data_8PTM
#
_model_server_result.job_id            GQmIApVf0U7cZnXEnrlpaQ 
_model_server_result.datetime_utc      '2024-11-27 11:28:55' 
_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          8ptm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":1000}' 
#
_entry.id    8PTM 
#
_exptl.entry_id    8PTM 
_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    3 
_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            8PTM 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8PTM 
_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    11-meric 
_pdbx_struct_assembly.oligomeric_count      11 
_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 
_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 L N N 
? 3 N N N 
? 3 P 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 C OG1 THR 185 C THR 185 1_555 M MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? 
metalc ? metalc2 L O3B ADP . C ADP 1000 1_555 M MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
metalc ? metalc3 D OG1 THR 185 D THR 185 1_555 O MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? 
metalc ? metalc4 N O2B ADP . D ADP 1000 1_555 O MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? 
#
_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                     8PTM 
_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
L 3 ADP C 1 1000 1000 ADP ADP . 
M 4 MG C 1 1001 1001 MG MG . 
N 3 ADP D 1 1000 1000 ADP ADP . 
O 4 MG D 1 1001 1001 MG MG . 
P 3 ADP E 1 1000 1000 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 . . . L 3 138.253 137.903 167.788 1 164.25 ? PB ADP 1000 C 1 
HETATM 2 O O1B ADP . . . L 3 138.112 138.653 166.486 1 150.77 ? O1B ADP 1000 C 1 
HETATM 3 O O2B ADP . . . L 3 138.377 138.787 169.005 1 155.71 ? O2B ADP 1000 C 1 
HETATM 4 O O3B ADP . . . L 3 139.23 136.754 167.742 1 157.51 ? O3B ADP 1000 C 1 
HETATM 5 P PA ADP . . . L 3 136.726 135.83 168.845 1 164.31 ? PA ADP 1000 C 1 
HETATM 6 O O1A ADP . . . L 3 136.853 134.656 167.907 1 152.5 ? O1A ADP 1000 C 1 
HETATM 7 O O2A ADP . . . L 3 137.651 135.954 170.03 1 157.74 ? O2A ADP 1000 C 1 
HETATM 8 O O3A ADP . . . L 3 136.83 137.18 167.978 1 153.76 ? O3A ADP 1000 C 1 
HETATM 9 O O5' ADP . . . L 3 135.214 135.879 169.387 1 156.22 ? O5' ADP 1000 C 1 
HETATM 10 C C5' ADP . . . L 3 134.808 135.001 170.433 1 152.93 ? C5' ADP 1000 C 1 
HETATM 11 C C4' ADP . . . L 3 133.353 135.266 170.791 1 153.4 ? C4' ADP 1000 C 1 
HETATM 12 O O4' ADP . . . L 3 132.515 135.008 169.663 1 156.48 ? O4' ADP 1000 C 1 
HETATM 13 C C3' ADP . . . L 3 132.898 134.357 171.92 1 152.78 ? C3' ADP 1000 C 1 
HETATM 14 O O3' ADP . . . L 3 132.632 135.128 173.094 1 152.07 ? O3' ADP 1000 C 1 
HETATM 15 C C2' ADP . . . L 3 131.629 133.691 171.432 1 155.74 ? C2' ADP 1000 C 1 
HETATM 16 O O2' ADP . . . L 3 130.535 134.042 172.283 1 155.93 ? O2' ADP 1000 C 1 
HETATM 17 C C1' ADP . . . L 3 131.379 134.221 170.029 1 156.46 ? C1' ADP 1000 C 1 
HETATM 18 N N9 ADP . . . L 3 131.237 133.09 169.079 1 155.13 ? N9 ADP 1000 C 1 
HETATM 19 C C8 ADP . . . L 3 132.009 132.88 167.997 1 151.62 ? C8 ADP 1000 C 1 
HETATM 20 N N7 ADP . . . L 3 131.626 131.764 167.327 1 147.44 ? N7 ADP 1000 C 1 
HETATM 21 C C5 ADP . . . L 3 130.579 131.239 167.987 1 148.79 ? C5 ADP 1000 C 1 
HETATM 22 C C6 ADP . . . L 3 129.697 130.062 167.818 1 152.88 ? C6 ADP 1000 C 1 
HETATM 23 N N6 ADP . . . L 3 129.864 129.205 166.783 1 152.39 ? N6 ADP 1000 C 1 
HETATM 24 N N1 ADP . . . L 3 128.719 129.874 168.731 1 155.41 ? N1 ADP 1000 C 1 
HETATM 25 C C2 ADP . . . L 3 128.543 130.718 169.764 1 153.51 ? C2 ADP 1000 C 1 
HETATM 26 N N3 ADP . . . L 3 129.307 131.805 169.977 1 154.15 ? N3 ADP 1000 C 1 
HETATM 27 C C4 ADP . . . L 3 130.323 132.117 169.138 1 152.71 ? C4 ADP 1000 C 1 
#
_model_server_stats.io_time_ms              74 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    94 
_model_server_stats.query_time_ms           733 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#