data_1IXF # _model_server_result.job_id h3rZo4_NFLzq88UfglrMEQ _model_server_result.datetime_utc '2024-11-08 04:37:10' _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 1ixf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":250}' # _entry.id 1IXF # _exptl.entry_id 1IXF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 3 _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 1IXF _cell.length_a 102.3 _cell.length_b 102.3 _cell.length_c 112.3 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1IXF _symmetry.cell_setting ? _symmetry.Int_Tables_number 177 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 6 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 102.3 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 51.15 88.594399 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 MAN GLC C1 O1 . O2 HO2 . sing 2 ? 2 3 2 GAL MAN C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B GLC 1 B 1 GLC B 400 GLC 2 n B MAN 2 B 2 MAN B 410 MAN 2 n B GAL 3 B 3 GAL B 420 GAL # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order covale ? covale1 A NZ LYS 216 A LYS 216 1_555 C C15 RET . A RET 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale2 E O3 L2P . A L2P 270 1_555 B C1 GLC . B GLC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 B O2 GLC . B GLC 1 1_555 B C1 MAN . B MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 B O6 MAN . B MAN 2 1_555 B C1 GAL . B GAL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? # _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 600 n n C1 C6 RET sing 601 n n C1 C16 RET sing 602 n n C1 C17 RET sing 603 n n C2 C3 RET sing 604 n n C2 H21 RET sing 605 n n C2 H22 RET sing 606 n n C3 C4 RET sing 607 n n C3 H31 RET sing 608 n n C3 H32 RET sing 609 n n C4 C5 RET sing 610 n n C4 H41 RET sing 611 n n C4 H42 RET sing 612 n n C5 C6 RET doub 613 n n C5 C18 RET sing 614 n n C6 C7 RET sing 615 n n C7 C8 RET doub 616 e n C7 H7 RET sing 617 n n C8 C9 RET sing 618 n n C8 H8 RET sing 619 n n C9 C10 RET doub 620 e n C9 C19 RET sing 621 n n C10 C11 RET sing 622 n n C10 H10 RET sing 623 n n C11 C12 RET doub 624 e n C11 H11 RET sing 625 n n C12 C13 RET sing 626 n n C12 H12 RET sing 627 n n C13 C14 RET doub 628 e n C13 C20 RET sing 629 n n C14 C15 RET sing 630 n n C14 H14 RET sing 631 n n C15 O1 RET doub 632 n n C15 H15 RET sing 633 n n C16 H161 RET sing 634 n n C16 H162 RET sing 635 n n C16 H163 RET sing 636 n n C17 H171 RET sing 637 n n C17 H172 RET sing 638 n n C17 H173 RET sing 639 n n C18 H181 RET sing 640 n n C18 H182 RET sing 641 n n C18 H183 RET sing 642 n n C19 H191 RET sing 643 n n C19 H192 RET sing 644 n n C19 H193 RET sing 645 n n C20 H201 RET sing 646 n n C20 H202 RET sing 647 n n C20 H203 RET sing 648 n n # _atom_sites.entry_id 1IXF _atom_sites.fract_transf_matrix[1][1] 0.009775 _atom_sites.fract_transf_matrix[1][2] 0.005644 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011287 _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] 0.008905 _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 C 3 RET A 1 250 250 RET RET . D 4 L3P A 1 260 260 L3P L3P . E 5 L2P A 1 270 270 L2P L2P . F 4 L3P A 1 280 280 L3P L3P . G 4 L3P A 1 290 290 L3P L3P . H 4 L3P A 1 300 300 L3P L3P . I 6 HOH A 1 600 600 HOH HOH . I 6 HOH A 2 601 601 HOH HOH . I 6 HOH A 3 602 602 HOH HOH . I 6 HOH A 4 603 603 HOH HOH . I 6 HOH A 5 604 604 HOH HOH . I 6 HOH A 6 605 605 HOH HOH . I 6 HOH A 7 606 606 HOH HOH . I 6 HOH A 8 607 607 HOH HOH . I 6 HOH A 9 608 608 HOH HOH . I 6 HOH A 10 609 609 HOH HOH . I 6 HOH A 11 610 610 HOH HOH . I 6 HOH A 12 611 611 HOH HOH . I 6 HOH A 13 612 612 HOH HOH . I 6 HOH A 14 613 613 HOH HOH . I 6 HOH A 15 614 614 HOH HOH . I 6 HOH A 16 615 615 HOH HOH . I 6 HOH A 17 616 616 HOH HOH . I 6 HOH A 18 617 617 HOH HOH . I 6 HOH A 19 618 618 HOH HOH . I 6 HOH A 20 619 619 HOH HOH . I 6 HOH A 21 620 620 HOH HOH . I 6 HOH A 22 621 621 HOH HOH . I 6 HOH A 23 622 622 HOH HOH . I 6 HOH A 24 623 623 HOH HOH . I 6 HOH A 25 624 624 HOH HOH . I 6 HOH A 26 625 625 HOH HOH . I 6 HOH A 27 626 626 HOH HOH . I 6 HOH A 28 627 627 HOH HOH . I 6 HOH A 29 628 628 HOH HOH . I 6 HOH A 30 629 629 HOH HOH . I 6 HOH A 31 630 630 HOH HOH . I 6 HOH A 32 631 631 HOH HOH . I 6 HOH A 33 632 632 HOH HOH . I 6 HOH A 34 633 633 HOH HOH . I 6 HOH A 35 634 634 HOH HOH . I 6 HOH A 36 635 635 HOH HOH . I 6 HOH A 37 636 636 HOH HOH . I 6 HOH A 38 637 637 HOH HOH . I 6 HOH A 39 638 638 HOH HOH . I 6 HOH A 40 639 639 HOH HOH . I 6 HOH A 41 640 640 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 . . . C 3 39.496 15.945 21.553 1 28.43 ? C1 RET 250 A 1 HETATM 2 C C2 RET . . . C 3 40.17 15.216 20.378 1 29.28 ? C2 RET 250 A 1 HETATM 3 C C3 RET . . . C 3 40.038 13.69 20.336 1 28.16 ? C3 RET 250 A 1 HETATM 4 C C4 RET . . . C 3 40.011 12.927 21.679 1 25.07 ? C4 RET 250 A 1 HETATM 5 C C5 RET . . . C 3 39.537 13.742 22.903 1 26.75 ? C5 RET 250 A 1 HETATM 6 C C6 RET . . . C 3 39.246 15.135 22.851 1 28.65 ? C6 RET 250 A 1 HETATM 7 C C7 RET . . . C 3 38.68 15.759 24.159 1 26.76 ? C7 RET 250 A 1 HETATM 8 C C8 RET . . . C 3 38.043 16.984 24.307 1 23.53 ? C8 RET 250 A 1 HETATM 9 C C9 RET . . . C 3 37.577 17.467 25.621 1 25.98 ? C9 RET 250 A 1 HETATM 10 C C10 RET . . . C 3 36.972 18.708 25.705 1 27.67 ? C10 RET 250 A 1 HETATM 11 C C11 RET . . . C 3 36.315 19.339 26.845 1 30.01 ? C11 RET 250 A 1 HETATM 12 C C12 RET . . . C 3 35.633 20.507 26.618 1 32.65 ? C12 RET 250 A 1 HETATM 13 C C13 RET . . . C 3 34.645 21.045 27.56 1 30.69 ? C13 RET 250 A 1 HETATM 14 C C14 RET . . . C 3 34.154 22.322 27.805 1 28.31 ? C14 RET 250 A 1 HETATM 15 C C15 RET . . . C 3 34.512 23.661 27.28 1 31.53 ? C15 RET 250 A 1 HETATM 16 C C16 RET . . . C 3 40.414 17.175 21.787 1 27.72 ? C16 RET 250 A 1 HETATM 17 C C17 RET . . . C 3 38.158 16.468 21.01 1 26.57 ? C17 RET 250 A 1 HETATM 18 C C18 RET . . . C 3 39.372 12.929 24.206 1 25.75 ? C18 RET 250 A 1 HETATM 19 C C19 RET . . . C 3 37.731 16.546 26.793 1 31.22 ? C19 RET 250 A 1 HETATM 20 C C20 RET . . . C 3 33.844 20.105 28.497 1 27.03 ? C20 RET 250 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 233 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #