data_6VM2
#
_model_server_result.job_id            vuj5RbWoAOicCrPwSWC3EA 
_model_server_result.datetime_utc      '2024-11-24 16:49:04' 
_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          6vm2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Y","auth_seq_id":903}' 
#
_entry.id    6VM2 
#
_exptl.entry_id    6VM2 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              746.566 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate' 
_entity.pdbx_number_of_molecules    5 
_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            6VM2 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VM2 
_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_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 
_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    ? 
_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 K N N 
? 3 O N N 
? 3 Q N N 
? 3 V N N 
? 3 Y 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 902 NAG 
2 n F NAG 2 F 2 NAG A 903 NAG 
2 n G NAG 1 G 1 NAG E 902 NAG 
2 n G NAG 2 G 2 NAG E 903 NAG 
2 n H NAG 1 H 1 NAG C 902 NAG 
2 n H NAG 2 H 2 NAG C 903 NAG 
2 n I NAG 1 I 1 NAG B 902 NAG 
2 n I NAG 2 I 2 NAG B 903 NAG 
2 n J NAG 1 J 1 NAG D 902 NAG 
2 n J NAG 2 J 2 NAG D 903 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
covale ? covale1 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale2 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale3 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale4 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale5 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
#
_chem_comp.formula           'C25 H49 O19 P3' 
_chem_comp.formula_weight    746.566 
_chem_comp.id                PIO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate' 
#
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
C1 O1 PIO sing 430 n n 
C1 C2 PIO sing 431 n n 
C1 C6 PIO sing 432 n n 
C1 H1 PIO sing 433 n n 
O1 P1 PIO sing 434 n n 
P1 O11 PIO sing 435 n n 
O11 H11 PIO sing 436 n n 
P1 O12 PIO doub 437 n n 
P1 O13 PIO sing 438 n n 
C2 O2 PIO sing 439 n n 
C2 C3 PIO sing 440 n n 
C2 H2 PIO sing 441 n n 
O2 HO2 PIO sing 442 n n 
C3 O3 PIO sing 443 n n 
C3 C4 PIO sing 444 n n 
C3 H3 PIO sing 445 n n 
O3 HO3 PIO sing 446 n n 
C4 O4 PIO sing 447 n n 
C4 C5 PIO sing 448 n n 
C4 H4 PIO sing 449 n n 
O4 P4 PIO sing 450 n n 
P4 O41 PIO sing 451 n n 
O41 H41 PIO sing 452 n n 
P4 O42 PIO doub 453 n n 
P4 O43 PIO sing 454 n n 
O43 H43 PIO sing 455 n n 
C5 O5 PIO sing 456 n n 
C5 C6 PIO sing 457 n n 
C5 H5 PIO sing 458 n n 
O5 P5 PIO sing 459 n n 
P5 O51 PIO sing 460 n n 
O51 H51 PIO sing 461 n n 
P5 O52 PIO sing 462 n n 
O52 H52 PIO sing 463 n n 
P5 O53 PIO doub 464 n n 
C6 O6 PIO sing 465 n n 
C6 H6 PIO sing 466 n n 
O6 HO6 PIO sing 467 n n 
O13 C1C PIO sing 468 n n 
C1A O1A PIO doub 469 n n 
C1A C2A PIO sing 470 n n 
C1A O2C PIO sing 471 n n 
C1B O1B PIO doub 472 n n 
C1B C2B PIO sing 473 n n 
C1B O3C PIO sing 474 n n 
C1C C2C PIO sing 475 n n 
C1C H1C PIO sing 476 n n 
C1C H1CA PIO sing 477 n n 
C2A C3A PIO sing 478 n n 
C2A H2A PIO sing 479 n n 
C2A H2AA PIO sing 480 n n 
C2B C3B PIO sing 481 n n 
C2B H2B PIO sing 482 n n 
C2B H2BA PIO sing 483 n n 
C2C O2C PIO sing 484 n n 
C2C C3C PIO sing 485 n n 
C2C H2C PIO sing 486 n n 
C3A C4A PIO sing 487 n n 
C3A H3A PIO sing 488 n n 
C3A H3AA PIO sing 489 n n 
C3B C4B PIO sing 490 n n 
C3B H3B PIO sing 491 n n 
C3B H3BA PIO sing 492 n n 
C3C O3C PIO sing 493 n n 
C3C H3C PIO sing 494 n n 
C3C H3CA PIO sing 495 n n 
C4A C5A PIO sing 496 n n 
C4A H4A PIO sing 497 n n 
C4A H4AA PIO sing 498 n n 
C4B C5B PIO sing 499 n n 
C4B H4B PIO sing 500 n n 
C4B H4BA PIO sing 501 n n 
C5A C6A PIO sing 502 n n 
C5A H5A PIO sing 503 n n 
C5A H5AA PIO sing 504 n n 
C5B C6B PIO sing 505 n n 
C5B H5B PIO sing 506 n n 
C5B H5BA PIO sing 507 n n 
C6A C7A PIO sing 508 n n 
C6A H6A PIO sing 509 n n 
C6A H6AA PIO sing 510 n n 
C6B C7B PIO sing 511 n n 
C6B H6B PIO sing 512 n n 
C6B H6BA PIO sing 513 n n 
C7A C8A PIO sing 514 n n 
C7A H7A PIO sing 515 n n 
C7A H7AA PIO sing 516 n n 
C7B C8B PIO sing 517 n n 
C7B H7B PIO sing 518 n n 
C7B H7BA PIO sing 519 n n 
C8A H8A PIO sing 520 n n 
C8A H8AA PIO sing 521 n n 
C8A H8AB PIO sing 522 n n 
C8B H8B PIO sing 523 n n 
C8B H8BA PIO sing 524 n n 
C8B H8BB PIO sing 525 n n 
#
_atom_sites.entry_id                     6VM2 
_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 PIO A 1 801 801 PIO PIO . 
L 4 GLY A 1 804 601 GLY GLY . 
M 5 IVM A 1 805 901 IVM IVM . 
N 5 IVM E 1 901 901 IVM IVM . 
O 3 PIO E 1 902 801 PIO PIO . 
P 4 GLY E 1 905 601 GLY GLY . 
Q 3 PIO C 1 801 801 PIO PIO . 
R 4 GLY C 1 804 601 GLY GLY . 
S 5 IVM C 1 805 901 IVM IVM . 
T 4 GLY B 1 601 601 GLY GLY . 
U 5 IVM B 1 602 901 IVM IVM . 
V 3 PIO B 1 603 801 PIO PIO . 
W 5 IVM D 1 901 901 IVM IVM . 
X 4 GLY D 1 902 601 GLY GLY . 
Y 3 PIO D 1 903 801 PIO PIO . 
#
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 PIO . . . Y 3 129.972 155.917 123.327 1 112.99 ? O1 PIO 903 D 1 
HETATM 2 P P1 PIO . . . Y 3 130.382 157.429 123.836 1 112.99 ? P1 PIO 903 D 1 
HETATM 3 O O11 PIO . . . Y 3 130.545 158.313 122.625 1 112.99 ? O11 PIO 903 D 1 
HETATM 4 O O12 PIO . . . Y 3 129.32 157.975 124.757 1 112.99 ? O12 PIO 903 D 1 
HETATM 5 O O13 PIO . . . Y 3 131.802 157.333 124.647 1 112.99 ? O13 PIO 903 D 1 
HETATM 6 C C1A PIO . . . Y 3 134.071 154.333 127.004 1 112.99 ? C1A PIO 903 D 1 
HETATM 7 O O1A PIO . . . Y 3 134.031 153.725 125.986 1 112.99 ? O1A PIO 903 D 1 
HETATM 8 C C1B PIO . . . Y 3 131.948 158.106 129.513 1 112.99 ? C1B PIO 903 D 1 
HETATM 9 O O1B PIO . . . Y 3 130.772 158.048 129.411 1 112.99 ? O1B PIO 903 D 1 
HETATM 10 C C1C PIO . . . Y 3 132 156.167 125.378 1 112.99 ? C1C PIO 903 D 1 
HETATM 11 C C2A PIO . . . Y 3 135.217 154.054 127.958 1 112.99 ? C2A PIO 903 D 1 
HETATM 12 C C2B PIO . . . Y 3 132.576 158.954 130.604 1 112.99 ? C2B PIO 903 D 1 
HETATM 13 C C2C PIO . . . Y 3 133.01 156.408 126.496 1 112.99 ? C2C PIO 903 D 1 
HETATM 14 O O2C PIO . . . Y 3 133.083 155.28 127.327 1 112.99 ? O2C PIO 903 D 1 
HETATM 15 C C3A PIO . . . Y 3 135.076 154.894 129.222 1 112.99 ? C3A PIO 903 D 1 
HETATM 16 C C3B PIO . . . Y 3 131.677 158.952 131.829 1 112.99 ? C3B PIO 903 D 1 
HETATM 17 C C3C PIO . . . Y 3 132.581 157.64 127.29 1 112.99 ? C3C PIO 903 D 1 
HETATM 18 O O3C PIO . . . Y 3 132.783 157.396 128.648 1 112.99 ? O3C PIO 903 D 1 
HETATM 19 C C4A PIO . . . Y 3 135.778 154.169 130.364 1 112.99 ? C4A PIO 903 D 1 
HETATM 20 C C4B PIO . . . Y 3 132.132 157.835 132.757 1 112.99 ? C4B PIO 903 D 1 
HETATM 21 C C5A PIO . . . Y 3 134.763 153.405 131.213 1 112.99 ? C5A PIO 903 D 1 
HETATM 22 C C5B PIO . . . Y 3 133.248 158.372 133.649 1 112.99 ? C5B PIO 903 D 1 
HETATM 23 C C6A PIO . . . Y 3 135.43 153.029 132.536 1 112.99 ? C6A PIO 903 D 1 
HETATM 24 C C6B PIO . . . Y 3 132.663 158.718 135.016 1 112.99 ? C6B PIO 903 D 1 
HETATM 25 C C7A PIO . . . Y 3 134.381 152.559 133.544 1 112.99 ? C7A PIO 903 D 1 
HETATM 26 C C7B PIO . . . Y 3 132.466 157.444 135.833 1 112.99 ? C7B PIO 903 D 1 
HETATM 27 C C8A PIO . . . Y 3 135.041 152.32 134.9 1 112.99 ? C8A PIO 903 D 1 
HETATM 28 C C8B PIO . . . Y 3 131.903 157.826 137.202 1 112.99 ? C8B PIO 903 D 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#