data_8Y5I
#
_model_server_result.job_id            VNYrnCDTyLkwPgE0RdU9fw 
_model_server_result.datetime_utc      '2024-11-14 14:40:23' 
_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          8y5i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":401}' 
#
_entry.id    8Y5I 
#
_exptl.entry_id    8Y5I 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_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            8Y5I 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8Y5I 
_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_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 
_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
? 5 F N N 
? 5 H 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 A OE1 GLN 96 A GLN 96 1_555 G MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? 
metalc ? metalc2 D OE1 GLN 96 D GLN 96 1_555 I MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? 
metalc ? metalc3 H O1G ATP . D ATP 401 1_555 I MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? 
#
_chem_comp.formula           'C10 H16 N5 O13 P3' 
_chem_comp.formula_weight    507.181 
_chem_comp.id                ATP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "ADENOSINE-5'-TRIPHOSPHATE" 
_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
PG O1G ATP doub 70 n n 
PG O2G ATP sing 71 n n 
PG O3G ATP sing 72 n n 
PG O3B ATP sing 73 n n 
O2G HOG2 ATP sing 74 n n 
O3G HOG3 ATP sing 75 n n 
PB O1B ATP doub 76 n n 
PB O2B ATP sing 77 n n 
PB O3B ATP sing 78 n n 
PB O3A ATP sing 79 n n 
O2B HOB2 ATP sing 80 n n 
PA O1A ATP doub 81 n n 
PA O2A ATP sing 82 n n 
PA O3A ATP sing 83 n n 
PA O5' ATP sing 84 n n 
O2A HOA2 ATP sing 85 n n 
O5' C5' ATP sing 86 n n 
C5' C4' ATP sing 87 n n 
C5' "H5'1" ATP sing 88 n n 
C5' "H5'2" ATP sing 89 n n 
C4' O4' ATP sing 90 n n 
C4' C3' ATP sing 91 n n 
C4' H4' ATP sing 92 n n 
O4' C1' ATP sing 93 n n 
C3' O3' ATP sing 94 n n 
C3' C2' ATP sing 95 n n 
C3' H3' ATP sing 96 n n 
O3' HO3' ATP sing 97 n n 
C2' O2' ATP sing 98 n n 
C2' C1' ATP sing 99 n n 
C2' H2' ATP sing 100 n n 
O2' HO2' ATP sing 101 n n 
C1' N9 ATP sing 102 n n 
C1' H1' ATP sing 103 n n 
N9 C8 ATP sing 104 n y 
N9 C4 ATP sing 105 n y 
C8 N7 ATP doub 106 n y 
C8 H8 ATP sing 107 n n 
N7 C5 ATP sing 108 n y 
C5 C6 ATP sing 109 n y 
C5 C4 ATP doub 110 n y 
C6 N6 ATP sing 111 n n 
C6 N1 ATP doub 112 n y 
N6 HN61 ATP sing 113 n n 
N6 HN62 ATP sing 114 n n 
N1 C2 ATP sing 115 n y 
C2 N3 ATP doub 116 n y 
C2 H2 ATP sing 117 n n 
N3 C4 ATP sing 118 n y 
#
_atom_sites.entry_id                     8Y5I 
_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 5 ATP A 1 401 401 ATP ATP . 
G 6 MG A 1 402 402 MG MG . 
H 5 ATP D 1 401 401 ATP ATP . 
I 6 MG D 1 402 402 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 PG ATP . . . H 5 117.766 108.884 164.985 1 47.96 ? PG ATP 401 D 1 
HETATM 2 O O1G ATP . . . H 5 117.125 109.86 164.036 1 47.73 ? O1G ATP 401 D 1 
HETATM 3 O O2G ATP . . . H 5 119.245 109.158 165.072 1 46.04 ? O2G ATP 401 D 1 
HETATM 4 O O3G ATP . . . H 5 117.143 109.019 166.35 1 48.58 ? O3G ATP 401 D 1 
HETATM 5 P PB ATP . . . H 5 118.219 106.937 162.987 1 46.03 ? PB ATP 401 D 1 
HETATM 6 O O1B ATP . . . H 5 117.771 107.928 161.942 1 47.77 ? O1B ATP 401 D 1 
HETATM 7 O O2B ATP . . . H 5 119.711 107.011 163.188 1 48.14 ? O2B ATP 401 D 1 
HETATM 8 O O3B ATP . . . H 5 117.531 107.361 164.408 1 46.37 ? O3B ATP 401 D 1 
HETATM 9 P PA ATP . . . H 5 117.804 104.889 160.954 1 46.02 ? PA ATP 401 D 1 
HETATM 10 O O1A ATP . . . H 5 117.955 106.054 160.022 1 46.71 ? O1A ATP 401 D 1 
HETATM 11 O O2A ATP . . . H 5 116.503 104.183 160.677 1 47.79 ? O2A ATP 401 D 1 
HETATM 12 O O3A ATP . . . H 5 117.817 105.408 162.525 1 45.94 ? O3A ATP 401 D 1 
HETATM 13 O O5' ATP . . . H 5 119.042 103.831 160.688 1 47.5 ? O5' ATP 401 D 1 
HETATM 14 C C5' ATP . . . H 5 120.314 104.123 161.212 1 47.26 ? C5' ATP 401 D 1 
HETATM 15 C C4' ATP . . . H 5 121.284 103.269 160.474 1 46.26 ? C4' ATP 401 D 1 
HETATM 16 O O4' ATP . . . H 5 120.852 103.136 159.258 1 45.72 ? O4' ATP 401 D 1 
HETATM 17 C C3' ATP . . . H 5 122.781 103.984 160.392 1 47.46 ? C3' ATP 401 D 1 
HETATM 18 O O3' ATP . . . H 5 123.807 102.95 160.614 1 48.45 ? O3' ATP 401 D 1 
HETATM 19 C C2' ATP . . . H 5 122.88 104.426 159.244 1 47.16 ? C2' ATP 401 D 1 
HETATM 20 O O2' ATP . . . H 5 124.317 104.427 158.808 1 47.99 ? O2' ATP 401 D 1 
HETATM 21 C C1' ATP . . . H 5 122.056 103.358 158.397 1 46.22 ? C1' ATP 401 D 1 
HETATM 22 N N9 ATP . . . H 5 121.698 103.838 157.229 1 46.7 ? N9 ATP 401 D 1 
HETATM 23 C C8 ATP . . . H 5 120.809 104.822 157.238 1 47.02 ? C8 ATP 401 D 1 
HETATM 24 N N7 ATP . . . H 5 120.572 105.167 155.971 1 47.17 ? N7 ATP 401 D 1 
HETATM 25 C C5 ATP . . . H 5 121.32 104.393 155.182 1 47.44 ? C5 ATP 401 D 1 
HETATM 26 C C6 ATP . . . H 5 121.462 104.325 153.818 1 47.87 ? C6 ATP 401 D 1 
HETATM 27 N N6 ATP . . . H 5 120.828 105.099 152.766 1 48.09 ? N6 ATP 401 D 1 
HETATM 28 N N1 ATP . . . H 5 122.282 103.449 153.275 1 47.74 ? N1 ATP 401 D 1 
HETATM 29 C C2 ATP . . . H 5 122.987 102.616 154.066 1 47.7 ? C2 ATP 401 D 1 
HETATM 30 N N3 ATP . . . H 5 122.85 102.679 155.406 1 48.14 ? N3 ATP 401 D 1 
HETATM 31 C C4 ATP . . . H 5 122.012 103.569 155.959 1 47.55 ? C4 ATP 401 D 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           36 
_model_server_stats.create_model_time_ms    75 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           31 
#