data_4A4M # _model_server_result.job_id sLD4VmsEi7Lf_uyMocU9ag _model_server_result.datetime_utc '2024-11-13 02:50:42' _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 4a4m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 4A4M # _exptl.entry_id 4A4M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 4 _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 4A4M _cell.length_a 242.19 _cell.length_b 242.19 _cell.length_c 109.829 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4A4M _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details 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' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 109.829 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 3 n C NAG 1 C 1 NAG A 1405 NAG 3 n C NAG 2 C 2 NAG A 1406 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 3 A CYS 2 1_555 A SG CYS 283 A CYS 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf2 A SG CYS 111 A CYS 110 1_555 A SG CYS 188 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? covale ? covale1 A C ACE 1 A ACE 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale2 A ND2 ASN 16 A ASN 15 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale3 A NZ LYS 297 A LYS 296 1_555 D C15 RET . A RET 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale4 A SG CYS 324 A CYS 323 1_555 G C1 PLM . A PLM 1404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.687 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 416 n n C1 C6 RET sing 417 n n C1 C16 RET sing 418 n n C1 C17 RET sing 419 n n C2 C3 RET sing 420 n n C2 H21 RET sing 421 n n C2 H22 RET sing 422 n n C3 C4 RET sing 423 n n C3 H31 RET sing 424 n n C3 H32 RET sing 425 n n C4 C5 RET sing 426 n n C4 H41 RET sing 427 n n C4 H42 RET sing 428 n n C5 C6 RET doub 429 n n C5 C18 RET sing 430 n n C6 C7 RET sing 431 n n C7 C8 RET doub 432 e n C7 H7 RET sing 433 n n C8 C9 RET sing 434 n n C8 H8 RET sing 435 n n C9 C10 RET doub 436 e n C9 C19 RET sing 437 n n C10 C11 RET sing 438 n n C10 H10 RET sing 439 n n C11 C12 RET doub 440 e n C11 H11 RET sing 441 n n C12 C13 RET sing 442 n n C12 H12 RET sing 443 n n C13 C14 RET doub 444 e n C13 C20 RET sing 445 n n C14 C15 RET sing 446 n n C14 H14 RET sing 447 n n C15 O1 RET doub 448 n n C15 H15 RET sing 449 n n C16 H161 RET sing 450 n n C16 H162 RET sing 451 n n C16 H163 RET sing 452 n n C17 H171 RET sing 453 n n C17 H172 RET sing 454 n n C17 H173 RET sing 455 n n C18 H181 RET sing 456 n n C18 H182 RET sing 457 n n C18 H183 RET sing 458 n n C19 H191 RET sing 459 n n C19 H192 RET sing 460 n n C19 H193 RET sing 461 n n C20 H201 RET sing 462 n n C20 H202 RET sing 463 n n C20 H203 RET sing 464 n n # _atom_sites.entry_id 4A4M _atom_sites.fract_transf_matrix[1][1] 0.004129 _atom_sites.fract_transf_matrix[1][2] 0.002384 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004768 _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] 0.009105 _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 RET A 1 401 401 RET RET . E 5 ACT A 1 1402 1402 ACT ACT . F 6 BOG A 1 1403 1403 BOG BOG . G 7 PLM A 1 1404 1404 PLM PLM . H 8 HOH A 1 2001 2001 HOH HOH . H 8 HOH A 2 2002 2002 HOH HOH . H 8 HOH A 3 2003 2003 HOH HOH . H 8 HOH A 4 2004 2004 HOH HOH . H 8 HOH A 5 2005 2005 HOH HOH . H 8 HOH A 6 2006 2006 HOH HOH . H 8 HOH A 7 2007 2007 HOH HOH . H 8 HOH A 8 2008 2008 HOH HOH . H 8 HOH A 9 2009 2009 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 . . . D 4 7.363 45.739 34.106 1 104.55 ? C1 RET 401 A 1 HETATM 2 C C2 RET . . . D 4 6.161 46.472 34.735 1 93.53 ? C2 RET 401 A 1 HETATM 3 C C3 RET . . . D 4 5.816 47.739 33.947 1 87.67 ? C3 RET 401 A 1 HETATM 4 C C4 RET . . . D 4 7.027 48.664 33.866 1 91.46 ? C4 RET 401 A 1 HETATM 5 C C5 RET . . . D 4 8.382 48.018 33.797 1 94.98 ? C5 RET 401 A 1 HETATM 6 C C6 RET . . . D 4 8.571 46.699 33.975 1 103.05 ? C6 RET 401 A 1 HETATM 7 C C7 RET . . . D 4 9.956 46.174 33.853 1 102.11 ? C7 RET 401 A 1 HETATM 8 C C8 RET . . . D 4 10.97 46.525 34.651 1 99.66 ? C8 RET 401 A 1 HETATM 9 C C9 RET . . . D 4 12.001 45.509 35.045 1 104.96 ? C9 RET 401 A 1 HETATM 10 C C10 RET . . . D 4 12.992 45.889 35.881 1 105.43 ? C10 RET 401 A 1 HETATM 11 C C11 RET . . . D 4 13.958 44.917 36.346 1 108.66 ? C11 RET 401 A 1 HETATM 12 C C12 RET . . . D 4 15.02 45.343 37.004 1 108.47 ? C12 RET 401 A 1 HETATM 13 C C13 RET . . . D 4 15.82 44.411 37.862 1 110.93 ? C13 RET 401 A 1 HETATM 14 C C14 RET . . . D 4 16.814 44.888 38.632 1 113.25 ? C14 RET 401 A 1 HETATM 15 C C15 RET . . . D 4 17.318 44.069 39.72 1 105.29 ? C15 RET 401 A 1 HETATM 16 C C16 RET . . . D 4 6.975 45.284 32.701 1 93.11 ? C16 RET 401 A 1 HETATM 17 C C17 RET . . . D 4 7.632 44.483 34.965 1 96.03 ? C17 RET 401 A 1 HETATM 18 C C18 RET . . . D 4 9.564 48.907 33.586 1 88.23 ? C18 RET 401 A 1 HETATM 19 C C19 RET . . . D 4 11.981 44.069 34.528 1 94.84 ? C19 RET 401 A 1 HETATM 20 C C20 RET . . . D 4 15.441 42.963 38.033 1 100.17 ? C20 RET 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #