data_3DDL # _model_server_result.job_id c8fk-FZI8SMCRN2o75HO9g _model_server_result.datetime_utc '2024-11-23 12:07:09' _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 3ddl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"BA","auth_seq_id":1415}' # _entry.id 3DDL # _exptl.entry_id 3DDL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 678.94 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 76.35 _cell.angle_beta 74.93 _cell.angle_gamma 64.08 _cell.entry_id 3DDL _cell.length_a 52.74 _cell.length_b 59.49 _cell.length_c 59.72 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DDL _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J,K,L,DA 1 1 B,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,EA 2 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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id BA _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 240 A LYS 240 1_555 L C15 RET . A RET 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale2 B NZ LYS 240 B LYS 240 1_555 AA C15 RET . B RET 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? # _chem_comp.formula 'C36 H73 N O8 P 1' _chem_comp.formula_weight 678.94 _chem_comp.id PX4 _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE _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 PX4 sing 402 n n O1 H1P PX4 sing 403 n n O2 P1 PX4 doub 404 n n P1 O3 PX4 sing 405 n n P1 O4 PX4 sing 406 n n O3 C1 PX4 sing 407 n n C1 C2 PX4 sing 408 n n C1 H1 PX4 sing 409 n n C1 H2 PX4 sing 410 n n C2 N1 PX4 sing 411 n n C2 H3 PX4 sing 412 n n C2 H4 PX4 sing 413 n n N1 C3 PX4 sing 414 n n N1 C4 PX4 sing 415 n n N1 C5 PX4 sing 416 n n C3 H5 PX4 sing 417 n n C3 H6 PX4 sing 418 n n C3 H7 PX4 sing 419 n n C4 H8 PX4 sing 420 n n C4 H9 PX4 sing 421 n n C4 H10 PX4 sing 422 n n C5 H11 PX4 sing 423 n n C5 H12 PX4 sing 424 n n C5 H13 PX4 sing 425 n n O4 C6 PX4 sing 426 n n C6 C7 PX4 sing 427 n n C6 H14 PX4 sing 428 n n C6 H15 PX4 sing 429 n n C7 C8 PX4 sing 430 n n C7 O7 PX4 sing 431 n n C7 H16 PX4 sing 432 n n C8 O5 PX4 sing 433 n n C8 H17 PX4 sing 434 n n C8 H18 PX4 sing 435 n n O5 C9 PX4 sing 436 n n C9 O6 PX4 doub 437 n n C9 C10 PX4 sing 438 n n C10 C11 PX4 sing 439 n n C10 H19 PX4 sing 440 n n C10 H20 PX4 sing 441 n n C11 C12 PX4 sing 442 n n C11 H21 PX4 sing 443 n n C11 H22 PX4 sing 444 n n C12 C13 PX4 sing 445 n n C12 H23 PX4 sing 446 n n C12 H24 PX4 sing 447 n n C13 C14 PX4 sing 448 n n C13 H25 PX4 sing 449 n n C13 H26 PX4 sing 450 n n C14 C15 PX4 sing 451 n n C14 H27 PX4 sing 452 n n C14 H28 PX4 sing 453 n n C15 C16 PX4 sing 454 n n C15 H29 PX4 sing 455 n n C15 H30 PX4 sing 456 n n C16 C17 PX4 sing 457 n n C16 H31 PX4 sing 458 n n C16 H32 PX4 sing 459 n n C17 C18 PX4 sing 460 n n C17 H33 PX4 sing 461 n n C17 H34 PX4 sing 462 n n C18 C19 PX4 sing 463 n n C18 H35 PX4 sing 464 n n C18 H36 PX4 sing 465 n n C19 C20 PX4 sing 466 n n C19 H37 PX4 sing 467 n n C19 H38 PX4 sing 468 n n C20 C21 PX4 sing 469 n n C20 H39 PX4 sing 470 n n C20 H40 PX4 sing 471 n n C21 C22 PX4 sing 472 n n C21 H41 PX4 sing 473 n n C21 H42 PX4 sing 474 n n C22 H43 PX4 sing 475 n n C22 H44 PX4 sing 476 n n C22 H45 PX4 sing 477 n n O7 C23 PX4 sing 478 n n C23 O8 PX4 doub 479 n n C23 C24 PX4 sing 480 n n C24 C25 PX4 sing 481 n n C24 H46 PX4 sing 482 n n C24 H47 PX4 sing 483 n n C25 C26 PX4 sing 484 n n C25 H48 PX4 sing 485 n n C25 H49 PX4 sing 486 n n C26 C27 PX4 sing 487 n n C26 H50 PX4 sing 488 n n C26 H51 PX4 sing 489 n n C27 C28 PX4 sing 490 n n C27 H52 PX4 sing 491 n n C27 H53 PX4 sing 492 n n C28 C29 PX4 sing 493 n n C28 H54 PX4 sing 494 n n C28 H55 PX4 sing 495 n n C29 C30 PX4 sing 496 n n C29 H56 PX4 sing 497 n n C29 H57 PX4 sing 498 n n C30 C31 PX4 sing 499 n n C30 H58 PX4 sing 500 n n C30 H59 PX4 sing 501 n n C31 C32 PX4 sing 502 n n C31 H60 PX4 sing 503 n n C31 H61 PX4 sing 504 n n C32 C33 PX4 sing 505 n n C32 H62 PX4 sing 506 n n C32 H63 PX4 sing 507 n n C33 C34 PX4 sing 508 n n C33 H64 PX4 sing 509 n n C33 H65 PX4 sing 510 n n C34 C35 PX4 sing 511 n n C34 H66 PX4 sing 512 n n C34 H67 PX4 sing 513 n n C35 C36 PX4 sing 514 n n C35 H68 PX4 sing 515 n n C35 H69 PX4 sing 516 n n C36 H70 PX4 sing 517 n n C36 H71 PX4 sing 518 n n C36 H72 PX4 sing 519 n n # _atom_sites.entry_id 3DDL _atom_sites.fract_transf_matrix[1][1] 0.018961 _atom_sites.fract_transf_matrix[1][2] -0.009215 _atom_sites.fract_transf_matrix[1][3] -0.003846 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01869 _atom_sites.fract_transf_matrix[2][3] -0.002659 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.017516 _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 C 2 SXN A 1 1401 1401 SXN SXN . D 3 UNL A 1 1402 1402 UNL UNL . E 3 UNL A 1 1403 1403 UNL UNL . F 3 UNL A 1 1404 1404 UNL UNL . G 3 UNL A 1 1405 1405 UNL UNL . H 3 UNL A 1 1406 1406 UNL UNL . I 3 UNL A 1 1407 1407 UNL UNL . J 3 UNL A 1 1408 1408 UNL UNL . K 3 UNL A 1 1409 1409 UNL UNL . L 4 RET A 1 1301 1301 RET RET . M 2 SXN B 1 1401 1401 SXN SXN . N 3 UNL B 1 1402 1402 UNL UNL . O 3 UNL B 1 1403 1403 UNL UNL . P 3 UNL B 1 1404 1404 UNL UNL . Q 3 UNL B 1 1405 1405 UNL UNL . R 3 UNL B 1 1406 1406 UNL UNL . S 3 UNL B 1 1407 1407 UNL UNL . T 3 UNL B 1 1408 1408 UNL UNL . U 3 UNL B 1 1409 1409 UNL UNL . V 3 UNL B 1 1410 1410 UNL UNL . W 3 UNL B 1 1411 1411 UNL UNL . X 3 UNL B 1 1412 1412 UNL UNL . Y 3 UNL B 1 1413 1413 UNL UNL . Z 3 UNL B 1 1414 1414 UNL UNL . AA 4 RET B 1 1301 1301 RET RET . BA 5 PX4 B 1 1415 1415 PX4 PX4 . CA 6 PCW B 1 1416 1416 PCW PCW . DA 7 HOH A 1 402 402 HOH HOH . DA 7 HOH A 2 413 413 HOH HOH . DA 7 HOH A 3 414 414 HOH HOH . DA 7 HOH A 4 415 415 HOH HOH . DA 7 HOH A 5 416 416 HOH HOH . DA 7 HOH A 6 417 417 HOH HOH . DA 7 HOH A 7 418 418 HOH HOH . DA 7 HOH A 8 419 419 HOH HOH . DA 7 HOH A 9 420 420 HOH HOH . DA 7 HOH A 10 421 421 HOH HOH . DA 7 HOH A 11 422 422 HOH HOH . DA 7 HOH A 12 423 423 HOH HOH . DA 7 HOH A 13 424 424 HOH HOH . DA 7 HOH A 14 425 425 HOH HOH . DA 7 HOH A 15 426 426 HOH HOH . DA 7 HOH A 16 427 427 HOH HOH . DA 7 HOH A 17 428 428 HOH HOH . DA 7 HOH A 18 429 429 HOH HOH . DA 7 HOH A 19 430 430 HOH HOH . DA 7 HOH A 20 431 431 HOH HOH . DA 7 HOH A 21 432 432 HOH HOH . DA 7 HOH A 22 433 433 HOH HOH . DA 7 HOH A 23 434 434 HOH HOH . DA 7 HOH A 24 435 435 HOH HOH . DA 7 HOH A 25 436 436 HOH HOH . DA 7 HOH A 26 437 437 HOH HOH . DA 7 HOH A 27 438 438 HOH HOH . DA 7 HOH A 28 439 439 HOH HOH . DA 7 HOH A 29 440 440 HOH HOH . DA 7 HOH A 30 441 441 HOH HOH . DA 7 HOH A 31 442 442 HOH HOH . DA 7 HOH A 32 443 443 HOH HOH . DA 7 HOH A 33 501 501 HOH HOH . DA 7 HOH A 34 502 502 HOH HOH . EA 7 HOH B 1 402 402 HOH HOH . EA 7 HOH B 2 420 420 HOH HOH . EA 7 HOH B 3 421 421 HOH HOH . EA 7 HOH B 4 422 422 HOH HOH . EA 7 HOH B 5 423 423 HOH HOH . EA 7 HOH B 6 424 424 HOH HOH . EA 7 HOH B 7 425 425 HOH HOH . EA 7 HOH B 8 426 426 HOH HOH . EA 7 HOH B 9 427 427 HOH HOH . EA 7 HOH B 10 428 428 HOH HOH . EA 7 HOH B 11 429 429 HOH HOH . EA 7 HOH B 12 430 430 HOH HOH . EA 7 HOH B 13 431 431 HOH HOH . EA 7 HOH B 14 432 432 HOH HOH . EA 7 HOH B 15 433 433 HOH HOH . EA 7 HOH B 16 434 434 HOH HOH . EA 7 HOH B 17 435 435 HOH HOH . EA 7 HOH B 18 436 436 HOH HOH . EA 7 HOH B 19 437 437 HOH HOH . EA 7 HOH B 20 438 438 HOH HOH . EA 7 HOH B 21 439 439 HOH HOH . EA 7 HOH B 22 440 440 HOH HOH . EA 7 HOH B 23 441 441 HOH HOH . EA 7 HOH B 24 442 442 HOH HOH . EA 7 HOH B 25 443 443 HOH HOH . EA 7 HOH B 26 444 444 HOH HOH . EA 7 HOH B 27 501 501 HOH HOH . EA 7 HOH B 28 502 502 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 O O1 PX4 . . . BA 5 38.676 52.609 74.528 1 81.6 ? O1 PX4 1415 B 1 HETATM 2 O O2 PX4 . . . BA 5 40.774 53.874 73.827 1 82.75 ? O2 PX4 1415 B 1 HETATM 3 P P1 PX4 . . . BA 5 40.036 52.435 73.883 1 83.18 ? P1 PX4 1415 B 1 HETATM 4 O O3 PX4 . . . BA 5 40.875 51.448 74.679 1 80.47 ? O3 PX4 1415 B 1 HETATM 5 O O4 PX4 . . . BA 5 39.854 51.886 72.374 1 81.5 ? O4 PX4 1415 B 1 HETATM 6 C C6 PX4 . . . BA 5 40.97 51.878 71.483 1 78.49 ? C6 PX4 1415 B 1 HETATM 7 C C7 PX4 . . . BA 5 40.493 51.639 70.049 1 76.95 ? C7 PX4 1415 B 1 HETATM 8 C C8 PX4 . . . BA 5 41.616 52.042 69.065 1 76.56 ? C8 PX4 1415 B 1 HETATM 9 O O5 PX4 . . . BA 5 41.245 53.207 68.303 1 76.53 ? O5 PX4 1415 B 1 HETATM 10 C C9 PX4 . . . BA 5 41.935 53.556 67.048 1 76.21 ? C9 PX4 1415 B 1 HETATM 11 O O6 PX4 . . . BA 5 43.141 53.77 67.049 1 77.59 ? O6 PX4 1415 B 1 HETATM 12 C C10 PX4 . . . BA 5 41.146 53.679 65.756 1 74.73 ? C10 PX4 1415 B 1 HETATM 13 C C11 PX4 . . . BA 5 41.859 52.977 64.612 1 72.94 ? C11 PX4 1415 B 1 HETATM 14 C C12 PX4 . . . BA 5 40.83 52.336 63.704 1 71.08 ? C12 PX4 1415 B 1 HETATM 15 C C13 PX4 . . . BA 5 41.537 51.806 62.476 1 70.63 ? C13 PX4 1415 B 1 HETATM 16 C C14 PX4 . . . BA 5 40.554 51.03 61.623 1 69.56 ? C14 PX4 1415 B 1 HETATM 17 C C15 PX4 . . . BA 5 41.328 50.207 60.608 1 69.42 ? C15 PX4 1415 B 1 HETATM 18 C C16 PX4 . . . BA 5 40.363 49.533 59.659 1 68.46 ? C16 PX4 1415 B 1 HETATM 19 O O7 PX4 . . . BA 5 39.267 52.384 69.795 1 74.09 ? O7 PX4 1415 B 1 HETATM 20 C C23 PX4 . . . BA 5 38.214 51.823 68.934 1 71.14 ? C23 PX4 1415 B 1 HETATM 21 O O8 PX4 . . . BA 5 37.264 51.215 69.426 1 71.99 ? O8 PX4 1415 B 1 HETATM 22 C C24 PX4 . . . BA 5 38.313 51.986 67.433 1 67.64 ? C24 PX4 1415 B 1 HETATM 23 C C25 PX4 . . . BA 5 37.074 52.658 66.88 1 62.98 ? C25 PX4 1415 B 1 HETATM 24 C C26 PX4 . . . BA 5 36.836 52.109 65.493 1 60.75 ? C26 PX4 1415 B 1 HETATM 25 C C27 PX4 . . . BA 5 35.933 53.058 64.725 1 59 ? C27 PX4 1415 B 1 HETATM 26 C C28 PX4 . . . BA 5 36.429 53.205 63.289 1 58.49 ? C28 PX4 1415 B 1 HETATM 27 C C29 PX4 . . . BA 5 36.183 51.914 62.515 1 57.52 ? C29 PX4 1415 B 1 HETATM 28 C C30 PX4 . . . BA 5 35.923 52.226 61.052 1 57.07 ? C30 PX4 1415 B 1 HETATM 29 C C31 PX4 . . . BA 5 36.798 51.324 60.212 1 58.3 ? C31 PX4 1415 B 1 HETATM 30 C C32 PX4 . . . BA 5 36.209 51.165 58.822 1 59.41 ? C32 PX4 1415 B 1 HETATM 31 C C33 PX4 . . . BA 5 37.331 51.352 57.805 1 61.63 ? C33 PX4 1415 B 1 HETATM 32 C C34 PX4 . . . BA 5 36.788 52.026 56.552 1 62.11 ? C34 PX4 1415 B 1 HETATM 33 C C35 PX4 . . . BA 5 36.894 51.06 55.374 1 61.85 ? C35 PX4 1415 B 1 HETATM 34 C C36 PX4 . . . BA 5 37.708 51.696 54.261 1 62.43 ? C36 PX4 1415 B 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 375 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 34 #