data_4MD1 # _model_server_result.job_id EUfJW1RbSdm33qRz9uDFGQ _model_server_result.datetime_utc '2024-10-18 20:27:36' _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 4md1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":1020}' # _entry.id 4MD1 # _exptl.entry_id 4MD1 _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 4MD1 _cell.length_a 60.91 _cell.length_b 60.91 _cell.length_c 110.1 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4MD1 _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,S,T,U,V _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_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 30.455 52.749607 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -30.455 52.749607 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id U _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 U C15 RET . A RET 1020 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.465 doub covale ? covale2 A NZ LYS 216 A LYS 216 1_555 U C15 RET . A RET 1020 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.515 doub # _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 376 n n C1 C6 RET sing 377 n n C1 C16 RET sing 378 n n C1 C17 RET sing 379 n n C2 C3 RET sing 380 n n C2 H21 RET sing 381 n n C2 H22 RET sing 382 n n C3 C4 RET sing 383 n n C3 H31 RET sing 384 n n C3 H32 RET sing 385 n n C4 C5 RET sing 386 n n C4 H41 RET sing 387 n n C4 H42 RET sing 388 n n C5 C6 RET doub 389 n n C5 C18 RET sing 390 n n C6 C7 RET sing 391 n n C7 C8 RET doub 392 e n C7 H7 RET sing 393 n n C8 C9 RET sing 394 n n C8 H8 RET sing 395 n n C9 C10 RET doub 396 e n C9 C19 RET sing 397 n n C10 C11 RET sing 398 n n C10 H10 RET sing 399 n n C11 C12 RET doub 400 e n C11 H11 RET sing 401 n n C12 C13 RET sing 402 n n C12 H12 RET sing 403 n n C13 C14 RET doub 404 e n C13 C20 RET sing 405 n n C14 C15 RET sing 406 n n C14 H14 RET sing 407 n n C15 O1 RET doub 408 n n C15 H15 RET sing 409 n n C16 H161 RET sing 410 n n C16 H162 RET sing 411 n n C16 H163 RET sing 412 n n C17 H171 RET sing 413 n n C17 H172 RET sing 414 n n C17 H173 RET sing 415 n n C18 H181 RET sing 416 n n C18 H182 RET sing 417 n n C18 H183 RET sing 418 n n C19 H191 RET sing 419 n n C19 H192 RET sing 420 n n C19 H193 RET sing 421 n n C20 H201 RET sing 422 n n C20 H202 RET sing 423 n n C20 H203 RET sing 424 n n # _atom_sites.entry_id 4MD1 _atom_sites.fract_transf_matrix[1][1] 0.016418 _atom_sites.fract_transf_matrix[1][2] 0.009479 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018957 _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] 0.009083 _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 L2P A 1 1001 1001 L2P L2P . C 3 SQL A 1 1002 1002 SQL SQN . D 2 L2P A 1 1003 1003 L2P L2P . E 2 L2P A 1 1004 1004 L2P L2P . F 2 L2P A 1 1005 1005 L2P L2P . G 2 L2P A 1 1006 1006 L2P L2P . H 2 L2P A 1 1007 1007 L2P L2P . I 2 L2P A 1 1008 1008 L2P L2P . J 2 L2P A 1 1009 1009 L2P L2P . K 2 L2P A 1 1010 1010 L2P L2P . L 2 L2P A 1 1011 1011 L2P L2P . M 2 L2P A 1 1012 1012 L2P L2P . N 2 L2P A 1 1013 1013 L2P L2P . O 2 L2P A 1 1014 1014 L2P L2P . P 2 L2P A 1 1015 1015 L2P L2P . Q 2 L2P A 1 1016 1016 L2P L2P . R 2 L2P A 1 1017 1017 L2P L2P . S 2 L2P A 1 1018 1018 L2P L2P . T 2 L2P A 1 1019 1019 L2P L2P . U 4 RET A 1 1020 216 RET LYR . V 5 HOH A 1 1101 401 HOH HOH . V 5 HOH A 2 1102 402 HOH HOH . V 5 HOH A 3 1103 403 HOH HOH . V 5 HOH A 4 1104 404 HOH HOH . V 5 HOH A 5 1105 405 HOH HOH . V 5 HOH A 6 1106 406 HOH HOH . V 5 HOH A 7 1107 407 HOH HOH . V 5 HOH A 8 1108 409 HOH HOH . V 5 HOH A 9 1109 411 HOH HOH . V 5 HOH A 10 1110 412 HOH HOH . V 5 HOH A 11 1111 414 HOH HOH . V 5 HOH A 12 1112 415 HOH HOH . V 5 HOH A 13 1113 416 HOH HOH . V 5 HOH A 14 1114 418 HOH HOH . V 5 HOH A 15 1115 419 HOH HOH . V 5 HOH A 16 1116 420 HOH HOH . V 5 HOH A 17 1117 421 HOH HOH . V 5 HOH A 18 1118 423 HOH HOH . V 5 HOH A 19 1119 424 HOH HOH . V 5 HOH A 20 1120 425 HOH HOH . V 5 HOH A 21 1121 427 HOH HOH . V 5 HOH A 22 1122 428 HOH HOH . V 5 HOH A 23 1123 430 HOH HOH . V 5 HOH A 24 1124 431 HOH HOH . V 5 HOH A 25 1125 432 HOH HOH . V 5 HOH A 26 1126 501 HOH HOH . V 5 HOH A 27 1127 502 HOH HOH . V 5 HOH A 28 1128 511 HOH HOH . V 5 HOH A 29 1129 512 HOH HOH . V 5 HOH A 30 1130 513 HOH HOH . V 5 HOH A 31 1131 514 HOH HOH . V 5 HOH A 32 1132 521 HOH HOH . V 5 HOH A 33 1133 522 HOH HOH . V 5 HOH A 34 1134 524 HOH HOH . V 5 HOH A 35 1135 526 HOH HOH . V 5 HOH A 36 1136 527 HOH HOH . V 5 HOH A 37 1137 530 HOH HOH . V 5 HOH A 38 1138 533 HOH HOH . V 5 HOH A 39 1139 538 HOH HOH . V 5 HOH A 40 1140 539 HOH HOH . V 5 HOH A 41 1141 544 HOH HOH . V 5 HOH A 42 1142 545 HOH HOH . V 5 HOH A 43 1143 649 HOH HOH . V 5 HOH A 44 1144 653 HOH HOH . V 5 HOH A 45 1145 655 HOH HOH . V 5 HOH A 46 1146 657 HOH HOH . V 5 HOH A 47 1147 658 HOH HOH . V 5 HOH A 48 1148 660 HOH HOH . V 5 HOH A 49 1149 670 HOH HOH . V 5 HOH A 50 1150 671 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 . U 4 -1.295 17.064 60.15 0.68 11.07 ? C1 RET 1020 A 1 HETATM 2 C C1 RET . B . U 4 -1.307 17.088 60.122 0.32 17.07 ? C1 RET 1020 A 1 HETATM 3 C C2 RET . A . U 4 -2.233 16.651 61.314 0.68 14.1 ? C2 RET 1020 A 1 HETATM 4 C C2 RET . B . U 4 -2.233 16.664 61.296 0.32 18.98 ? C2 RET 1020 A 1 HETATM 5 C C3 RET . A . U 4 -3.645 16.633 61.047 0.68 13.75 ? C3 RET 1020 A 1 HETATM 6 C C3 RET . B . U 4 -3.646 16.629 61.04 0.32 23.34 ? C3 RET 1020 A 1 HETATM 7 C C4 RET . A . U 4 -4.036 15.88 59.798 0.68 10.75 ? C4 RET 1020 A 1 HETATM 8 C C4 RET . B . U 4 -4.029 15.882 59.786 0.32 14.73 ? C4 RET 1020 A 1 HETATM 9 C C5 RET . A . U 4 -3.047 16.023 58.712 0.68 9.23 ? C5 RET 1020 A 1 HETATM 10 C C5 RET . B . U 4 -3.041 16.025 58.691 0.32 10.78 ? C5 RET 1020 A 1 HETATM 11 C C6 RET . A . U 4 -1.774 16.507 58.806 0.68 10.38 ? C6 RET 1020 A 1 HETATM 12 C C6 RET . B . U 4 -1.767 16.523 58.759 0.32 14.19 ? C6 RET 1020 A 1 HETATM 13 C C7 RET . A . U 4 -1.032 16.489 57.641 0.68 10.19 ? C7 RET 1020 A 1 HETATM 14 C C7 RET . B . U 4 -1.045 16.568 57.557 0.32 15.32 ? C7 RET 1020 A 1 HETATM 15 C C8 RET . A . U 4 0.288 16.941 57.5 0.68 10.09 ? C8 RET 1020 A 1 HETATM 16 C C8 RET . B . U 4 0.265 17.007 57.438 0.32 15.03 ? C8 RET 1020 A 1 HETATM 17 C C9 RET . A . U 4 0.995 16.9 56.279 0.68 8.97 ? C9 RET 1020 A 1 HETATM 18 C C9 RET . B . U 4 0.934 16.948 56.179 0.32 13.69 ? C9 RET 1020 A 1 HETATM 19 C C10 RET . A . U 4 2.316 17.38 56.277 0.68 9.36 ? C10 RET 1020 A 1 HETATM 20 C C10 RET . B . U 4 2.229 17.402 56.162 0.32 13.68 ? C10 RET 1020 A 1 HETATM 21 C C11 RET . A . U 4 3.201 17.438 55.2 0.68 8.99 ? C11 RET 1020 A 1 HETATM 22 C C11 RET . B . U 4 3.102 17.435 55.004 0.32 13.19 ? C11 RET 1020 A 1 HETATM 23 C C12 RET . A . U 4 4.421 18.009 55.534 0.68 9.57 ? C12 RET 1020 A 1 HETATM 24 C C12 RET . B . U 4 4.367 17.877 55.461 0.32 15.5 ? C12 RET 1020 A 1 HETATM 25 C C13 RET . A . U 4 5.415 18.277 54.613 0.68 9.18 ? C13 RET 1020 A 1 HETATM 26 C C13 RET . B . U 4 5.331 18.249 54.578 0.32 11.93 ? C13 RET 1020 A 1 HETATM 27 C C14 RET . A . U 4 6.586 18.847 55.053 0.68 11.85 ? C14 RET 1020 A 1 HETATM 28 C C14 RET . B . U 4 6.587 18.688 55.111 0.32 16.93 ? C14 RET 1020 A 1 HETATM 29 C C15 RET . A . U 4 7.649 19.157 54.212 0.68 14.86 ? C15 RET 1020 A 1 HETATM 30 C C15 RET . B . U 4 7.598 19.074 54.36 0.32 18.15 ? C15 RET 1020 A 1 HETATM 31 C C16 RET . A . U 4 0.039 16.478 60.509 0.68 9.74 ? C16 RET 1020 A 1 HETATM 32 C C16 RET . B . U 4 0.024 16.492 60.495 0.32 13.49 ? C16 RET 1020 A 1 HETATM 33 C C17 RET . A . U 4 -1.172 18.558 59.932 0.68 12.49 ? C17 RET 1020 A 1 HETATM 34 C C17 RET . B . U 4 -1.175 18.574 59.919 0.32 18.99 ? C17 RET 1020 A 1 HETATM 35 C C18 RET . A . U 4 -3.572 15.444 57.423 0.68 9.25 ? C18 RET 1020 A 1 HETATM 36 C C18 RET . B . U 4 -3.574 15.423 57.418 0.32 12.44 ? C18 RET 1020 A 1 HETATM 37 C C19 RET . A . U 4 0.427 16.24 55.003 0.68 8 ? C19 RET 1020 A 1 HETATM 38 C C19 RET . B . U 4 0.309 16.144 54.938 0.32 12.8 ? C19 RET 1020 A 1 HETATM 39 C C20 RET . A . U 4 5.314 17.698 53.188 0.68 8.28 ? C20 RET 1020 A 1 HETATM 40 C C20 RET . B . U 4 5.33 17.654 53.126 0.32 12.24 ? C20 RET 1020 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 40 #