data_6PDY
#
_model_server_result.job_id            dvSsSh8OV4JewuM9uFZrMg 
_model_server_result.datetime_utc      '2025-07-08 07:22:20' 
_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          6pdy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"T","auth_seq_id":502}' 
#
_entry.id    6PDY 
#
_exptl.entry_id    6PDY 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          3 
_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            6PDY 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PDY 
_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    heptameric 
_pdbx_struct_assembly.oligomeric_count      7 
_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 
_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 H N N 
? 3 K N N 
? 3 N N N 
? 3 Q N N 
? 3 T 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 B OD1 ASP 185 A ASP 213 1_555 J MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.757 ? 
metalc ? metalc2 B OD2 ASP 185 A ASP 213 1_555 J MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc3 C OG1 THR 133 B THR 161 1_555 M MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
metalc ? metalc4 K O1B ADP . B ADP 501 1_555 M MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? 
metalc ? metalc5 K O2B ADP . B ADP 501 1_555 M MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? 
metalc ? metalc6 K O2A ADP . B ADP 501 1_555 M MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc7 D OG1 THR 133 C THR 161 1_555 P MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc8 D OD1 ASP 185 C ASP 213 1_555 P MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? 
metalc ? metalc9 E OG1 THR 133 D THR 161 1_555 R MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? 
metalc ? metalc10 E OD1 ASP 185 D ASP 213 1_555 R MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
metalc ? metalc11 E OD2 ASP 185 D ASP 213 1_555 R MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? 
#
_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                     6PDY 
_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
H 3 ADP A 1 501 501 ADP ADP . 
I 4 BEF A 1 502 502 BEF BEF . 
J 5 MG A 1 503 601 MG MG . 
K 3 ADP B 1 501 501 ADP ADP . 
L 4 BEF B 1 502 502 BEF BEF . 
M 5 MG B 1 503 601 MG MG . 
N 3 ADP C 1 501 501 ADP ADP . 
O 4 BEF C 1 502 502 BEF BEF . 
P 5 MG C 1 503 601 MG MG . 
Q 3 ADP D 1 501 501 ADP ADP . 
R 5 MG D 1 502 601 MG MG . 
S 4 BEF E 1 501 502 BEF BEF . 
T 3 ADP E 1 502 501 ADP ADP . 
#
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 . . . T 3 144.068 133.608 166.499 1 96.37 ? PB ADP 502 E 1 
HETATM 2 O O1B ADP . . . T 3 145.476 133.849 166.012 1 96.37 ? O1B ADP 502 E 1 
HETATM 3 O O2B ADP . . . T 3 143.059 134.622 166.017 1 96.37 ? O2B ADP 502 E 1 
HETATM 4 O O3B ADP . . . T 3 143.591 132.18 166.379 1 96.37 ? O3B ADP 502 E 1 
HETATM 5 P PA ADP . . . T 3 142.87 133.651 169.03 1 96.37 ? PA ADP 502 E 1 
HETATM 6 O O1A ADP . . . T 3 141.815 132.946 168.215 1 96.37 ? O1A ADP 502 E 1 
HETATM 7 O O2A ADP . . . T 3 142.557 134.968 169.696 1 96.37 ? O2A ADP 502 E 1 
HETATM 8 O O3A ADP . . . T 3 144.157 133.86 168.088 1 96.37 ? O3A ADP 502 E 1 
HETATM 9 O O5' ADP . . . T 3 143.426 132.636 170.149 1 96.37 ? O5' ADP 502 E 1 
HETATM 10 C C5' ADP . . . T 3 143.406 131.225 169.943 1 96.37 ? C5' ADP 502 E 1 
HETATM 11 C C4' ADP . . . T 3 142.579 130.513 171.009 1 96.37 ? C4' ADP 502 E 1 
HETATM 12 O O4' ADP . . . T 3 143.207 130.599 172.289 1 96.37 ? O4' ADP 502 E 1 
HETATM 13 C C3' ADP . . . T 3 141.17 131.074 171.166 1 96.37 ? C3' ADP 502 E 1 
HETATM 14 O O3' ADP . . . T 3 140.218 130.244 170.497 1 96.37 ? O3' ADP 502 E 1 
HETATM 15 C C2' ADP . . . T 3 140.917 131.102 172.662 1 96.37 ? C2' ADP 502 E 1 
HETATM 16 O O2' ADP . . . T 3 139.845 130.228 173.027 1 96.37 ? O2' ADP 502 E 1 
HETATM 17 C C1' ADP . . . T 3 142.211 130.642 173.313 1 96.37 ? C1' ADP 502 E 1 
HETATM 18 N N9 ADP . . . T 3 142.612 131.587 174.38 1 96.37 ? N9 ADP 502 E 1 
HETATM 19 C C8 ADP . . . T 3 143.675 132.411 174.338 1 96.37 ? C8 ADP 502 E 1 
HETATM 20 N N7 ADP . . . T 3 143.759 133.141 175.479 1 96.37 ? N7 ADP 502 E 1 
HETATM 21 C C5 ADP . . . T 3 142.734 132.779 176.268 1 96.37 ? C5 ADP 502 E 1 
HETATM 22 C C6 ADP . . . T 3 142.235 133.157 177.605 1 96.37 ? C6 ADP 502 E 1 
HETATM 23 N N6 ADP . . . T 3 142.877 134.095 178.335 1 96.37 ? N6 ADP 502 E 1 
HETATM 24 N N1 ADP . . . T 3 141.128 132.536 178.062 1 96.37 ? N1 ADP 502 E 1 
HETATM 25 C C2 ADP . . . T 3 140.483 131.599 177.341 1 96.37 ? C2 ADP 502 E 1 
HETATM 26 N N3 ADP . . . T 3 140.885 131.212 176.118 1 96.37 ? N3 ADP 502 E 1 
HETATM 27 C C4 ADP . . . T 3 141.982 131.752 175.541 1 96.37 ? C4 ADP 502 E 1 
HETATM 28 H "H5'1" ADP . . . T 3 143.018 130.979 168.955 1 96.37 ? "H5'1" ADP 502 E 1 
HETATM 29 H "H5'2" ADP . . . T 3 144.432 130.854 169.987 1 96.37 ? "H5'2" ADP 502 E 1 
HETATM 30 H H4' ADP . . . T 3 142.491 129.457 170.721 1 96.37 ? H4' ADP 502 E 1 
HETATM 31 H H3' ADP . . . T 3 141.119 132.098 170.773 1 96.37 ? H3' ADP 502 E 1 
HETATM 32 H HO3' ADP . . . T 3 139.373 130.71 170.439 1 96.37 ? HO3' ADP 502 E 1 
HETATM 33 H H2' ADP . . . T 3 140.696 132.13 172.976 1 96.37 ? H2' ADP 502 E 1 
HETATM 34 H HO2' ADP . . . T 3 139.006 130.605 172.732 1 96.37 ? HO2' ADP 502 E 1 
HETATM 35 H H1' ADP . . . T 3 142.057 129.64 173.735 1 96.37 ? H1' ADP 502 E 1 
HETATM 36 H H8 ADP . . . T 3 144.366 132.482 173.508 1 96.37 ? H8 ADP 502 E 1 
HETATM 37 H HN61 ADP . . . T 3 142.532 134.35 179.248 1 96.37 ? HN61 ADP 502 E 1 
HETATM 38 H HN62 ADP . . . T 3 143.701 134.539 177.961 1 96.37 ? HN62 ADP 502 E 1 
HETATM 39 H H2 ADP . . . T 3 139.599 131.137 177.762 1 96.37 ? H2 ADP 502 E 1 
#
_model_server_stats.io_time_ms              73 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    36 
_model_server_stats.query_time_ms           238 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           39 
#