data_9BU3 # _model_server_result.job_id Gm9BjmwT6OY_XWXPPfMtDg _model_server_result.datetime_utc '2024-12-04 06:44:14' _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 9bu3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"UA","auth_seq_id":506}' # _entry.id 9BU3 # _exptl.entry_id 9BU3 _exptl.method 'ELECTRON MICROSCOPY' # _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 20 _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 9BU3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9BU3 _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB _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 ? 5 Q N N ? 5 S N N ? 5 T N N ? 5 U N N ? 5 AA N N ? 5 CA N N ? 5 DA N N ? 5 EA N N ? 5 KA N N ? 5 MA N N ? 5 NA N N ? 5 OA N N ? 5 UA N N ? 5 WA N N ? 5 XA N N ? 5 YA N N ? 5 AB N N ? 5 BB N N ? 5 CB N N ? 5 HB N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 2 n F NAG 1 F 1 NAG A 502 NAG 2 n F NAG 2 F 2 NAG A 503 NAG 2 n G NAG 1 G 1 NAG B 502 NAG 2 n G NAG 2 G 2 NAG B 503 NAG 2 n H NAG 1 H 1 NAG C 502 NAG 2 n H NAG 2 H 2 NAG C 503 NAG 2 n I NAG 1 I 1 NAG D 502 NAG 2 n I NAG 2 I 2 NAG D 503 NAG 2 n J NAG 1 J 1 NAG E 502 NAG 2 n J NAG 2 J 2 NAG E 503 NAG # 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 231 A CYS 198 1_555 A SG CYS 242 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 B SG CYS 231 B CYS 198 1_555 B SG CYS 242 B CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 C SG CYS 231 C CYS 198 1_555 C SG CYS 242 C CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 D SG CYS 231 D CYS 198 1_555 D SG CYS 242 D CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 E SG CYS 231 E CYS 198 1_555 E SG CYS 242 E CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 71 A ASN 38 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 B ND2 ASN 71 B ASN 38 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 C ND2 ASN 71 C ASN 38 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 D ND2 ASN 71 D ASN 38 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 E ND2 ASN 71 E ASN 38 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale8 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale9 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 403 n n O1 H1P PX4 sing 404 n n O2 P1 PX4 doub 405 n n P1 O3 PX4 sing 406 n n P1 O4 PX4 sing 407 n n O3 C1 PX4 sing 408 n n C1 C2 PX4 sing 409 n n C1 H1 PX4 sing 410 n n C1 H2 PX4 sing 411 n n C2 N1 PX4 sing 412 n n C2 H3 PX4 sing 413 n n C2 H4 PX4 sing 414 n n N1 C3 PX4 sing 415 n n N1 C4 PX4 sing 416 n n N1 C5 PX4 sing 417 n n C3 H5 PX4 sing 418 n n C3 H6 PX4 sing 419 n n C3 H7 PX4 sing 420 n n C4 H8 PX4 sing 421 n n C4 H9 PX4 sing 422 n n C4 H10 PX4 sing 423 n n C5 H11 PX4 sing 424 n n C5 H12 PX4 sing 425 n n C5 H13 PX4 sing 426 n n O4 C6 PX4 sing 427 n n C6 C7 PX4 sing 428 n n C6 H14 PX4 sing 429 n n C6 H15 PX4 sing 430 n n C7 C8 PX4 sing 431 n n C7 O7 PX4 sing 432 n n C7 H16 PX4 sing 433 n n C8 O5 PX4 sing 434 n n C8 H17 PX4 sing 435 n n C8 H18 PX4 sing 436 n n O5 C9 PX4 sing 437 n n C9 O6 PX4 doub 438 n n C9 C10 PX4 sing 439 n n C10 C11 PX4 sing 440 n n C10 H19 PX4 sing 441 n n C10 H20 PX4 sing 442 n n C11 C12 PX4 sing 443 n n C11 H21 PX4 sing 444 n n C11 H22 PX4 sing 445 n n C12 C13 PX4 sing 446 n n C12 H23 PX4 sing 447 n n C12 H24 PX4 sing 448 n n C13 C14 PX4 sing 449 n n C13 H25 PX4 sing 450 n n C13 H26 PX4 sing 451 n n C14 C15 PX4 sing 452 n n C14 H27 PX4 sing 453 n n C14 H28 PX4 sing 454 n n C15 C16 PX4 sing 455 n n C15 H29 PX4 sing 456 n n C15 H30 PX4 sing 457 n n C16 C17 PX4 sing 458 n n C16 H31 PX4 sing 459 n n C16 H32 PX4 sing 460 n n C17 C18 PX4 sing 461 n n C17 H33 PX4 sing 462 n n C17 H34 PX4 sing 463 n n C18 C19 PX4 sing 464 n n C18 H35 PX4 sing 465 n n C18 H36 PX4 sing 466 n n C19 C20 PX4 sing 467 n n C19 H37 PX4 sing 468 n n C19 H38 PX4 sing 469 n n C20 C21 PX4 sing 470 n n C20 H39 PX4 sing 471 n n C20 H40 PX4 sing 472 n n C21 C22 PX4 sing 473 n n C21 H41 PX4 sing 474 n n C21 H42 PX4 sing 475 n n C22 H43 PX4 sing 476 n n C22 H44 PX4 sing 477 n n C22 H45 PX4 sing 478 n n O7 C23 PX4 sing 479 n n C23 O8 PX4 doub 480 n n C23 C24 PX4 sing 481 n n C24 C25 PX4 sing 482 n n C24 H46 PX4 sing 483 n n C24 H47 PX4 sing 484 n n C25 C26 PX4 sing 485 n n C25 H48 PX4 sing 486 n n C25 H49 PX4 sing 487 n n C26 C27 PX4 sing 488 n n C26 H50 PX4 sing 489 n n C26 H51 PX4 sing 490 n n C27 C28 PX4 sing 491 n n C27 H52 PX4 sing 492 n n C27 H53 PX4 sing 493 n n C28 C29 PX4 sing 494 n n C28 H54 PX4 sing 495 n n C28 H55 PX4 sing 496 n n C29 C30 PX4 sing 497 n n C29 H56 PX4 sing 498 n n C29 H57 PX4 sing 499 n n C30 C31 PX4 sing 500 n n C30 H58 PX4 sing 501 n n C30 H59 PX4 sing 502 n n C31 C32 PX4 sing 503 n n C31 H60 PX4 sing 504 n n C31 H61 PX4 sing 505 n n C32 C33 PX4 sing 506 n n C32 H62 PX4 sing 507 n n C32 H63 PX4 sing 508 n n C33 C34 PX4 sing 509 n n C33 H64 PX4 sing 510 n n C33 H65 PX4 sing 511 n n C34 C35 PX4 sing 512 n n C34 H66 PX4 sing 513 n n C34 H67 PX4 sing 514 n n C35 C36 PX4 sing 515 n n C35 H68 PX4 sing 516 n n C35 H69 PX4 sing 517 n n C36 H70 PX4 sing 518 n n C36 H71 PX4 sing 519 n n C36 H72 PX4 sing 520 n n # _atom_sites.entry_id 9BU3 _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 K 3 GLY A 1 501 501 GLY GLY . L 3 GLY A 1 502 501 GLY GLY . M 4 PIO A 1 503 504 PIO PIO . N 4 PIO A 1 504 506 PIO PIO . O 4 PIO A 1 505 507 PIO PIO . P 4 PIO A 1 506 508 PIO PIO . Q 5 PX4 A 1 507 509 PX4 PX4 . R 4 PIO A 1 508 505 PIO PIO . S 5 PX4 A 1 509 513 PX4 PX4 . T 5 PX4 A 1 510 514 PX4 PX4 . U 5 PX4 A 1 511 515 PX4 PX4 . V 3 GLY B 1 501 501 GLY GLY . W 4 PIO B 1 502 504 PIO PIO . X 4 PIO B 1 503 506 PIO PIO . Y 4 PIO B 1 504 507 PIO PIO . Z 4 PIO B 1 505 508 PIO PIO . AA 5 PX4 B 1 506 509 PX4 PX4 . BA 4 PIO B 1 507 505 PIO PIO . CA 5 PX4 B 1 508 513 PX4 PX4 . DA 5 PX4 B 1 509 514 PX4 PX4 . EA 5 PX4 B 1 510 515 PX4 PX4 . FA 3 GLY C 1 501 501 GLY GLY . GA 4 PIO C 1 502 504 PIO PIO . HA 4 PIO C 1 503 506 PIO PIO . IA 4 PIO C 1 504 507 PIO PIO . JA 4 PIO C 1 505 508 PIO PIO . KA 5 PX4 C 1 506 509 PX4 PX4 . LA 4 PIO C 1 507 505 PIO PIO . MA 5 PX4 C 1 508 513 PX4 PX4 . NA 5 PX4 C 1 509 514 PX4 PX4 . OA 5 PX4 C 1 510 515 PX4 PX4 . PA 3 GLY D 1 501 501 GLY GLY . QA 4 PIO D 1 502 504 PIO PIO . RA 4 PIO D 1 503 506 PIO PIO . SA 4 PIO D 1 504 507 PIO PIO . TA 4 PIO D 1 505 508 PIO PIO . UA 5 PX4 D 1 506 509 PX4 PX4 . VA 4 PIO D 1 507 505 PIO PIO . WA 5 PX4 D 1 508 513 PX4 PX4 . XA 5 PX4 D 1 509 514 PX4 PX4 . YA 5 PX4 D 1 510 515 PX4 PX4 . ZA 4 PIO E 1 501 505 PIO PIO . AB 5 PX4 E 1 502 513 PX4 PX4 . BB 5 PX4 E 1 503 514 PX4 PX4 . CB 5 PX4 E 1 504 515 PX4 PX4 . DB 4 PIO E 1 505 504 PIO PIO . EB 4 PIO E 1 506 506 PIO PIO . FB 4 PIO E 1 507 507 PIO PIO . GB 4 PIO E 1 508 508 PIO PIO . HB 5 PX4 E 1 509 509 PX4 PX4 . IB 6 HOH A 1 601 504 HOH HOH . IB 6 HOH A 2 602 505 HOH HOH . IB 6 HOH A 3 603 506 HOH HOH . JB 6 HOH B 1 601 504 HOH HOH . JB 6 HOH B 2 602 506 HOH HOH . JB 6 HOH B 3 603 505 HOH HOH . KB 6 HOH C 1 601 504 HOH HOH . KB 6 HOH C 2 602 505 HOH HOH . KB 6 HOH C 3 603 506 HOH HOH . LB 6 HOH D 1 601 504 HOH HOH . LB 6 HOH D 2 602 506 HOH HOH . LB 6 HOH D 3 603 505 HOH HOH . MB 6 HOH E 1 601 504 HOH HOH . MB 6 HOH E 2 602 506 HOH HOH . MB 6 HOH E 3 603 505 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 O7 PX4 . . . UA 5 146.373 184.306 124.435 1 84.88 ? O7 PX4 506 D 1 HETATM 2 C C23 PX4 . . . UA 5 147.742 184.734 124.756 1 84.88 ? C23 PX4 506 D 1 HETATM 3 O O8 PX4 . . . UA 5 148.14 185.858 124.405 1 84.88 ? O8 PX4 506 D 1 HETATM 4 C C24 PX4 . . . UA 5 148.719 183.751 125.565 1 84.88 ? C24 PX4 506 D 1 HETATM 5 C C25 PX4 . . . UA 5 148.098 183.465 127.016 1 84.88 ? C25 PX4 506 D 1 HETATM 6 C C26 PX4 . . . UA 5 148.948 182.322 127.753 1 84.88 ? C26 PX4 506 D 1 HETATM 7 C C27 PX4 . . . UA 5 148.531 182.278 129.298 1 84.88 ? C27 PX4 506 D 1 HETATM 8 C C28 PX4 . . . UA 5 149.295 181.083 130.036 1 84.88 ? C28 PX4 506 D 1 HETATM 9 C C29 PX4 . . . UA 5 148.849 181.055 131.575 1 84.88 ? C29 PX4 506 D 1 HETATM 10 C C30 PX4 . . . UA 5 149.318 179.683 132.255 1 84.88 ? C30 PX4 506 D 1 HETATM 11 C C31 PX4 . . . UA 5 148.347 179.358 133.489 1 84.88 ? C31 PX4 506 D 1 HETATM 12 C C32 PX4 . . . UA 5 148.783 177.973 134.171 1 84.88 ? C32 PX4 506 D 1 HETATM 13 C C33 PX4 . . . UA 5 147.62 177.477 135.161 1 84.88 ? C33 PX4 506 D 1 HETATM 14 C C34 PX4 . . . UA 5 147.157 178.698 136.097 1 84.88 ? C34 PX4 506 D 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 52 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #