data_7KRA # _model_server_result.job_id gNCd24UXsnz0roWELtWqGg _model_server_result.datetime_utc '2025-01-22 04:22:12' _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 7kra # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":301}' # _entry.id 7KRA # _exptl.entry_id 7KRA _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 524.648 _entity.id 13 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2~{R})-1-octanoyloxy-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propan-2-yl] nonanoate' _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 90 _cell.entry_id 7KRA _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7KRA _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details author_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 _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 ? _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 # _struct_asym.details ? _struct_asym.entity_id 13 _struct_asym.id P _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 disulf ? disulf1 A SG CYS 701 A CYS 701 1_555 A SG CYS 709 A CYS 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 I SG CYS 24 I CYS 24 1_555 I SG CYS 97 I CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 I SG CYS 152 I CYS 152 1_555 I SG CYS 208 I CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 J SG CYS 39 J CYS 39 1_555 J SG CYS 109 J CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 J SG CYS 154 J CYS 154 1_555 J SG CYS 214 J CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 73 A ASN 73 1_555 O C1 NAG . A NAG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 106 A ASN 106 1_555 N C1 NAG . A NAG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale3 A ND2 ASN 192 A ASN 192 1_555 M C1 NAG . A NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale4 G ND2 ASN 53 G ASN 53 1_555 R C1 NAG . G NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale5 G ND2 ASN 115 G ASN 115 1_555 Q C1 NAG . G NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? # _chem_comp.formula 'C25 H51 N O8 P' _chem_comp.formula_weight 524.648 _chem_comp.id X3P _chem_comp.mon_nstd_flag . _chem_comp.name '[(2~{R})-1-octanoyloxy-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propan-2-yl] nonanoate' _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 C13 N X3P sing 404 n n C11 C12 X3P sing 405 n n C11 O12 X3P sing 406 n n C12 N X3P sing 407 n n N C15 X3P sing 408 n n N C14 X3P sing 409 n n O12 P X3P sing 410 n n O13 P X3P doub 411 n n P O14 X3P sing 412 n n P O11 X3P sing 413 n n O31 C31 X3P sing 414 n n O31 C3 X3P sing 415 n n O32 C31 X3P doub 416 n n C31 C32 X3P sing 417 n n O11 C1 X3P sing 418 n n C1 C2 X3P sing 419 n n C2 C3 X3P sing 420 n n C2 O21 X3P sing 421 n n O22 C21 X3P doub 422 n n C32 C33 X3P sing 423 n n O21 C21 X3P sing 424 n n C21 C22 X3P sing 425 n n C33 C34 X3P sing 426 n n C22 C23 X3P sing 427 n n C23 C24 X3P sing 428 n n C24 C25 X3P sing 429 n n C34 C35 X3P sing 430 n n C25 C26 X3P sing 431 n n C27 C26 X3P sing 432 n n C27 C28 X3P sing 433 n n C35 C36 X3P sing 434 n n C36 C37 X3P sing 435 n n C28 C29 X3P sing 436 n n C37 C38 X3P sing 437 n n C1 H1 X3P sing 438 n n C1 H2 X3P sing 439 n n C2 H3 X3P sing 440 n n C3 H4 X3P sing 441 n n C3 H5 X3P sing 442 n n C11 H6 X3P sing 443 n n C11 H7 X3P sing 444 n n C12 H8 X3P sing 445 n n C12 H9 X3P sing 446 n n C13 H10 X3P sing 447 n n C13 H11 X3P sing 448 n n C13 H12 X3P sing 449 n n C14 H13 X3P sing 450 n n C14 H14 X3P sing 451 n n C14 H15 X3P sing 452 n n O14 H16 X3P sing 453 n n C15 H17 X3P sing 454 n n C15 H18 X3P sing 455 n n C15 H19 X3P sing 456 n n C22 H20 X3P sing 457 n n C22 H21 X3P sing 458 n n C23 H22 X3P sing 459 n n C23 H23 X3P sing 460 n n C24 H24 X3P sing 461 n n C24 H25 X3P sing 462 n n C25 H26 X3P sing 463 n n C25 H27 X3P sing 464 n n C26 H28 X3P sing 465 n n C26 H29 X3P sing 466 n n C27 H30 X3P sing 467 n n C27 H31 X3P sing 468 n n C28 H32 X3P sing 469 n n C28 H33 X3P sing 470 n n C29 H34 X3P sing 471 n n C29 H35 X3P sing 472 n n C29 H36 X3P sing 473 n n C32 H37 X3P sing 474 n n C32 H38 X3P sing 475 n n C33 H39 X3P sing 476 n n C33 H40 X3P sing 477 n n C34 H41 X3P sing 478 n n C34 H42 X3P sing 479 n n C35 H43 X3P sing 480 n n C35 H44 X3P sing 481 n n C36 H45 X3P sing 482 n n C36 H46 X3P sing 483 n n C37 H47 X3P sing 484 n n C37 H48 X3P sing 485 n n C38 H49 X3P sing 486 n n C38 H50 X3P sing 487 n n C38 H51 X3P sing 488 n n # _atom_sites.entry_id 7KRA _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 M 12 NAG A 1 801 762 NAG NAG . N 12 NAG A 1 802 765 NAG NAG . O 12 NAG A 1 803 766 NAG NAG . P 13 X3P C 1 301 201 X3P PCW . Q 12 NAG G 1 301 273 NAG NAG . R 12 NAG G 1 302 275 NAG NAG . # 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 N N X3P . . . P 13 223.689 210.169 206.114 1 103.26 ? N X3P 301 C 1 HETATM 2 P P X3P . . . P 13 226.342 207.122 207.577 1 103.26 ? P X3P 301 C 1 HETATM 3 C C1 X3P . . . P 13 224.641 205.737 209.053 1 103.26 ? C1 X3P 301 C 1 HETATM 4 C C2 X3P . . . P 13 223.222 206.284 209.105 1 103.26 ? C2 X3P 301 C 1 HETATM 5 C C3 X3P . . . P 13 222.235 205.123 209.324 1 103.26 ? C3 X3P 301 C 1 HETATM 6 C C11 X3P . . . P 13 225.415 208.371 205.395 1 103.26 ? C11 X3P 301 C 1 HETATM 7 O O11 X3P . . . P 13 225.571 206.815 209.028 1 103.26 ? O11 X3P 301 C 1 HETATM 8 C C12 X3P . . . P 13 225.124 209.831 205.906 1 103.26 ? C12 X3P 301 C 1 HETATM 9 O O12 X3P . . . P 13 225.18 207.394 206.411 1 103.26 ? O12 X3P 301 C 1 HETATM 10 C C13 X3P . . . P 13 222.953 210.167 204.853 1 103.26 ? C13 X3P 301 C 1 HETATM 11 O O13 X3P . . . P 13 227.177 205.918 207.188 1 103.26 ? O13 X3P 301 C 1 HETATM 12 C C14 X3P . . . P 13 223.052 209.249 207.071 1 103.26 ? C14 X3P 301 C 1 HETATM 13 O O14 X3P . . . P 13 227.234 208.334 207.718 1 103.26 ? O14 X3P 301 C 1 HETATM 14 C C15 X3P . . . P 13 223.638 211.497 206.676 1 103.26 ? C15 X3P 301 C 1 HETATM 15 C C21 X3P . . . P 13 221.843 207.843 210.29 1 103.26 ? C21 X3P 301 C 1 HETATM 16 O O21 X3P . . . P 13 223.121 207.203 210.166 1 103.26 ? O21 X3P 301 C 1 HETATM 17 C C22 X3P . . . P 13 221.234 208.111 211.703 1 103.26 ? C22 X3P 301 C 1 HETATM 18 O O22 X3P . . . P 13 221.251 208.174 209.319 1 103.26 ? O22 X3P 301 C 1 HETATM 19 C C23 X3P . . . P 13 219.802 207.511 211.77 1 103.26 ? C23 X3P 301 C 1 HETATM 20 C C24 X3P . . . P 13 219.892 206.025 212.18 1 103.26 ? C24 X3P 301 C 1 HETATM 21 C C25 X3P . . . P 13 218.467 205.411 212.253 1 103.26 ? C25 X3P 301 C 1 HETATM 22 C C26 X3P . . . P 13 217.945 205.473 213.717 1 103.26 ? C26 X3P 301 C 1 HETATM 23 C C27 X3P . . . P 13 216.399 205.527 213.711 1 103.26 ? C27 X3P 301 C 1 HETATM 24 C C28 X3P . . . P 13 215.867 205.149 215.123 1 103.26 ? C28 X3P 301 C 1 HETATM 25 C C29 X3P . . . P 13 215.503 203.647 215.149 1 103.26 ? C29 X3P 301 C 1 HETATM 26 C C31 X3P . . . P 13 222.101 202.783 209.004 1 103.26 ? C31 X3P 301 C 1 HETATM 27 O O31 X3P . . . P 13 222.602 204.022 208.499 1 103.26 ? O31 X3P 301 C 1 HETATM 28 C C32 X3P . . . P 13 223.014 201.918 209.916 1 103.26 ? C32 X3P 301 C 1 HETATM 29 O O32 X3P . . . P 13 221.007 202.423 208.732 1 103.26 ? O32 X3P 301 C 1 HETATM 30 C C33 X3P . . . P 13 222.554 202.087 211.382 1 103.26 ? C33 X3P 301 C 1 HETATM 31 C C34 X3P . . . P 13 223.761 202.525 212.249 1 103.26 ? C34 X3P 301 C 1 HETATM 32 C C35 X3P . . . P 13 223.339 202.62 213.73 1 103.26 ? C35 X3P 301 C 1 HETATM 33 C C36 X3P . . . P 13 223.268 201.197 214.352 1 103.26 ? C36 X3P 301 C 1 HETATM 34 C C37 X3P . . . P 13 223.047 201.307 215.898 1 103.26 ? C37 X3P 301 C 1 HETATM 35 C C38 X3P . . . P 13 223.429 199.955 216.581 1 103.26 ? C38 X3P 301 C 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 357 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 35 #