data_7PMD
#
_model_server_result.job_id            X5GFgBtlG6Hs63Uc1MIHbw 
_model_server_result.datetime_utc      '2025-09-04 15:06:45' 
_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          7pmd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":401}' 
#
_entry.id    7PMD 
#
_exptl.entry_id    7PMD 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          7 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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            7PMD 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7PMD 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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    ? 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      7 
_struct_asym.id                             H 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
covale ? covale1 B C GLU 74 C GLU 72 1_555 B N HIC 75 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale2 B C HIC 75 C HIC 73 1_555 B N GLY 76 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? 
covale ? covale3 C C TRP 1 H TRP 1 1_555 C N EEP 2 H EEP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.305 ? 
covale ? covale4 C CD1 TRP 1 H TRP 1 1_555 C SG CYS 5 H CYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.728 ? 
covale ? covale5 C N TRP 1 H TRP 1 1_555 C C ALA 7 H ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? 
covale ? covale6 C C EEP 2 H EEP 2 1_555 C N ALA 3 H ALA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.303 ? 
covale ? covale7 C C ALA 3 H ALA 3 1_555 C N DTH 4 H DTH 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.313 ? 
covale ? covale8 C C DTH 4 H DTH 4 1_555 C N CYS 5 H CYS 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale9 C C CYS 5 H CYS 5 1_555 C N HYP 6 H HYP 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale10 C C HYP 6 H HYP 6 1_555 C N ALA 7 H ALA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.373 ? 
metalc ? metalc1 A OG SER 218 A SER 218 1_555 F MG MG . A MG 1902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.903 ? 
metalc ? metalc2 E O2G ANP . A ANP 1901 1_555 F MG MG . A MG 1902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.919 ? 
metalc ? metalc3 E O3G ANP . A ANP 1901 1_555 F MG MG . A MG 1902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? 
metalc ? metalc4 E O1B ANP . A ANP 1901 1_555 G MG MG . A MG 1903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? 
metalc ? metalc5 E O1A ANP . A ANP 1901 1_555 G MG MG . A MG 1903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? 
metalc ? metalc6 H O3B ADP . C ADP 401 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? 
#
_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     ? 
#
_atom_sites.entry_id                     7PMD 
_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
E 5 ANP A 1 1901 793 ANP ANP . 
F 6 MG A 1 1902 794 MG MG . 
G 6 MG A 1 1903 795 MG MG . 
H 7 ADP C 1 401 376 ADP ADP . 
I 6 MG C 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 7 135.053 201.127 145.233 1 60.62 ? PB ADP 401 C 1 
HETATM 2 O O1B ADP . . . H 7 135.899 200.053 144.639 1 60.62 ? O1B ADP 401 C 1 
HETATM 3 O O2B ADP . . . H 7 133.604 200.938 144.95 1 60.62 ? O2B ADP 401 C 1 
HETATM 4 O O3B ADP . . . H 7 135.366 201.482 146.661 1 60.62 ? O3B ADP 401 C 1 
HETATM 5 P PA ADP . . . H 7 136.942 202.955 144.373 1 60.62 ? PA ADP 401 C 1 
HETATM 6 O O1A ADP . . . H 7 137.782 202.161 143.437 1 60.62 ? O1A ADP 401 C 1 
HETATM 7 O O2A ADP . . . H 7 137.389 203.131 145.783 1 60.62 ? O2A ADP 401 C 1 
HETATM 8 O O3A ADP . . . H 7 135.453 202.394 144.367 1 60.62 ? O3A ADP 401 C 1 
HETATM 9 O O5' ADP . . . H 7 136.652 204.369 143.714 1 60.62 ? O5' ADP 401 C 1 
HETATM 10 C C5' ADP . . . H 7 136.361 204.41 142.329 1 60.62 ? C5' ADP 401 C 1 
HETATM 11 C C4' ADP . . . H 7 135.512 205.641 142.112 1 60.62 ? C4' ADP 401 C 1 
HETATM 12 O O4' ADP . . . H 7 136.28 206.794 142.423 1 60.62 ? O4' ADP 401 C 1 
HETATM 13 C C3' ADP . . . H 7 135.118 205.83 140.679 1 60.62 ? C3' ADP 401 C 1 
HETATM 14 O O3' ADP . . . H 7 133.936 206.612 140.63 1 60.62 ? O3' ADP 401 C 1 
HETATM 15 C C2' ADP . . . H 7 136.21 206.66 140.101 1 60.62 ? C2' ADP 401 C 1 
HETATM 16 O O2' ADP . . . H 7 135.62 207.485 139.106 1 60.62 ? O2' ADP 401 C 1 
HETATM 17 C C1' ADP . . . H 7 136.59 207.54 141.253 1 60.62 ? C1' ADP 401 C 1 
HETATM 18 N N9 ADP . . . H 7 138.029 207.841 141.182 1 60.62 ? N9 ADP 401 C 1 
HETATM 19 C C8 ADP . . . H 7 139.014 206.954 141.021 1 60.62 ? C8 ADP 401 C 1 
HETATM 20 N N7 ADP . . . H 7 140.214 207.572 140.995 1 60.62 ? N7 ADP 401 C 1 
HETATM 21 C C5 ADP . . . H 7 139.989 208.881 141.138 1 60.62 ? C5 ADP 401 C 1 
HETATM 22 C C6 ADP . . . H 7 140.812 210.093 141.194 1 60.62 ? C6 ADP 401 C 1 
HETATM 23 N N6 ADP . . . H 7 142.154 210.019 141.087 1 60.62 ? N6 ADP 401 C 1 
HETATM 24 N N1 ADP . . . H 7 140.185 211.266 141.351 1 60.62 ? N1 ADP 401 C 1 
HETATM 25 C C2 ADP . . . H 7 138.854 211.344 141.455 1 60.62 ? C2 ADP 401 C 1 
HETATM 26 N N3 ADP . . . H 7 138.045 210.287 141.413 1 60.62 ? N3 ADP 401 C 1 
HETATM 27 C C4 ADP . . . H 7 138.548 209.053 141.257 1 60.62 ? C4 ADP 401 C 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           344 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#