data_5VB2 # _model_server_result.job_id Gpc77pTAIzD6LpszyytbYw _model_server_result.datetime_utc '2024-10-27 12:30:29' _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":"N","auth_seq_id":2304}' # _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 . . . N 3 -3.413 137.837 13.142 1 108 ? O1 PX4 2304 B 1 HETATM 2 O O2 PX4 . . . N 3 -5.559 138.63 12.208 1 108.35 ? O2 PX4 2304 B 1 HETATM 3 P P1 PX4 . . . N 3 -4.276 139.05 12.885 1 109.04 ? P1 PX4 2304 B 1 HETATM 4 O O3 PX4 . . . N 3 -3.47 140.111 11.919 1 109.38 ? O3 PX4 2304 B 1 HETATM 5 C C1 PX4 . . . N 3 -2.703 139.611 10.863 1 111.53 ? C1 PX4 2304 B 1 HETATM 6 C C2 PX4 . . . N 3 -3.295 140.061 9.522 1 112.51 ? C2 PX4 2304 B 1 HETATM 7 N N1 PX4 . . . N 3 -3.003 141.455 9.199 1 112.84 ? N1 PX4 2304 B 1 HETATM 8 C C3 PX4 . . . N 3 -3.642 141.768 7.93 1 113.21 ? C3 PX4 2304 B 1 HETATM 9 C C4 PX4 . . . N 3 -1.57 141.644 9.028 1 111.84 ? C4 PX4 2304 B 1 HETATM 10 C C5 PX4 . . . N 3 -3.522 142.342 10.231 1 112.71 ? C5 PX4 2304 B 1 HETATM 11 O O4 PX4 . . . N 3 -4.631 139.818 14.3 1 108.52 ? O4 PX4 2304 B 1 HETATM 12 C C6 PX4 . . . N 3 -4.8 139.103 15.489 1 107.05 ? C6 PX4 2304 B 1 HETATM 13 C C7 PX4 . . . N 3 -5.01 140.112 16.62 1 104.01 ? C7 PX4 2304 B 1 HETATM 14 C C8 PX4 . . . N 3 -5.934 139.508 17.681 1 106.21 ? C8 PX4 2304 B 1 HETATM 15 O O5 PX4 . . . N 3 -5.814 138.114 17.686 1 106.96 ? O5 PX4 2304 B 1 HETATM 16 O O7 PX4 . . . N 3 -3.786 140.461 17.211 1 98.44 ? O7 PX4 2304 B 1 HETATM 17 C C23 PX4 . . . N 3 -2.875 141.132 16.378 1 92.7 ? C23 PX4 2304 B 1 HETATM 18 O O8 PX4 . . . N 3 -2.526 140.634 15.365 1 93.26 ? O8 PX4 2304 B 1 HETATM 19 C C24 PX4 . . . N 3 -2.303 142.5 16.75 1 87.44 ? C24 PX4 2304 B 1 HETATM 20 C C25 PX4 . . . N 3 -3.266 143.272 17.649 1 84.33 ? C25 PX4 2304 B 1 HETATM 21 C C26 PX4 . . . N 3 -2.507 143.834 18.851 1 80.77 ? C26 PX4 2304 B 1 HETATM 22 C C27 PX4 . . . N 3 -3.534 144.25 19.898 1 80.77 ? C27 PX4 2304 B 1 HETATM 23 C C28 PX4 . . . N 3 -2.847 144.686 21.187 1 80.77 ? C28 PX4 2304 B 1 HETATM 24 C C29 PX4 . . . N 3 -3.939 145.025 22.196 1 80.77 ? C29 PX4 2304 B 1 HETATM 25 C C30 PX4 . . . N 3 -3.417 144.804 23.614 1 83.28 ? C30 PX4 2304 B 1 HETATM 26 C C31 PX4 . . . N 3 -4.089 145.779 24.578 1 85.01 ? C31 PX4 2304 B 1 HETATM 27 C C32 PX4 . . . N 3 -3.26 145.847 25.856 1 89.71 ? C32 PX4 2304 B 1 HETATM 28 C C33 PX4 . . . N 3 -3.51 147.18 26.554 1 94.66 ? C33 PX4 2304 B 1 HETATM 29 C C34 PX4 . . . N 3 -3.031 147.092 28.005 1 98.66 ? C34 PX4 2304 B 1 HETATM 30 C C35 PX4 . . . N 3 -1.845 148.025 28.259 1 101.69 ? C35 PX4 2304 B 1 HETATM 31 C C36 PX4 . . . N 3 -1.973 148.624 29.659 1 103.07 ? C36 PX4 2304 B 1 HETATM 32 H H1 PX4 . . . N 3 -2.696 138.642 10.902 1 133.84 ? H1 PX4 2304 B 1 HETATM 33 H H2 PX4 . . . N 3 -1.795 139.942 10.94 1 133.84 ? H2 PX4 2304 B 1 HETATM 34 H H3 PX4 . . . N 3 -2.935 139.497 8.819 1 135.02 ? H3 PX4 2304 B 1 HETATM 35 H H4 PX4 . . . N 3 -4.257 139.944 9.552 1 135.02 ? H4 PX4 2304 B 1 HETATM 36 H H5 PX4 . . . N 3 -3.188 141.296 7.215 1 135.85 ? H5 PX4 2304 B 1 HETATM 37 H H6 PX4 . . . N 3 -3.594 142.723 7.77 1 135.85 ? H6 PX4 2304 B 1 HETATM 38 H H7 PX4 . . . N 3 -4.572 141.492 7.96 1 135.85 ? H7 PX4 2304 B 1 HETATM 39 H H8 PX4 . . . N 3 -1.141 141.669 9.897 1 134.2 ? H8 PX4 2304 B 1 HETATM 40 H H9 PX4 . . . N 3 -1.407 142.479 8.562 1 134.2 ? H9 PX4 2304 B 1 HETATM 41 H H10 PX4 . . . N 3 -1.207 140.908 8.509 1 134.2 ? H10 PX4 2304 B 1 HETATM 42 H H11 PX4 . . . N 3 -2.814 142.559 10.858 1 135.25 ? H11 PX4 2304 B 1 HETATM 43 H H12 PX4 . . . N 3 -4.246 141.901 10.702 1 135.25 ? H12 PX4 2304 B 1 HETATM 44 H H13 PX4 . . . N 3 -3.852 143.157 9.822 1 135.25 ? H13 PX4 2304 B 1 HETATM 45 H H14 PX4 . . . N 3 -5.575 138.525 15.417 1 128.46 ? H14 PX4 2304 B 1 HETATM 46 H H15 PX4 . . . N 3 -4.009 138.571 15.667 1 128.46 ? H15 PX4 2304 B 1 HETATM 47 H H16 PX4 . . . N 3 -5.425 140.911 16.258 1 124.81 ? H16 PX4 2304 B 1 HETATM 48 H H17 PX4 . . . N 3 -6.852 139.751 17.484 1 127.45 ? H17 PX4 2304 B 1 HETATM 49 H H18 PX4 . . . N 3 -5.691 139.854 18.554 1 127.45 ? H18 PX4 2304 B 1 HETATM 50 H H46 PX4 . . . N 3 -2.146 143.01 15.94 1 104.92 ? H46 PX4 2304 B 1 HETATM 51 H H47 PX4 . . . N 3 -1.461 142.377 17.217 1 104.92 ? H47 PX4 2304 B 1 HETATM 52 H H48 PX4 . . . N 3 -3.966 142.676 17.959 1 101.2 ? H48 PX4 2304 B 1 HETATM 53 H H49 PX4 . . . N 3 -3.661 144.001 17.147 1 101.2 ? H49 PX4 2304 B 1 HETATM 54 H H50 PX4 . . . N 3 -1.984 144.605 18.579 1 96.92 ? H50 PX4 2304 B 1 HETATM 55 H H51 PX4 . . . N 3 -1.921 143.153 19.218 1 96.92 ? H51 PX4 2304 B 1 HETATM 56 H H52 PX4 . . . N 3 -4.12 143.5 20.087 1 96.92 ? H52 PX4 2304 B 1 HETATM 57 H H53 PX4 . . . N 3 -4.061 144.988 19.553 1 96.92 ? H53 PX4 2304 B 1 HETATM 58 H H54 PX4 . . . N 3 -2.298 145.468 21.02 1 96.92 ? H54 PX4 2304 B 1 HETATM 59 H H55 PX4 . . . N 3 -2.296 143.963 21.527 1 96.92 ? H55 PX4 2304 B 1 HETATM 60 H H56 PX4 . . . N 3 -4.708 144.453 22.043 1 96.92 ? H56 PX4 2304 B 1 HETATM 61 H H57 PX4 . . . N 3 -4.2 145.953 22.089 1 96.92 ? H57 PX4 2304 B 1 HETATM 62 H H58 PX4 . . . N 3 -2.458 144.947 23.63 1 99.94 ? H58 PX4 2304 B 1 HETATM 63 H H59 PX4 . . . N 3 -3.611 143.895 23.89 1 99.94 ? H59 PX4 2304 B 1 HETATM 64 H H60 PX4 . . . N 3 -4.984 145.467 24.786 1 102.01 ? H60 PX4 2304 B 1 HETATM 65 H H61 PX4 . . . N 3 -4.136 146.659 24.173 1 102.01 ? H61 PX4 2304 B 1 HETATM 66 H H62 PX4 . . . N 3 -2.318 145.77 25.635 1 107.65 ? H62 PX4 2304 B 1 HETATM 67 H H63 PX4 . . . N 3 -3.514 145.12 26.446 1 107.65 ? H63 PX4 2304 B 1 HETATM 68 H H64 PX4 . . . N 3 -4.459 147.38 26.538 1 113.59 ? H64 PX4 2304 B 1 HETATM 69 H H65 PX4 . . . N 3 -3.024 147.882 26.095 1 113.59 ? H65 PX4 2304 B 1 HETATM 70 H H66 PX4 . . . N 3 -2.762 146.179 28.196 1 118.4 ? H66 PX4 2304 B 1 HETATM 71 H H67 PX4 . . . N 3 -3.76 147.338 28.596 1 118.4 ? H67 PX4 2304 B 1 HETATM 72 H H68 PX4 . . . N 3 -1.845 148.736 27.6 1 122.03 ? H68 PX4 2304 B 1 HETATM 73 H H69 PX4 . . . N 3 -1.018 147.523 28.196 1 122.03 ? H69 PX4 2304 B 1 HETATM 74 H H70 PX4 . . . N 3 -1.185 149.155 29.857 1 123.69 ? H70 PX4 2304 B 1 HETATM 75 H H71 PX4 . . . N 3 -2.054 147.91 30.311 1 123.69 ? H71 PX4 2304 B 1 HETATM 76 H H72 PX4 . . . N 3 -2.761 149.189 29.698 1 123.69 ? H72 PX4 2304 B 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 76 #