HETATM 41 H H182 RET . . . B 2 -16.412 -5.184 -2.006 1 47.72 ? H182 RET 300 A 1 HETATM 42 H H183 RET . . . B 2 -14.757 -4.998 -2.469 1 47.72 ? H183 RET 300 A 1 HETATM 43 H H191 RET . . . B 2 -14.926 -7.995 -0.22 1 41.68 ? H191 RET 300 A 1 HETATM 44 H H192 RET . . . B 2 -13.406 -8.812 -0.103 1 41.68 ? H192 RET 300 A 1 HETATM 45 H H193 RET . . . B 2 -14.821 -9.516 0.597 1 41.68 ? H193 RET 300 A 1 HETATM 46 H H201 RET . . . B 2 -12.237 -13.439 1.622 1 45.69 ? H201 RET 300 A 1 HETATM 47 H H202 RET . . . B 2 -13.883 -13.036 1.967 1 45.69 ? H202 RET 300 A 1 HETATM 48 H H203 RET . . . B 2 -13.313 -14.647 2.234 1 45.69 ? H203 RET 300 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 48 #