data_5EJ1 # _model_server_result.job_id '_dNa4S6S9ruhfeDeyAc4sQ' _model_server_result.datetime_utc '2024-11-22 10:09:31' _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 5ej1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":801}' # _entry.id 5EJ1 # _exptl.entry_id 5EJ1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 482.568 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(4S,7R)-7-(heptanoyloxy)-4-hydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphahexadecan-1-aminium 4-oxide' _entity.pdbx_number_of_molecules 2 _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 90 _cell.entry_id 5EJ1 _cell.length_a 67.355 _cell.length_b 218.23 _cell.length_c 220.765 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EJ1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 G N N ? 6 J N N # _pdbx_entity_branch.entity_id 4 _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 ? 4 2 1 BGC BGC C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BGC BGC C1 O1 . O4 HO4 . sing 3 ? 4 4 3 BGC BGC C1 O1 . O4 HO4 . sing 4 ? 4 5 4 BGC BGC C1 O1 . O4 HO4 . sing 5 ? 4 6 5 BGC BGC C1 O1 . O4 HO4 . sing 6 ? 4 7 6 BGC BGC C1 O1 . O4 HO4 . sing 7 ? 4 8 7 BGC BGC C1 O1 . O4 HO4 . sing 8 ? 4 9 8 BGC BGC C1 O1 . O4 HO4 . sing 9 ? 4 10 9 BGC BGC C1 O1 . O4 HO4 . sing 10 ? 4 11 10 BGC BGC C1 O1 . O4 HO4 . sing 11 ? 4 12 11 BGC BGC C1 O1 . O4 HO4 . sing 12 ? 4 13 12 BGC BGC C1 O1 . O4 HO4 . sing 13 ? 4 14 13 BGC BGC C1 O1 . O4 HO4 . sing 14 ? 4 15 14 BGC BGC C1 O1 . O4 HO4 . sing 15 ? 4 16 15 BGC BGC C1 O1 . O4 HO4 . sing 16 ? 4 17 16 BGC BGC C1 O1 . O4 HO4 . sing 17 ? 4 18 17 BGC BGC 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 4 n D BGC 1 C 1 BGC A 901 BGC 4 n D BGC 2 C 2 BGC A 902 BGC 4 n D BGC 3 C 3 BGC A 903 BGC 4 n D BGC 4 C 4 BGC A 904 BGC 4 n D BGC 5 C 5 BGC A 905 BGC 4 n D BGC 6 C 6 BGC A 906 BGC 4 n D BGC 7 C 7 BGC A 907 BGC 4 n D BGC 8 C 8 BGC A 908 BGC 4 n D BGC 9 C 9 BGC A 909 BGC 4 n D BGC 10 C 10 BGC A 910 BGC 4 n D BGC 11 C 11 BGC A 911 BGC 4 n D BGC 12 C 12 BGC A 912 BGC 4 n D BGC 13 C 13 BGC A 913 BGC 4 n D BGC 14 C 14 BGC A 914 BGC 4 n D BGC 15 C 15 BGC A 915 BGC 4 n D BGC 16 C 16 BGC A 916 BGC 4 n D BGC 17 C 17 BGC A 917 BGC 4 n D BGC 18 C 18 BGC A 918 BGC # 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 B SG CYS 112 B CYS 163 1_555 B SG CYS 379 B CYS 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 C C UNK 1 D UNK 170 1_555 C N UNK 2 D UNK 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 C C UNK 2 D UNK 171 1_555 C N UNK 3 D UNK 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 C C UNK 3 D UNK 172 1_555 C N UNK 4 D UNK 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 C C UNK 5 D UNK 175 1_555 C N UNK 6 D UNK 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 C C UNK 6 D UNK 176 1_555 C N UNK 7 D UNK 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 D O4 BGC . C BGC 1 1_555 D C1 BGC . C BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 D O4 BGC . C BGC 2 1_555 D C1 BGC . C BGC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale8 D O4 BGC . C BGC 3 1_555 D C1 BGC . C BGC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale9 D O4 BGC . C BGC 4 1_555 D C1 BGC . C BGC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale10 D O4 BGC . C BGC 5 1_555 D C1 BGC . C BGC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale11 D O4 BGC . C BGC 6 1_555 D C1 BGC . C BGC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale12 D O4 BGC . C BGC 7 1_555 D C1 BGC . C BGC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale13 D O4 BGC . C BGC 8 1_555 D C1 BGC . C BGC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale14 D O4 BGC . C BGC 9 1_555 D C1 BGC . C BGC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale15 D O4 BGC . C BGC 10 1_555 D C1 BGC . C BGC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale16 D O4 BGC . C BGC 11 1_555 D C1 BGC . C BGC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale17 D O4 BGC . C BGC 12 1_555 D C1 BGC . C BGC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale18 D O4 BGC . C BGC 13 1_555 D C1 BGC . C BGC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale19 D O4 BGC . C BGC 14 1_555 D C1 BGC . C BGC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale20 D O4 BGC . C BGC 15 1_555 D C1 BGC . C BGC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale21 D O4 BGC . C BGC 16 1_555 D C1 BGC . C BGC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale22 D O4 BGC . C BGC 17 1_555 D C1 BGC . C BGC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? # _chem_comp.formula 'C22 H45 N O8 P 1' _chem_comp.formula_weight 482.568 _chem_comp.id XP5 _chem_comp.mon_nstd_flag . _chem_comp.name '(4S,7R)-7-(heptanoyloxy)-4-hydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphahexadecan-1-aminium 4-oxide' _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 O1 P1 XP5 doub 606 n n O2 P1 XP5 sing 607 n n P1 O3 XP5 sing 608 n n P1 O4 XP5 sing 609 n n O3 C1 XP5 sing 610 n n C1 C2 XP5 sing 611 n n C2 N1 XP5 sing 612 n n N1 C3 XP5 sing 613 n n N1 C4 XP5 sing 614 n n N1 C5 XP5 sing 615 n n O4 C6 XP5 sing 616 n n C6 CAM XP5 sing 617 n n C8 O5 XP5 sing 618 n n C8 CAM XP5 sing 619 n n O5 C9 XP5 sing 620 n n C9 O6 XP5 doub 621 n n C9 C10 XP5 sing 622 n n C10 C11 XP5 sing 623 n n C11 C12 XP5 sing 624 n n C12 C13 XP5 sing 625 n n C13 C14 XP5 sing 626 n n C14 C15 XP5 sing 627 n n O7 C17 XP5 doub 628 n n C17 O8 XP5 sing 629 n n C17 C18 XP5 sing 630 n n O8 CAM XP5 sing 631 n n C18 C19 XP5 sing 632 n n C19 C20 XP5 sing 633 n n C20 C21 XP5 sing 634 n n C21 C22 XP5 sing 635 n n C22 C23 XP5 sing 636 n n O2 H2 XP5 sing 637 n n C1 H11C XP5 sing 638 n n C1 H12C XP5 sing 639 n n C2 H21C XP5 sing 640 n n C2 H22C XP5 sing 641 n n C3 H31C XP5 sing 642 n n C3 H32C XP5 sing 643 n n C3 H33C XP5 sing 644 n n C4 H41C XP5 sing 645 n n C4 H42C XP5 sing 646 n n C4 H43C XP5 sing 647 n n C5 H51C XP5 sing 648 n n C5 H52C XP5 sing 649 n n C5 H53C XP5 sing 650 n n C6 H61C XP5 sing 651 n n C6 H62C XP5 sing 652 n n CAM HAM XP5 sing 653 n n C8 H81C XP5 sing 654 n n C8 H82C XP5 sing 655 n n C10 H101 XP5 sing 656 n n C10 H102 XP5 sing 657 n n C11 H111 XP5 sing 658 n n C11 H112 XP5 sing 659 n n C12 H121 XP5 sing 660 n n C12 H122 XP5 sing 661 n n C13 H131 XP5 sing 662 n n C13 H132 XP5 sing 663 n n C14 H141 XP5 sing 664 n n C14 H142 XP5 sing 665 n n C15 H151 XP5 sing 666 n n C15 H152 XP5 sing 667 n n C15 H153 XP5 sing 668 n n C18 H181 XP5 sing 669 n n C18 H182 XP5 sing 670 n n C19 H191 XP5 sing 671 n n C19 H192 XP5 sing 672 n n C20 H201 XP5 sing 673 n n C20 H202 XP5 sing 674 n n C21 H211 XP5 sing 675 n n C21 H212 XP5 sing 676 n n C22 H221 XP5 sing 677 n n C22 H222 XP5 sing 678 n n C23 H231 XP5 sing 679 n n C23 H232 XP5 sing 680 n n C23 H233 XP5 sing 681 n n # _atom_sites.entry_id 5EJ1 _atom_sites.fract_transf_matrix[1][1] 0.014847 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004582 _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] 0.00453 _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 E 5 C2E A 1 919 919 C2E C2E . F 5 C2E A 1 920 920 C2E C2E . G 6 XP5 A 1 921 922 XP5 PLC . H 7 3PE A 1 922 923 3PE 3PE . I 7 3PE A 1 923 1 3PE 3PE . J 6 XP5 B 1 801 1 XP5 PLC . # 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 O O1 XP5 . . . J 6 -6.729 33.074 -67.703 1 212.93 ? O1 XP5 801 B 1 HETATM 2 O O2 XP5 . . . J 6 -6.773 33.29 -65.248 1 212.53 ? O2 XP5 801 B 1 HETATM 3 P P1 XP5 . . . J 6 -6.841 32.316 -66.402 1 212.86 ? P1 XP5 801 B 1 HETATM 4 O O3 XP5 . . . J 6 -8.282 31.514 -66.372 1 212.08 ? O3 XP5 801 B 1 HETATM 5 C C1 XP5 . . . J 6 -9.001 31.469 -65.172 1 211.45 ? C1 XP5 801 B 1 HETATM 6 C C2 XP5 . . . J 6 -8.286 30.536 -64.195 1 211.26 ? C2 XP5 801 B 1 HETATM 7 N N1 XP5 . . . J 6 -8.671 30.88 -62.835 1 209.89 ? N1 XP5 801 B 1 HETATM 8 C C3 XP5 . . . J 6 -8.271 32.246 -62.55 1 209.75 ? C3 XP5 801 B 1 HETATM 9 C C4 XP5 . . . J 6 -10.111 30.757 -62.7 1 208.96 ? C4 XP5 801 B 1 HETATM 10 C C5 XP5 . . . J 6 -8.015 29.977 -61.908 1 209.85 ? C5 XP5 801 B 1 HETATM 11 O O4 XP5 . . . J 6 -5.598 31.238 -66.282 1 213.81 ? O4 XP5 801 B 1 HETATM 12 C C6 XP5 . . . J 6 -4.285 31.719 -66.219 1 214.1 ? C6 XP5 801 B 1 HETATM 13 C C8 XP5 . . . J 6 -3.279 29.441 -65.921 1 214.92 ? C8 XP5 801 B 1 HETATM 14 O O5 XP5 . . . J 6 -2.187 28.639 -66.272 1 215.18 ? O5 XP5 801 B 1 HETATM 15 C C9 XP5 . . . J 6 -2.109 27.429 -65.576 1 214.56 ? C9 XP5 801 B 1 HETATM 16 O O6 XP5 . . . J 6 -2.777 27.251 -64.613 1 213.76 ? O6 XP5 801 B 1 HETATM 17 C C10 XP5 . . . J 6 -1.163 26.333 -66.054 1 214.93 ? C10 XP5 801 B 1 HETATM 18 O O8 XP5 . . . J 6 -3.754 30.332 -68.091 1 214.86 ? O8 XP5 801 B 1 HETATM 19 C CAM XP5 . . . J 6 -3.323 30.686 -66.808 1 214.94 ? CAM XP5 801 B 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #