data_5VB2 # _model_server_result.job_id Mcv6tQrqhoSGg9tXed5GUw _model_server_result.datetime_utc '2024-10-27 12:29:23' _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 5vb2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1303}' # _entry.id 5VB2 # _exptl.entry_id 5VB2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 678.94 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE _entity.pdbx_number_of_molecules 13 _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 5VB2 _cell.length_a 125.963 _cell.length_b 129.853 _cell.length_c 196.128 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VB2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA _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 ? 3 G N N ? 3 H N N ? 3 I N N ? 3 M N N ? 3 N N N ? 3 O N N ? 3 P N N ? 3 T N N ? 3 U N N ? 3 V N N ? 3 AA N N ? 3 BA N N ? 3 CA N N # _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 371 n n O1 H1P PX4 sing 372 n n O2 P1 PX4 doub 373 n n P1 O3 PX4 sing 374 n n P1 O4 PX4 sing 375 n n O3 C1 PX4 sing 376 n n C1 C2 PX4 sing 377 n n C1 H1 PX4 sing 378 n n C1 H2 PX4 sing 379 n n C2 N1 PX4 sing 380 n n C2 H3 PX4 sing 381 n n C2 H4 PX4 sing 382 n n N1 C3 PX4 sing 383 n n N1 C4 PX4 sing 384 n n N1 C5 PX4 sing 385 n n C3 H5 PX4 sing 386 n n C3 H6 PX4 sing 387 n n C3 H7 PX4 sing 388 n n C4 H8 PX4 sing 389 n n C4 H9 PX4 sing 390 n n C4 H10 PX4 sing 391 n n C5 H11 PX4 sing 392 n n C5 H12 PX4 sing 393 n n C5 H13 PX4 sing 394 n n O4 C6 PX4 sing 395 n n C6 C7 PX4 sing 396 n n C6 H14 PX4 sing 397 n n C6 H15 PX4 sing 398 n n C7 C8 PX4 sing 399 n n C7 O7 PX4 sing 400 n n C7 H16 PX4 sing 401 n n C8 O5 PX4 sing 402 n n C8 H17 PX4 sing 403 n n C8 H18 PX4 sing 404 n n O5 C9 PX4 sing 405 n n C9 O6 PX4 doub 406 n n C9 C10 PX4 sing 407 n n C10 C11 PX4 sing 408 n n C10 H19 PX4 sing 409 n n C10 H20 PX4 sing 410 n n C11 C12 PX4 sing 411 n n C11 H21 PX4 sing 412 n n C11 H22 PX4 sing 413 n n C12 C13 PX4 sing 414 n n C12 H23 PX4 sing 415 n n C12 H24 PX4 sing 416 n n C13 C14 PX4 sing 417 n n C13 H25 PX4 sing 418 n n C13 H26 PX4 sing 419 n n C14 C15 PX4 sing 420 n n C14 H27 PX4 sing 421 n n C14 H28 PX4 sing 422 n n C15 C16 PX4 sing 423 n n C15 H29 PX4 sing 424 n n C15 H30 PX4 sing 425 n n C16 C17 PX4 sing 426 n n C16 H31 PX4 sing 427 n n C16 H32 PX4 sing 428 n n C17 C18 PX4 sing 429 n n C17 H33 PX4 sing 430 n n C17 H34 PX4 sing 431 n n C18 C19 PX4 sing 432 n n C18 H35 PX4 sing 433 n n C18 H36 PX4 sing 434 n n C19 C20 PX4 sing 435 n n C19 H37 PX4 sing 436 n n C19 H38 PX4 sing 437 n n C20 C21 PX4 sing 438 n n C20 H39 PX4 sing 439 n n C20 H40 PX4 sing 440 n n C21 C22 PX4 sing 441 n n C21 H41 PX4 sing 442 n n C21 H42 PX4 sing 443 n n C22 H43 PX4 sing 444 n n C22 H44 PX4 sing 445 n n C22 H45 PX4 sing 446 n n O7 C23 PX4 sing 447 n n C23 O8 PX4 doub 448 n n C23 C24 PX4 sing 449 n n C24 C25 PX4 sing 450 n n C24 H46 PX4 sing 451 n n C24 H47 PX4 sing 452 n n C25 C26 PX4 sing 453 n n C25 H48 PX4 sing 454 n n C25 H49 PX4 sing 455 n n C26 C27 PX4 sing 456 n n C26 H50 PX4 sing 457 n n C26 H51 PX4 sing 458 n n C27 C28 PX4 sing 459 n n C27 H52 PX4 sing 460 n n C27 H53 PX4 sing 461 n n C28 C29 PX4 sing 462 n n C28 H54 PX4 sing 463 n n C28 H55 PX4 sing 464 n n C29 C30 PX4 sing 465 n n C29 H56 PX4 sing 466 n n C29 H57 PX4 sing 467 n n C30 C31 PX4 sing 468 n n C30 H58 PX4 sing 469 n n C30 H59 PX4 sing 470 n n C31 C32 PX4 sing 471 n n C31 H60 PX4 sing 472 n n C31 H61 PX4 sing 473 n n C32 C33 PX4 sing 474 n n C32 H62 PX4 sing 475 n n C32 H63 PX4 sing 476 n n C33 C34 PX4 sing 477 n n C33 H64 PX4 sing 478 n n C33 H65 PX4 sing 479 n n C34 C35 PX4 sing 480 n n C34 H66 PX4 sing 481 n n C34 H67 PX4 sing 482 n n C35 C36 PX4 sing 483 n n C35 H68 PX4 sing 484 n n C35 H69 PX4 sing 485 n n C36 H70 PX4 sing 486 n n C36 H71 PX4 sing 487 n n C36 H72 PX4 sing 488 n n # _atom_sites.entry_id 5VB2 _atom_sites.fract_transf_matrix[1][1] 0.007939 _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] 0.007701 _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] 0.005099 _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 2 CPS A 1 1301 1301 CPS CPS . F 2 CPS A 1 1302 1302 CPS CPS . G 3 PX4 A 1 1303 1303 PX4 PX4 . H 3 PX4 A 1 1304 1304 PX4 PX4 . I 3 PX4 A 1 1305 1305 PX4 PX4 . J 4 PO4 A 1 1306 1306 PO4 PO4 . K 2 CPS B 1 2301 2301 CPS CPS . L 2 CPS B 1 2302 2302 CPS CPS . M 3 PX4 B 1 2303 2303 PX4 PX4 . N 3 PX4 B 1 2304 2304 PX4 PX4 . O 3 PX4 B 1 2305 2305 PX4 PX4 . P 3 PX4 B 1 2306 2306 PX4 PX4 . Q 4 PO4 B 1 2307 2307 PO4 PO4 . R 2 CPS C 1 1301 1301 CPS CPS . S 2 CPS C 1 1302 1302 CPS CPS . T 3 PX4 C 1 1303 1303 PX4 PX4 . U 3 PX4 C 1 1304 1304 PX4 PX4 . V 3 PX4 C 1 1305 1305 PX4 PX4 . W 4 PO4 C 1 1306 1306 PO4 PO4 . X 5 CL C 1 1307 1307 CL CL . Y 2 CPS D 1 2301 2301 CPS CPS . Z 2 CPS D 1 2302 2302 CPS CPS . AA 3 PX4 D 1 2303 2303 PX4 PX4 . BA 3 PX4 D 1 2304 2304 PX4 PX4 . CA 3 PX4 D 1 2305 2305 PX4 PX4 . DA 4 PO4 D 1 2306 2306 PO4 PO4 . EA 6 HOH A 1 1401 1401 HOH HOH . EA 6 HOH A 2 1402 1402 HOH HOH . EA 6 HOH A 3 1403 1403 HOH HOH . EA 6 HOH A 4 1404 1404 HOH HOH . EA 6 HOH A 5 1405 1405 HOH HOH . EA 6 HOH A 6 1406 1406 HOH HOH . EA 6 HOH A 7 1407 1407 HOH HOH . EA 6 HOH A 8 1408 1408 HOH HOH . FA 6 HOH B 1 2401 2401 HOH HOH . FA 6 HOH B 2 2402 2402 HOH HOH . FA 6 HOH B 3 2403 2403 HOH HOH . FA 6 HOH B 4 2404 2404 HOH HOH . FA 6 HOH B 5 2405 2405 HOH HOH . FA 6 HOH B 6 2406 2406 HOH HOH . GA 6 HOH C 1 1401 1401 HOH HOH . GA 6 HOH C 2 1402 1402 HOH HOH . GA 6 HOH C 3 1403 1403 HOH HOH . GA 6 HOH C 4 1404 1404 HOH HOH . GA 6 HOH C 5 1405 1405 HOH HOH . HA 6 HOH D 1 2401 2401 HOH HOH . HA 6 HOH D 2 2402 2402 HOH HOH . HA 6 HOH D 3 2403 2403 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 . . . G 3 -21.629 166.223 14.491 1 111.1 ? O1 PX4 1303 A 1 HETATM 2 O O2 PX4 . . . G 3 -20.757 168.39 13.722 1 113.03 ? O2 PX4 1303 A 1 HETATM 3 P P1 PX4 . . . G 3 -20.424 167.133 14.488 1 112.44 ? P1 PX4 1303 A 1 HETATM 4 O O3 PX4 . . . G 3 -19.142 166.372 13.784 1 113.16 ? O3 PX4 1303 A 1 HETATM 5 C C1 PX4 . . . G 3 -19.267 165.04 13.372 1 114.58 ? C1 PX4 1303 A 1 HETATM 6 C C2 PX4 . . . G 3 -19.621 164.943 11.88 1 114.54 ? C2 PX4 1303 A 1 HETATM 7 N N1 PX4 . . . G 3 -18.571 165.441 10.994 1 114.02 ? N1 PX4 1303 A 1 HETATM 8 C C3 PX4 . . . G 3 -17.32 164.746 11.232 1 113.06 ? C3 PX4 1303 A 1 HETATM 9 C C4 PX4 . . . G 3 -18.957 165.164 9.618 1 113.55 ? C4 PX4 1303 A 1 HETATM 10 C C5 PX4 . . . G 3 -18.392 166.868 11.177 1 114.59 ? C5 PX4 1303 A 1 HETATM 11 O O4 PX4 . . . G 3 -20.035 167.531 16.038 1 110.39 ? O4 PX4 1303 A 1 HETATM 12 C C6 PX4 . . . G 3 -20.058 166.508 16.989 1 108.18 ? C6 PX4 1303 A 1 HETATM 13 C C7 PX4 . . . G 3 -19.086 166.817 18.125 1 104.87 ? C7 PX4 1303 A 1 HETATM 14 C C8 PX4 . . . G 3 -17.683 166.353 17.733 1 101.23 ? C8 PX4 1303 A 1 HETATM 15 O O5 PX4 . . . G 3 -16.731 167.148 18.379 1 98.65 ? O5 PX4 1303 A 1 HETATM 16 C C9 PX4 . . . G 3 -15.875 166.463 19.25 1 96.71 ? C9 PX4 1303 A 1 HETATM 17 O O6 PX4 . . . G 3 -15.432 165.408 18.946 1 97.37 ? O6 PX4 1303 A 1 HETATM 18 C C10 PX4 . . . G 3 -15.52 167.084 20.6 1 94.12 ? C10 PX4 1303 A 1 HETATM 19 C C11 PX4 . . . G 3 -14.293 166.405 21.211 1 91.97 ? C11 PX4 1303 A 1 HETATM 20 C C12 PX4 . . . G 3 -14.344 166.474 22.738 1 89.8 ? C12 PX4 1303 A 1 HETATM 21 C C13 PX4 . . . G 3 -13.318 167.468 23.278 1 87.78 ? C13 PX4 1303 A 1 HETATM 22 C C14 PX4 . . . G 3 -13.372 167.42 24.803 1 86.49 ? C14 PX4 1303 A 1 HETATM 23 C C15 PX4 . . . G 3 -12.335 168.362 25.41 1 84.34 ? C15 PX4 1303 A 1 HETATM 24 C C16 PX4 . . . G 3 -12.382 168.24 26.932 1 81.71 ? C16 PX4 1303 A 1 HETATM 25 C C17 PX4 . . . G 3 -10.962 168.158 27.484 1 80.77 ? C17 PX4 1303 A 1 HETATM 26 O O7 PX4 . . . G 3 -19.075 168.194 18.369 1 105.36 ? O7 PX4 1303 A 1 HETATM 27 H H1 PX4 . . . G 3 -19.966 164.612 13.892 1 137.49 ? H1 PX4 1303 A 1 HETATM 28 H H2 PX4 . . . G 3 -18.428 164.579 13.529 1 137.49 ? H2 PX4 1303 A 1 HETATM 29 H H3 PX4 . . . G 3 -20.429 165.455 11.72 1 137.45 ? H3 PX4 1303 A 1 HETATM 30 H H4 PX4 . . . G 3 -19.794 164.014 11.663 1 137.45 ? H4 PX4 1303 A 1 HETATM 31 H H5 PX4 . . . G 3 -17.475 163.788 11.221 1 135.68 ? H5 PX4 1303 A 1 HETATM 32 H H6 PX4 . . . G 3 -16.965 165.006 12.096 1 135.68 ? H6 PX4 1303 A 1 HETATM 33 H H7 PX4 . . . G 3 -16.684 164.979 10.537 1 135.68 ? H7 PX4 1303 A 1 HETATM 34 H H8 PX4 . . . G 3 -18.424 165.708 9.017 1 136.26 ? H8 PX4 1303 A 1 HETATM 35 H H9 PX4 . . . G 3 -19.896 165.373 9.497 1 136.26 ? H9 PX4 1303 A 1 HETATM 36 H H10 PX4 . . . G 3 -18.806 164.225 9.423 1 136.26 ? H10 PX4 1303 A 1 HETATM 37 H H11 PX4 . . . G 3 -17.658 167.026 11.791 1 137.51 ? H11 PX4 1303 A 1 HETATM 38 H H12 PX4 . . . G 3 -19.206 167.252 11.539 1 137.51 ? H12 PX4 1303 A 1 HETATM 39 H H13 PX4 . . . G 3 -18.192 167.282 10.322 1 137.51 ? H13 PX4 1303 A 1 HETATM 40 H H14 PX4 . . . G 3 -20.955 166.424 17.348 1 129.81 ? H14 PX4 1303 A 1 HETATM 41 H H15 PX4 . . . G 3 -19.803 165.673 16.566 1 129.81 ? H15 PX4 1303 A 1 HETATM 42 H H16 PX4 . . . G 3 -19.368 166.349 18.926 1 125.85 ? H16 PX4 1303 A 1 HETATM 43 H H17 PX4 . . . G 3 -17.575 166.437 16.773 1 121.47 ? H17 PX4 1303 A 1 HETATM 44 H H18 PX4 . . . G 3 -17.563 165.427 17.993 1 121.47 ? H18 PX4 1303 A 1 HETATM 45 H H19 PX4 . . . G 3 -16.273 166.985 21.204 1 112.94 ? H19 PX4 1303 A 1 HETATM 46 H H20 PX4 . . . G 3 -15.332 168.028 20.477 1 112.94 ? H20 PX4 1303 A 1 HETATM 47 H H21 PX4 . . . G 3 -13.491 166.851 20.898 1 110.37 ? H21 PX4 1303 A 1 HETATM 48 H H22 PX4 . . . G 3 -14.271 165.475 20.934 1 110.37 ? H22 PX4 1303 A 1 HETATM 49 H H23 PX4 . . . G 3 -14.157 165.594 23.103 1 107.76 ? H23 PX4 1303 A 1 HETATM 50 H H24 PX4 . . . G 3 -15.232 166.751 23.015 1 107.76 ? H24 PX4 1303 A 1 HETATM 51 H H25 PX4 . . . G 3 -13.534 168.362 22.971 1 105.34 ? H25 PX4 1303 A 1 HETATM 52 H H26 PX4 . . . G 3 -12.431 167.221 22.974 1 105.34 ? H26 PX4 1303 A 1 HETATM 53 H H27 PX4 . . . G 3 -13.194 166.514 25.1 1 103.79 ? H27 PX4 1303 A 1 HETATM 54 H H28 PX4 . . . G 3 -14.257 167.685 25.099 1 103.79 ? H28 PX4 1303 A 1 HETATM 55 H H29 PX4 . . . G 3 -12.534 169.275 25.151 1 101.2 ? H29 PX4 1303 A 1 HETATM 56 H H30 PX4 . . . G 3 -11.451 168.12 25.093 1 101.2 ? H30 PX4 1303 A 1 HETATM 57 H H31 PX4 . . . G 3 -12.871 167.439 27.177 1 98.05 ? H31 PX4 1303 A 1 HETATM 58 H H32 PX4 . . . G 3 -12.829 169.017 27.304 1 98.05 ? H32 PX4 1303 A 1 HETATM 59 H H33 PX4 . . . G 3 -10.995 167.967 28.434 1 96.92 ? H33 PX4 1303 A 1 HETATM 60 H H34 PX4 . . . G 3 -10.51 169.004 27.34 1 96.92 ? H34 PX4 1303 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 49 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 60 #