data_9DVM
#
_model_server_result.job_id            Fcf-S9xEaNggyRVi9iSoMw 
_model_server_result.datetime_utc      '2025-04-24 09:11:03' 
_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          9dvm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":705}' 
#
_entry.id    9DVM 
#
_exptl.entry_id    9DVM 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              819.995 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)]' 
_entity.pdbx_number_of_molecules    4 
_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            9DVM 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9DVM 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 F N N 
? 3 G N N 
? 3 M N N 
? 3 N N 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
disulf ? disulf1 A SG CYS 415 A CYS 415 1_555 A SG CYS 440 A CYS 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf2 B SG CYS 415 B CYS 415 1_555 B SG CYS 440 B CYS 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
#
_chem_comp.formula           'C6 H20 O30 P8' 
_chem_comp.formula_weight    819.995 
_chem_comp.id                I8P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)]' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '1D-myo-inositol 1,5-bisdiphosphate 2,3,4,6-tetrakisphosphate' 
#
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
O11 C1 I8P sing 360 n n 
C2 C1 I8P sing 361 n n 
C1 C6 I8P sing 362 n n 
C1 H1 I8P sing 363 n n 
O12 C2 I8P sing 364 n n 
C2 C3 I8P sing 365 n n 
C2 H2 I8P sing 366 n n 
O13 C3 I8P sing 367 n n 
C3 C4 I8P sing 368 n n 
C3 H3 I8P sing 369 n n 
C4 C5 I8P sing 370 n n 
C4 O14 I8P sing 371 n n 
C4 H4 I8P sing 372 n n 
C6 C5 I8P sing 373 n n 
C5 O15 I8P sing 374 n n 
C5 H5 I8P sing 375 n n 
C6 O16 I8P sing 376 n n 
C6 H6 I8P sing 377 n n 
PA1 O11 I8P sing 378 n n 
PA2 O12 I8P sing 379 n n 
O13 PA3 I8P sing 380 n n 
O14 PA4 I8P sing 381 n n 
O15 PA5 I8P sing 382 n n 
PA6 O16 I8P sing 383 n n 
O21 PA1 I8P doub 384 n n 
O22 PA2 I8P sing 385 n n 
O22 HO22 I8P sing 386 n n 
PA3 O23 I8P sing 387 n n 
O23 HO23 I8P sing 388 n n 
O24 PA4 I8P sing 389 n n 
O24 HO24 I8P sing 390 n n 
PA5 O25 I8P doub 391 n n 
PA6 O26 I8P sing 392 n n 
O26 HO26 I8P sing 393 n n 
O31 PA1 I8P sing 394 n n 
O31 HO31 I8P sing 395 n n 
O32 PA2 I8P doub 396 n n 
O33 PA3 I8P doub 397 n n 
O34 PA4 I8P doub 398 n n 
PA5 O35 I8P sing 399 n n 
O35 HO35 I8P sing 400 n n 
PA6 O36 I8P sing 401 n n 
O36 HO36 I8P sing 402 n n 
PA1 O41 I8P sing 403 n n 
O41 PB1 I8P sing 404 n n 
PA2 O42 I8P sing 405 n n 
O42 HO42 I8P sing 406 n n 
O43 PA3 I8P sing 407 n n 
O43 HO43 I8P sing 408 n n 
PA4 O44 I8P sing 409 n n 
O44 HO44 I8P sing 410 n n 
O45 PA5 I8P sing 411 n n 
O45 PB5 I8P sing 412 n n 
O46 PA6 I8P doub 413 n n 
O51 PB1 I8P sing 414 n n 
O51 HO51 I8P sing 415 n n 
O55 PB5 I8P doub 416 n n 
O61 PB1 I8P doub 417 n n 
O65 PB5 I8P sing 418 n n 
O65 HO65 I8P sing 419 n n 
PB1 O71 I8P sing 420 n n 
O71 HO71 I8P sing 421 n n 
PB5 O75 I8P sing 422 n n 
O75 HO75 I8P sing 423 n n 
#
_atom_sites.entry_id                     9DVM 
_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
C 2 PO4 A 1 701 701 PO4 PO4 . 
D 2 PO4 A 1 702 702 PO4 PO4 . 
E 2 PO4 A 1 703 703 PO4 PO4 . 
F 3 I8P A 1 704 704 I8P I8P . 
G 3 I8P A 1 705 706 I8P I8P . 
H 4 CLR A 1 706 707 CLR CLR . 
I 5 CPL A 1 707 708 CPL CPL . 
J 2 PO4 B 1 701 701 PO4 PO4 . 
K 2 PO4 B 1 702 702 PO4 PO4 . 
L 2 PO4 B 1 703 703 PO4 PO4 . 
M 3 I8P B 1 704 704 I8P I8P . 
N 3 I8P B 1 705 706 I8P I8P . 
O 4 CLR B 1 706 707 CLR CLR . 
P 5 CPL B 1 707 708 CPL CPL . 
Q 6 HOH A 1 801 705 HOH HOH . 
R 6 HOH B 1 801 705 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 C C1 I8P . . . N 3 162.935 154.896 155.899 1 354.84 ? C1 I8P 705 B 1 
HETATM 2 C C2 I8P . . . N 3 162.393 154.525 157.304 1 348.32 ? C2 I8P 705 B 1 
HETATM 3 C C3 I8P . . . N 3 160.838 154.504 157.208 1 350.05 ? C3 I8P 705 B 1 
HETATM 4 C C4 I8P . . . N 3 160.402 153.297 156.312 1 351.64 ? C4 I8P 705 B 1 
HETATM 5 C C5 I8P . . . N 3 161.148 153.352 154.92 1 354.16 ? C5 I8P 705 B 1 
HETATM 6 C C6 I8P . . . N 3 162.675 153.707 154.931 1 354.14 ? C6 I8P 705 B 1 
HETATM 7 O O11 I8P . . . N 3 164.298 155.171 155.994 1 349.87 ? O11 I8P 705 B 1 
HETATM 8 O O12 I8P . . . N 3 162.899 153.338 157.772 1 346.49 ? O12 I8P 705 B 1 
HETATM 9 O O13 I8P . . . N 3 160.345 154.405 158.487 1 351.18 ? O13 I8P 705 B 1 
HETATM 10 O O14 I8P . . . N 3 159.032 153.383 156.067 1 353.09 ? O14 I8P 705 B 1 
HETATM 11 O O15 I8P . . . N 3 161.051 152.071 154.398 1 352.79 ? O15 I8P 705 B 1 
HETATM 12 O O16 I8P . . . N 3 162.975 154.101 153.634 1 347.91 ? O16 I8P 705 B 1 
HETATM 13 O O21 I8P . . . N 3 165.377 155.077 158.445 1 348.7 ? O21 I8P 705 B 1 
HETATM 14 O O22 I8P . . . N 3 162.188 153.601 160.306 1 354.26 ? O22 I8P 705 B 1 
HETATM 15 O O23 I8P . . . N 3 157.647 154.331 158.426 1 347.72 ? O23 I8P 705 B 1 
HETATM 16 O O24 I8P . . . N 3 159.09 156.088 155.592 1 353.13 ? O24 I8P 705 B 1 
HETATM 17 O O25 I8P . . . N 3 160.495 150.574 152.27 1 345.81 ? O25 I8P 705 B 1 
HETATM 18 O O26 I8P . . . N 3 163.553 151.702 152.661 1 347.79 ? O26 I8P 705 B 1 
HETATM 19 O O31 I8P . . . N 3 166.386 156.507 156.784 1 345.55 ? O31 I8P 705 B 1 
HETATM 20 O O32 I8P . . . N 3 161.385 151.585 159.075 1 348.86 ? O32 I8P 705 B 1 
HETATM 21 O O33 I8P . . . N 3 158.826 156.476 158.204 1 350.26 ? O33 I8P 705 B 1 
HETATM 22 O O34 I8P . . . N 3 156.906 154.982 156.003 1 345.97 ? O34 I8P 705 B 1 
HETATM 23 O O35 I8P . . . N 3 158.64 151.264 153.966 1 348.9 ? O35 I8P 705 B 1 
HETATM 24 O O36 I8P . . . N 3 165.37 153.533 152.682 1 352.73 ? O36 I8P 705 B 1 
HETATM 25 O O41 I8P . . . N 3 164.136 157.147 157.705 1 352.56 ? O41 I8P 705 B 1 
HETATM 26 O O42 I8P . . . N 3 163.727 151.753 159.824 1 348.34 ? O42 I8P 705 B 1 
HETATM 27 O O43 I8P . . . N 3 158.793 155.398 160.429 1 345.97 ? O43 I8P 705 B 1 
HETATM 28 O O44 I8P . . . N 3 158.304 154.62 153.885 1 345.59 ? O44 I8P 705 B 1 
HETATM 29 O O45 I8P . . . N 3 159.548 152.871 152.514 1 349.39 ? O45 I8P 705 B 1 
HETATM 30 O O46 I8P . . . N 3 163.437 153.583 151.124 1 351.5 ? O46 I8P 705 B 1 
HETATM 31 O O51 I8P . . . N 3 164.424 159.568 156.925 1 344.94 ? O51 I8P 705 B 1 
HETATM 32 O O55 I8P . . . N 3 160.963 152.884 150.271 1 352.1 ? O55 I8P 705 B 1 
HETATM 33 O O61 I8P . . . N 3 162.97 159.191 158.84 1 353.56 ? O61 I8P 705 B 1 
HETATM 34 O O65 I8P . . . N 3 161.104 154.814 151.827 1 347.59 ? O65 I8P 705 B 1 
HETATM 35 O O71 I8P . . . N 3 162.159 158.506 156.599 1 351.61 ? O71 I8P 705 B 1 
HETATM 36 O O75 I8P . . . N 3 159.048 154.529 150.65 1 354.72 ? O75 I8P 705 B 1 
HETATM 37 P PA1 I8P . . . N 3 165.043 155.9 157.232 1 346.42 ? PA1 I8P 705 B 1 
HETATM 38 P PA2 I8P . . . N 3 162.589 152.569 159.259 1 352.99 ? PA2 I8P 705 B 1 
HETATM 39 P PA3 I8P . . . N 3 158.849 155.113 158.887 1 351.4 ? PA3 I8P 705 B 1 
HETATM 40 P PA4 I8P . . . N 3 158.293 154.812 155.447 1 348.01 ? PA4 I8P 705 B 1 
HETATM 41 P PA5 I8P . . . N 3 159.98 151.557 153.312 1 349.37 ? PA5 I8P 705 B 1 
HETATM 42 P PA6 I8P . . . N 3 163.916 153.182 152.546 1 349.53 ? PA6 I8P 705 B 1 
HETATM 43 P PB1 I8P . . . N 3 163.405 158.568 157.495 1 351.82 ? PB1 I8P 705 B 1 
HETATM 44 P PB5 I8P . . . N 3 160.182 153.675 151.306 1 353.97 ? PB5 I8P 705 B 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    67 
_model_server_stats.query_time_ms           532 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           44 
#