data_3DDL
#
_model_server_result.job_id            UKXJsPq63Id82_pB8zbusQ 
_model_server_result.datetime_utc      '2024-11-08 05:47:35' 
_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              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           34 
#