data_3J8I
#
_model_server_result.job_id            PUCqJaTvIuLqFBB4VQa5hw 
_model_server_result.datetime_utc      '2024-11-17 10:45:13' 
_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          3j8i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":401}' 
#
_entry.id    3J8I 
#
_exptl.entry_id    3J8I 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_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            3J8I 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3J8I 
_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 
_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
? 2 F N N 
? 2 H N N 
? 2 J N N 
? 2 L N N 
? 2 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
metalc ? metalc1 F O1B ADP . D ADP 401 1_555 G MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.978 ? 
metalc ? metalc2 H O1B ADP . E ADP 401 1_555 I MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? 
metalc ? metalc3 J O1B ADP . F ADP 401 1_555 K MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? 
metalc ? metalc4 L O1B ADP . G ADP 401 1_555 M MG MG . G MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.967 ? 
metalc ? metalc5 N O1B ADP . H ADP 401 1_555 O MG MG . H MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.976 ? 
#
_chem_comp.formula           'C10 H15 N5 O10 P2' 
_chem_comp.formula_weight    427.201 
_chem_comp.id                ADP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "ADENOSINE-5'-DIPHOSPHATE" 
_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
PB O1B ADP doub 1 n n 
PB O2B ADP sing 2 n n 
PB O3B ADP sing 3 n n 
PB O3A ADP sing 4 n n 
O2B HOB2 ADP sing 5 n n 
O3B HOB3 ADP sing 6 n n 
PA O1A ADP doub 7 n n 
PA O2A ADP sing 8 n n 
PA O3A ADP sing 9 n n 
PA O5' ADP sing 10 n n 
O2A HOA2 ADP sing 11 n n 
O5' C5' ADP sing 12 n n 
C5' C4' ADP sing 13 n n 
C5' "H5'1" ADP sing 14 n n 
C5' "H5'2" ADP sing 15 n n 
C4' O4' ADP sing 16 n n 
C4' C3' ADP sing 17 n n 
C4' H4' ADP sing 18 n n 
O4' C1' ADP sing 19 n n 
C3' O3' ADP sing 20 n n 
C3' C2' ADP sing 21 n n 
C3' H3' ADP sing 22 n n 
O3' HO3' ADP sing 23 n n 
C2' O2' ADP sing 24 n n 
C2' C1' ADP sing 25 n n 
C2' H2' ADP sing 26 n n 
O2' HO2' ADP sing 27 n n 
C1' N9 ADP sing 28 n n 
C1' H1' ADP sing 29 n n 
N9 C8 ADP sing 30 n y 
N9 C4 ADP sing 31 n y 
C8 N7 ADP doub 32 n y 
C8 H8 ADP sing 33 n n 
N7 C5 ADP sing 34 n y 
C5 C6 ADP sing 35 n y 
C5 C4 ADP doub 36 n y 
C6 N6 ADP sing 37 n n 
C6 N1 ADP doub 38 n y 
N6 HN61 ADP sing 39 n n 
N6 HN62 ADP sing 40 n n 
N1 C2 ADP sing 41 n y 
C2 N3 ADP doub 42 n y 
C2 H2 ADP sing 43 n n 
N3 C4 ADP sing 44 n y 
#
_atom_sites.entry_id                     3J8I 
_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
F 2 ADP D 1 401 376 ADP ADP . 
G 3 MG D 1 402 377 MG MG . 
H 2 ADP E 1 401 376 ADP ADP . 
I 3 MG E 1 402 377 MG MG . 
J 2 ADP F 1 401 376 ADP ADP . 
K 3 MG F 1 402 377 MG MG . 
L 2 ADP G 1 401 376 ADP ADP . 
M 3 MG G 1 402 377 MG MG . 
N 2 ADP H 1 401 376 ADP ADP . 
O 3 MG H 1 402 377 MG MG . 
#
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 P PB ADP . . . H 2 17.705 4.797 20.013 1 92.85 ? PB ADP 401 E 1 
HETATM 2 O O1B ADP . . . H 2 18.738 5.188 19.028 1 98.23 ? O1B ADP 401 E 1 
HETATM 3 O O2B ADP . . . H 2 17.646 5.828 21.242 1 88.73 ? O2B ADP 401 E 1 
HETATM 4 O O3B ADP . . . H 2 16.393 4.718 19.317 1 85.88 ? O3B ADP 401 E 1 
HETATM 5 P PA ADP . . . H 2 17.984 2.015 19.921 1 116.16 ? PA ADP 401 E 1 
HETATM 6 O O1A ADP . . . H 2 17.388 2.123 18.582 1 118.15 ? O1A ADP 401 E 1 
HETATM 7 O O2A ADP . . . H 2 19.323 1.43 19.807 1 127.23 ? O2A ADP 401 E 1 
HETATM 8 O O3A ADP . . . H 2 18.075 3.407 20.571 1 82.39 ? O3A ADP 401 E 1 
HETATM 9 O O5' ADP . . . H 2 17.135 1.066 20.881 1 120.42 ? O5' ADP 401 E 1 
HETATM 10 C C5' ADP . . . H 2 16.545 1.33 22.157 1 95.4 ? C5' ADP 401 E 1 
HETATM 11 C C4' ADP . . . H 2 15.81 -0.012 22.556 1 119.73 ? C4' ADP 401 E 1 
HETATM 12 O O4' ADP . . . H 2 16.608 -1.181 22.239 1 95.95 ? O4' ADP 401 E 1 
HETATM 13 C C3' ADP . . . H 2 15.477 -0.159 24.065 1 118.09 ? C3' ADP 401 E 1 
HETATM 14 O O3' ADP . . . H 2 14.128 -0.613 24.319 1 147.83 ? O3' ADP 401 E 1 
HETATM 15 C C2' ADP . . . H 2 16.498 -1.132 24.609 1 90.77 ? C2' ADP 401 E 1 
HETATM 16 O O2' ADP . . . H 2 16.072 -1.776 25.816 1 48.41 ? O2' ADP 401 E 1 
HETATM 17 C C1' ADP . . . H 2 16.728 -2.026 23.411 1 66.52 ? C1' ADP 401 E 1 
HETATM 18 N N9 ADP . . . H 2 18.069 -2.685 23.403 1 78.45 ? N9 ADP 401 E 1 
HETATM 19 C C8 ADP . . . H 2 19.268 -2.065 23.199 1 80.82 ? C8 ADP 401 E 1 
HETATM 20 N N7 ADP . . . H 2 20.236 -2.958 23.285 1 65.34 ? N7 ADP 401 E 1 
HETATM 21 C C5 ADP . . . H 2 19.683 -4.132 23.518 1 90.14 ? C5 ADP 401 E 1 
HETATM 22 C C6 ADP . . . H 2 20.163 -5.436 23.737 1 115.79 ? C6 ADP 401 E 1 
HETATM 23 N N6 ADP . . . H 2 21.477 -5.639 23.663 1 168.84 ? N6 ADP 401 E 1 
HETATM 24 N N1 ADP . . . H 2 19.293 -6.505 23.977 1 74.14 ? N1 ADP 401 E 1 
HETATM 25 C C2 ADP . . . H 2 17.962 -6.319 24.057 1 12.3 ? C2 ADP 401 E 1 
HETATM 26 N N3 ADP . . . H 2 17.477 -5.055 23.867 1 58.44 ? N3 ADP 401 E 1 
HETATM 27 C C4 ADP . . . H 2 18.292 -3.952 23.628 1 79.61 ? C4 ADP 401 E 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           349 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           27 
#