data_8XDM
#
_model_server_result.job_id            oVxl1YE1wFCdxQtsp4_vpA 
_model_server_result.datetime_utc      '2024-12-19 03:38:59' 
_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          8xdm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":401}' 
#
_entry.id    8XDM 
#
_exptl.entry_id    8XDM 
_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    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_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
? 2 D N N 
? 2 F N N 
? 2 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
covale ? covale1 A C GLU 74 A GLU 72 1_555 A N HIC 75 A HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale2 A C HIC 75 A HIC 73 1_555 A N GLY 76 A GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale3 B C GLU 74 B GLU 72 1_555 B N HIC 75 B HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale4 B C HIC 75 B HIC 73 1_555 B N GLY 76 B GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale5 C C GLU 74 C GLU 72 1_555 C N HIC 75 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale6 C C HIC 75 C HIC 73 1_555 C N GLY 76 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
metalc ? metalc1 D O2B ADP . A ADP 401 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? 
metalc ? metalc2 F O2B ADP . B ADP 401 1_555 G MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? 
metalc ? metalc3 H O2B ADP . C ADP 401 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? 
#
_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                     8XDM 
_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
D 2 ADP A 1 401 376 ADP ADP . 
E 3 MG A 1 402 378 MG MG . 
F 2 ADP B 1 401 376 ADP ADP . 
G 3 MG B 1 402 378 MG MG . 
H 2 ADP C 1 401 376 ADP ADP . 
I 3 MG C 1 402 378 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 . . . F 2 231.73 209.81 203.749 1 22.13 ? PB ADP 401 B 1 
HETATM 2 O O1B ADP . . . F 2 231.593 208.847 202.597 1 22.13 ? O1B ADP 401 B 1 
HETATM 3 O O2B ADP . . . F 2 232.18 209.177 205.044 1 22.13 ? O2B ADP 401 B 1 
HETATM 4 O O3B ADP . . . F 2 230.552 210.739 203.901 1 22.13 ? O3B ADP 401 B 1 
HETATM 5 P PA ADP . . . F 2 233.12 212.308 203.631 1 22.13 ? PA ADP 401 B 1 
HETATM 6 O O1A ADP . . . F 2 234.599 212.606 203.686 1 22.13 ? O1A ADP 401 B 1 
HETATM 7 O O2A ADP . . . F 2 232.28 212.646 204.839 1 22.13 ? O2A ADP 401 B 1 
HETATM 8 O O3A ADP . . . F 2 232.985 210.731 203.318 1 22.13 ? O3A ADP 401 B 1 
HETATM 9 O O5' ADP . . . F 2 232.535 213.085 202.343 1 22.13 ? O5' ADP 401 B 1 
HETATM 10 C C5' ADP . . . F 2 231.132 213.201 202.122 1 22.13 ? C5' ADP 401 B 1 
HETATM 11 C C4' ADP . . . F 2 230.782 214.517 201.431 1 22.13 ? C4' ADP 401 B 1 
HETATM 12 O O4' ADP . . . F 2 231.709 215.558 201.753 1 22.13 ? O4' ADP 401 B 1 
HETATM 13 C C3' ADP . . . F 2 230.78 214.415 199.913 1 22.13 ? C3' ADP 401 B 1 
HETATM 14 O O3' ADP . . . F 2 229.44 214.28 199.435 1 22.13 ? O3' ADP 401 B 1 
HETATM 15 C C2' ADP . . . F 2 231.364 215.724 199.422 1 22.13 ? C2' ADP 401 B 1 
HETATM 16 O O2' ADP . . . F 2 230.395 216.432 198.645 1 22.13 ? O2' ADP 401 B 1 
HETATM 17 C C1' ADP . . . F 2 231.7 216.506 200.682 1 22.13 ? C1' ADP 401 B 1 
HETATM 18 N N9 ADP . . . F 2 233 217.205 200.521 1 22.13 ? N9 ADP 401 B 1 
HETATM 19 C C8 ADP . . . F 2 234.215 216.631 200.435 1 22.13 ? C8 ADP 401 B 1 
HETATM 20 N N7 ADP . . . F 2 235.187 217.568 200.284 1 22.13 ? N7 ADP 401 B 1 
HETATM 21 C C5 ADP . . . F 2 234.589 218.774 200.267 1 22.13 ? C5 ADP 401 B 1 
HETATM 22 C C6 ADP . . . F 2 235.024 220.185 200.137 1 22.13 ? C6 ADP 401 B 1 
HETATM 23 N N6 ADP . . . F 2 236.333 220.505 199.992 1 22.13 ? N6 ADP 401 B 1 
HETATM 24 N N1 ADP . . . F 2 234.072 221.144 200.17 1 22.13 ? N1 ADP 401 B 1 
HETATM 25 C C2 ADP . . . F 2 232.769 220.841 200.313 1 22.13 ? C2 ADP 401 B 1 
HETATM 26 N N3 ADP . . . F 2 232.303 219.586 200.436 1 22.13 ? N3 ADP 401 B 1 
HETATM 27 C C4 ADP . . . F 2 233.148 218.527 200.419 1 22.13 ? C4 ADP 401 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           334 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           27 
#