data_5VB2
#
_model_server_result.job_id            AUKHFmS5lJf0C_v4wNanXg 
_model_server_result.datetime_utc      '2024-10-27 12:30:34' 
_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":"M","auth_seq_id":2303}' 
#
_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 . . . M 3 8.111 133.802 5.006 1 131.39 ? O1 PX4 2303 B 1 
HETATM 2 O O2 PX4 . . . M 3 6.097 134.122 6.375 1 129.42 ? O2 PX4 2303 B 1 
HETATM 3 P P1 PX4 . . . M 3 7.174 134.833 5.591 1 132.61 ? P1 PX4 2303 B 1 
HETATM 4 O O3 PX4 . . . M 3 6.464 135.718 4.395 1 136.04 ? O3 PX4 2303 B 1 
HETATM 5 C C1 PX4 . . . M 3 6.102 135.067 3.212 1 141.52 ? C1 PX4 2303 B 1 
HETATM 6 C C2 PX4 . . . M 3 6.507 135.917 2.003 1 143.62 ? C2 PX4 2303 B 1 
HETATM 7 N N1 PX4 . . . M 3 7.854 135.62 1.513 1 146 ? N1 PX4 2303 B 1 
HETATM 8 C C3 PX4 . . . M 3 7.898 134.298 0.907 1 147.15 ? C3 PX4 2303 B 1 
HETATM 9 C C4 PX4 . . . M 3 8.192 136.585 0.476 1 144.87 ? C4 PX4 2303 B 1 
HETATM 10 C C5 PX4 . . . M 3 8.822 135.706 2.595 1 145.19 ? C5 PX4 2303 B 1 
HETATM 11 O O4 PX4 . . . M 3 8.036 135.833 6.579 1 123.85 ? O4 PX4 2303 B 1 
HETATM 12 C C6 PX4 . . . M 3 8.947 135.264 7.475 1 117.68 ? C6 PX4 2303 B 1 
HETATM 13 C C7 PX4 . . . M 3 8.495 135.539 8.908 1 108.85 ? C7 PX4 2303 B 1 
HETATM 14 C C8 PX4 . . . M 3 8.561 137.038 9.183 1 106 ? C8 PX4 2303 B 1 
HETATM 15 O O5 PX4 . . . M 3 7.991 137.293 10.432 1 102.79 ? O5 PX4 2303 B 1 
HETATM 16 C C9 PX4 . . . M 3 8.275 138.56 10.944 1 99.45 ? C9 PX4 2303 B 1 
HETATM 17 O O6 PX4 . . . M 3 8.196 139.512 10.244 1 96.96 ? O6 PX4 2303 B 1 
HETATM 18 C C10 PX4 . . . M 3 8.697 138.716 12.403 1 99.17 ? C10 PX4 2303 B 1 
HETATM 19 C C11 PX4 . . . M 3 8.087 137.604 13.254 1 97.05 ? C11 PX4 2303 B 1 
HETATM 20 C C12 PX4 . . . M 3 8.259 137.936 14.736 1 94.85 ? C12 PX4 2303 B 1 
HETATM 21 O O7 PX4 . . . M 3 7.175 135.115 9.083 1 103.27 ? O7 PX4 2303 B 1 
HETATM 22 C C23 PX4 . . . M 3 6.995 134.115 10.049 1 97.65 ? C23 PX4 2303 B 1 
HETATM 23 O O8 PX4 . . . M 3 7.529 133.066 9.927 1 96.38 ? O8 PX4 2303 B 1 
HETATM 24 C C24 PX4 . . . M 3 6.102 134.387 11.257 1 94.41 ? C24 PX4 2303 B 1 
HETATM 25 C C25 PX4 . . . M 3 6.816 133.935 12.529 1 92.87 ? C25 PX4 2303 B 1 
HETATM 26 C C26 PX4 . . . M 3 5.935 134.232 13.744 1 91.78 ? C26 PX4 2303 B 1 
HETATM 27 C C27 PX4 . . . M 3 6.803 134.329 14.999 1 90.65 ? C27 PX4 2303 B 1 
HETATM 28 C C28 PX4 . . . M 3 5.933 134.14 16.242 1 89.79 ? C28 PX4 2303 B 1 
HETATM 29 H H1 PX4 . . . M 3 5.142 134.928 3.201 1 169.83 ? H1 PX4 2303 B 1 
HETATM 30 H H2 PX4 . . . M 3 6.552 134.208 3.167 1 169.83 ? H2 PX4 2303 B 1 
HETATM 31 H H3 PX4 . . . M 3 6.467 136.853 2.253 1 172.34 ? H3 PX4 2303 B 1 
HETATM 32 H H4 PX4 . . . M 3 5.874 135.759 1.285 1 172.34 ? H4 PX4 2303 B 1 
HETATM 33 H H5 PX4 . . . M 3 7.175 134.212 0.266 1 176.58 ? H5 PX4 2303 B 1 
HETATM 34 H H6 PX4 . . . M 3 7.801 133.623 1.596 1 176.58 ? H6 PX4 2303 B 1 
HETATM 35 H H7 PX4 . . . M 3 8.747 134.178 0.454 1 176.58 ? H7 PX4 2303 B 1 
HETATM 36 H H8 PX4 . . . M 3 9.151 136.581 0.331 1 173.84 ? H8 PX4 2303 B 1 
HETATM 37 H H9 PX4 . . . M 3 7.912 137.471 0.756 1 173.84 ? H9 PX4 2303 B 1 
HETATM 38 H H10 PX4 . . . M 3 7.739 136.348 -0.347 1 173.84 ? H10 PX4 2303 B 1 
HETATM 39 H H11 PX4 . . . M 3 8.984 134.82 2.955 1 174.23 ? H11 PX4 2303 B 1 
HETATM 40 H H12 PX4 . . . M 3 8.473 136.28 3.295 1 174.23 ? H12 PX4 2303 B 1 
HETATM 41 H H13 PX4 . . . M 3 9.653 136.076 2.258 1 174.23 ? H13 PX4 2303 B 1 
HETATM 42 H H14 PX4 . . . M 3 8.99 134.306 7.328 1 141.22 ? H14 PX4 2303 B 1 
HETATM 43 H H15 PX4 . . . M 3 9.825 135.652 7.334 1 141.22 ? H15 PX4 2303 B 1 
HETATM 44 H H16 PX4 . . . M 3 9.073 135.069 9.528 1 130.62 ? H16 PX4 2303 B 1 
HETATM 45 H H17 PX4 . . . M 3 8.077 137.523 8.497 1 127.2 ? H17 PX4 2303 B 1 
HETATM 46 H H18 PX4 . . . M 3 9.488 137.324 9.187 1 127.2 ? H18 PX4 2303 B 1 
HETATM 47 H H19 PX4 . . . M 3 8.394 139.575 12.734 1 119.01 ? H19 PX4 2303 B 1 
HETATM 48 H H20 PX4 . . . M 3 9.664 138.672 12.463 1 119.01 ? H20 PX4 2303 B 1 
HETATM 49 H H21 PX4 . . . M 3 8.534 136.765 13.058 1 116.46 ? H21 PX4 2303 B 1 
HETATM 50 H H22 PX4 . . . M 3 7.143 137.522 13.05 1 116.46 ? H22 PX4 2303 B 1 
HETATM 51 H H23 PX4 . . . M 3 7.988 138.854 14.894 1 113.81 ? H23 PX4 2303 B 1 
HETATM 52 H H24 PX4 . . . M 3 9.19 137.826 14.986 1 113.81 ? H24 PX4 2303 B 1 
HETATM 53 H H46 PX4 . . . M 3 5.27 133.897 11.161 1 113.29 ? H46 PX4 2303 B 1 
HETATM 54 H H47 PX4 . . . M 3 5.913 135.337 11.312 1 113.29 ? H47 PX4 2303 B 1 
HETATM 55 H H48 PX4 . . . M 3 7.656 134.412 12.615 1 111.44 ? H48 PX4 2303 B 1 
HETATM 56 H H49 PX4 . . . M 3 6.989 132.982 12.481 1 111.44 ? H49 PX4 2303 B 1 
HETATM 57 H H50 PX4 . . . M 3 5.287 133.519 13.854 1 110.13 ? H50 PX4 2303 B 1 
HETATM 58 H H51 PX4 . . . M 3 5.47 135.072 13.607 1 110.13 ? H51 PX4 2303 B 1 
HETATM 59 H H52 PX4 . . . M 3 7.227 135.201 15.031 1 108.78 ? H52 PX4 2303 B 1 
HETATM 60 H H53 PX4 . . . M 3 7.485 133.64 14.974 1 108.78 ? H53 PX4 2303 B 1 
#
_model_server_stats.io_time_ms              29 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    39 
_model_server_stats.query_time_ms           356 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           60 
#