data_6GAG # _model_server_result.job_id 9xY3Yl7XsCgfS9fWwiAu_A _model_server_result.datetime_utc '2024-11-27 04:07:39' _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 6gag # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 6GAG # _exptl.entry_id 6GAG _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 6GAG _cell.length_a 62.1 _cell.length_b 62.1 _cell.length_c 110.5 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6GAG _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 _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 -62.1 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 -31.05 -53.780178 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 # 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 B C15 RET . A RET 301 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.343 ? covale ? covale2 A NZ LYS 216 A LYS 216 1_555 B C15 RET . A RET 301 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.309 ? # _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 6GAG _atom_sites.fract_transf_matrix[1][1] 0.016103 _atom_sites.fract_transf_matrix[1][2] 0.009297 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018594 _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] 0.00905 _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 1 301 300 RET RET . C 3 L2P A 1 302 600 L2P L2P . D 4 TRD A 1 303 601 TRD TRD . E 5 D10 A 1 304 602 D10 D10 . F 6 HP6 A 1 305 603 HP6 HP6 . G 7 OCT A 1 306 604 OCT OCT . H 7 OCT A 1 307 605 OCT OCT . I 8 MYS A 1 308 606 MYS MYS . J 9 UND A 1 309 607 UND UND . K 3 L2P A 1 310 608 L2P L2P . L 3 L2P A 1 311 609 L2P L2P . M 10 DD9 A 1 312 611 DD9 DD9 . N 11 C14 A 1 313 612 C14 C14 . O 7 OCT A 1 314 613 OCT OCT . P 9 UND A 1 315 614 UND UND . Q 12 HOH A 1 401 636 HOH HOH . Q 12 HOH A 2 402 611 HOH HOH . Q 12 HOH A 3 403 627 HOH HOH . Q 12 HOH A 4 404 618 HOH HOH . Q 12 HOH A 5 405 613 HOH HOH . Q 12 HOH A 6 406 616 HOH HOH . Q 12 HOH A 7 407 610 HOH HOH . Q 12 HOH A 8 408 402 HOH HOH . Q 12 HOH A 9 409 631 HOH HOH . Q 12 HOH A 10 410 617 HOH HOH . Q 12 HOH A 11 411 406 HOH HOH . Q 12 HOH A 12 412 403 HOH HOH . Q 12 HOH A 13 413 401 HOH HOH . Q 12 HOH A 14 414 620 HOH HOH . Q 12 HOH A 15 415 630 HOH HOH . Q 12 HOH A 16 416 633 HOH HOH . Q 12 HOH A 17 417 614 HOH HOH . Q 12 HOH A 18 418 609 HOH HOH . Q 12 HOH A 19 419 606 HOH HOH . Q 12 HOH A 20 420 635 HOH HOH . Q 12 HOH A 21 421 407 HOH HOH . Q 12 HOH A 22 422 612 HOH HOH . Q 12 HOH A 23 423 626 HOH HOH . Q 12 HOH A 24 424 404 HOH HOH . Q 12 HOH A 25 425 501 HOH HOH . Q 12 HOH A 26 426 619 HOH HOH . Q 12 HOH A 27 427 622 HOH HOH . Q 12 HOH A 28 428 615 HOH HOH . Q 12 HOH A 29 429 628 HOH HOH . Q 12 HOH A 30 430 624 HOH HOH . Q 12 HOH A 31 431 621 HOH HOH . Q 12 HOH A 32 432 629 HOH HOH . Q 12 HOH A 33 433 623 HOH HOH . Q 12 HOH A 34 434 634 HOH HOH . Q 12 HOH A 35 435 638 HOH HOH . Q 12 HOH A 36 436 637 HOH HOH . Q 12 HOH A 37 437 632 HOH HOH . Q 12 HOH A 38 438 625 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 -15.998 -7.587 -5.342 0.85 21.81 ? C1 RET 301 A 1 HETATM 2 C C1 RET . B . B 2 -16.244 -7.658 -5.408 0.15 13.72 ? C1 RET 301 A 1 HETATM 3 C C2 RET . A . B 2 -16.46 -6.693 -6.481 0.85 27.02 ? C2 RET 301 A 1 HETATM 4 C C2 RET . B . B 2 -16.762 -6.655 -6.423 0.15 13.72 ? C2 RET 301 A 1 HETATM 5 C C3 RET . A . B 2 -15.945 -5.292 -6.415 0.85 27.39 ? C3 RET 301 A 1 HETATM 6 C C3 RET . B . B 2 -15.875 -5.437 -6.437 0.15 13.72 ? C3 RET 301 A 1 HETATM 7 C C4 RET . A . B 2 -16.34 -4.641 -5.106 0.85 21.21 ? C4 RET 301 A 1 HETATM 8 C C4 RET . B . B 2 -16.087 -4.701 -5.128 0.15 13.72 ? C4 RET 301 A 1 HETATM 9 C C5 RET . A . B 2 -15.915 -5.503 -3.942 0.85 21.64 ? C5 RET 301 A 1 HETATM 10 C C5 RET . B . B 2 -15.885 -5.631 -3.95 0.15 13.72 ? C5 RET 301 A 1 HETATM 11 C C6 RET . A . B 2 -15.743 -6.836 -4.027 0.85 20.44 ? C6 RET 301 A 1 HETATM 12 C C6 RET . B . B 2 -15.866 -6.978 -4.084 0.15 13.72 ? C6 RET 301 A 1 HETATM 13 C C7 RET . A . B 2 -15.288 -7.542 -2.782 0.85 18.52 ? C7 RET 301 A 1 HETATM 14 C C7 RET . B . B 2 -15.346 -7.708 -2.886 0.15 13.72 ? C7 RET 301 A 1 HETATM 15 C C8 RET . A . B 2 -15.086 -8.857 -2.67 0.85 20.82 ? C8 RET 301 A 1 HETATM 16 C C8 RET . B . B 2 -15.185 -9.001 -2.595 0.15 13.72 ? C8 RET 301 A 1 HETATM 17 C C9 RET . A . B 2 -14.614 -9.541 -1.451 0.85 19.58 ? C9 RET 301 A 1 HETATM 18 C C9 RET . B . B 2 -14.678 -9.606 -1.362 0.15 13.72 ? C9 RET 301 A 1 HETATM 19 C C10 RET . A . B 2 -14.413 -10.864 -1.531 0.85 21.77 ? C10 RET 301 A 1 HETATM 20 C C10 RET . B . B 2 -14.723 -10.943 -1.339 0.15 13.72 ? C10 RET 301 A 1 HETATM 21 C C11 RET . A . B 2 -13.949 -11.737 -0.453 0.85 19.31 ? C11 RET 301 A 1 HETATM 22 C C11 RET . B . B 2 -13.889 -11.794 -0.506 0.15 13.72 ? C11 RET 301 A 1 HETATM 23 C C12 RET . A . B 2 -13.844 -13.015 -0.816 0.85 20.76 ? C12 RET 301 A 1 HETATM 24 C C12 RET . B . B 2 -13.887 -13.087 -0.808 0.15 13.72 ? C12 RET 301 A 1 HETATM 25 C C13 RET . A . B 2 -13.446 -14.088 0.109 0.85 22.86 ? C13 RET 301 A 1 HETATM 26 C C13 RET . B . B 2 -13.309 -14.1 0.085 0.15 13.72 ? C13 RET 301 A 1 HETATM 27 C C14 RET . A . B 2 -13.523 -15.35 -0.351 0.85 21.02 ? C14 RET 301 A 1 HETATM 28 C C14 RET . B . B 2 -13.029 -15.31 -0.417 0.15 13.72 ? C14 RET 301 A 1 HETATM 29 C C15 RET . A . B 2 -13.199 -16.489 0.487 0.85 22.97 ? C15 RET 301 A 1 HETATM 30 C C15 RET . B . B 2 -13.387 -16.529 0.297 0.15 13.72 ? C15 RET 301 A 1 HETATM 31 C C16 RET . A . B 2 -17.185 -8.538 -5.203 0.85 22.2 ? C16 RET 301 A 1 HETATM 32 C C16 RET . B . B 2 -17.39 -8.659 -5.269 0.15 13.72 ? C16 RET 301 A 1 HETATM 33 C C17 RET . A . B 2 -14.753 -8.335 -5.832 0.85 22.69 ? C17 RET 301 A 1 HETATM 34 C C17 RET . B . B 2 -15.015 -8.323 -6.022 0.15 13.72 ? C17 RET 301 A 1 HETATM 35 C C18 RET . A . B 2 -15.696 -4.749 -2.66 0.85 20.82 ? C18 RET 301 A 1 HETATM 36 C C18 RET . B . B 2 -15.673 -4.946 -2.63 0.15 13.72 ? C18 RET 301 A 1 HETATM 37 C C19 RET . A . B 2 -14.351 -8.746 -0.197 0.85 20.32 ? C19 RET 301 A 1 HETATM 38 C C19 RET . B . B 2 -14.3 -8.783 -0.167 0.15 13.72 ? C19 RET 301 A 1 HETATM 39 C C20 RET . A . B 2 -13.021 -13.765 1.517 0.85 19.86 ? C20 RET 301 A 1 HETATM 40 C C20 RET . B . B 2 -12.762 -13.692 1.42 0.15 13.72 ? C20 RET 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 40 #