data_3PXO # _model_server_result.job_id ibWFoAI3RRFQonTancgsCQ _model_server_result.datetime_utc '2024-11-22 14:46:52' _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 3pxo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":801}' # _entry.id 3PXO # _exptl.entry_id 3PXO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 6 _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 3PXO _cell.length_a 241.82 _cell.length_b 241.82 _cell.length_c 111.8 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PXO _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # 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' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 111.8 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . 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 NAG 1 B 1 NAG A 401 NAG 2 n B NAG 2 B 2 NAG A 402 NAG 2 n B BMA 3 B 3 BMA A 403 BMA 2 n B MAN 4 B 4 MAN A 404 MAN 3 n C NAG 1 C 1 NAG A 501 NAG 3 n C NAG 2 C 2 NAG A 502 NAG # 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 disulf ? disulf1 A SG CYS 110 A CYS 110 1_555 A SG CYS 187 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 A ND2 ASN 2 A ASN 2 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale2 A ND2 ASN 15 A ASN 15 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale3 A NZ LYS 296 A LYS 296 1_555 G C15 RET . A RET 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale4 A SG CYS 323 A CYS 323 1_555 F C1 PLM . A PLM 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.837 ? covale ? covale5 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale6 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale7 B O3 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale8 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? # _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 452 n n C1 C6 RET sing 453 n n C1 C16 RET sing 454 n n C1 C17 RET sing 455 n n C2 C3 RET sing 456 n n C2 H21 RET sing 457 n n C2 H22 RET sing 458 n n C3 C4 RET sing 459 n n C3 H31 RET sing 460 n n C3 H32 RET sing 461 n n C4 C5 RET sing 462 n n C4 H41 RET sing 463 n n C4 H42 RET sing 464 n n C5 C6 RET doub 465 n n C5 C18 RET sing 466 n n C6 C7 RET sing 467 n n C7 C8 RET doub 468 e n C7 H7 RET sing 469 n n C8 C9 RET sing 470 n n C8 H8 RET sing 471 n n C9 C10 RET doub 472 e n C9 C19 RET sing 473 n n C10 C11 RET sing 474 n n C10 H10 RET sing 475 n n C11 C12 RET doub 476 e n C11 H11 RET sing 477 n n C12 C13 RET sing 478 n n C12 H12 RET sing 479 n n C13 C14 RET doub 480 e n C13 C20 RET sing 481 n n C14 C15 RET sing 482 n n C14 H14 RET sing 483 n n C15 O1 RET doub 484 n n C15 H15 RET sing 485 n n C16 H161 RET sing 486 n n C16 H162 RET sing 487 n n C16 H163 RET sing 488 n n C17 H171 RET sing 489 n n C17 H172 RET sing 490 n n C17 H173 RET sing 491 n n C18 H181 RET sing 492 n n C18 H182 RET sing 493 n n C18 H183 RET sing 494 n n C19 H191 RET sing 495 n n C19 H192 RET sing 496 n n C19 H193 RET sing 497 n n C20 H201 RET sing 498 n n C20 H202 RET sing 499 n n C20 H203 RET sing 500 n n # _atom_sites.entry_id 3PXO _atom_sites.fract_transf_matrix[1][1] 0.004135 _atom_sites.fract_transf_matrix[1][2] 0.002388 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004775 _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] 0.008945 _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 D 4 BOG A 1 601 601 BOG BOG . E 4 BOG A 1 602 602 BOG BOG . F 5 PLM A 1 701 701 PLM PLM . G 6 RET A 1 801 801 RET RET . H 7 HOH A 1 349 1 HOH HOH . H 7 HOH A 2 350 2 HOH HOH . H 7 HOH A 3 351 3 HOH HOH . H 7 HOH A 4 352 4 HOH HOH . H 7 HOH A 5 353 5 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 . . . G 6 -43.137 -16.091 34.573 1 69.47 ? C1 RET 801 A 1 HETATM 2 C C2 RET . . . G 6 -43.403 -17.632 34.691 1 69.47 ? C2 RET 801 A 1 HETATM 3 C C3 RET . . . G 6 -44.631 -18.091 34.082 1 75.42 ? C3 RET 801 A 1 HETATM 4 C C4 RET . . . G 6 -45.849 -17.295 34.371 1 74.23 ? C4 RET 801 A 1 HETATM 5 C C5 RET . . . G 6 -45.641 -15.813 34.274 1 71.94 ? C5 RET 801 A 1 HETATM 6 C C6 RET . . . G 6 -44.446 -15.269 34.526 1 75.28 ? C6 RET 801 A 1 HETATM 7 C C7 RET . . . G 6 -44.266 -13.812 34.735 1 75.47 ? C7 RET 801 A 1 HETATM 8 C C8 RET . . . G 6 -44.965 -13.011 35.523 1 67.93 ? C8 RET 801 A 1 HETATM 9 C C9 RET . . . G 6 -44.749 -11.577 35.697 1 64.73 ? C9 RET 801 A 1 HETATM 10 C C10 RET . . . G 6 -45.313 -10.999 36.765 1 63.51 ? C10 RET 801 A 1 HETATM 11 C C11 RET . . . G 6 -45.282 -9.635 37.198 1 61.37 ? C11 RET 801 A 1 HETATM 12 C C12 RET . . . G 6 -46.021 -9.215 38.247 1 69.1 ? C12 RET 801 A 1 HETATM 13 C C13 RET . . . G 6 -46.084 -7.886 38.802 1 74.14 ? C13 RET 801 A 1 HETATM 14 C C14 RET . . . G 6 -46.966 -7.644 39.806 1 71.07 ? C14 RET 801 A 1 HETATM 15 C C15 RET . . . G 6 -47.183 -6.386 40.492 1 71.44 ? C15 RET 801 A 1 HETATM 16 C C16 RET . . . G 6 -42.251 -15.672 33.449 1 62.43 ? C16 RET 801 A 1 HETATM 17 C C17 RET . . . G 6 -42.398 -15.898 35.883 1 70.66 ? C17 RET 801 A 1 HETATM 18 C C18 RET . . . G 6 -46.87 -15.038 33.849 1 67.1 ? C18 RET 801 A 1 HETATM 19 C C19 RET . . . G 6 -43.915 -10.86 34.676 1 63.33 ? C19 RET 801 A 1 HETATM 20 C C20 RET . . . G 6 -45.164 -6.837 38.241 1 77.12 ? C20 RET 801 A 1 # _model_server_stats.io_time_ms 117 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #