data_8D3W
#
_model_server_result.job_id            Xgp1TBYAfOdhDcOT95ar5Q 
_model_server_result.datetime_utc      '2024-12-26 11:32:27' 
_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          8d3w 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":2001}' 
#
_entry.id    8D3W 
#
_exptl.entry_id    8D3W 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              505.208 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' 
_entity.pdbx_number_of_molecules    1 
_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 
_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                      4 
_struct_asym.id                             D 
_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
disulf ? disulf1 B SG CYS 126 B CYS 126 1_555 B SG CYS 149 B CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf2 B SG CYS 213 B CYS 213 1_555 B SG CYS 276 B CYS 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
#
_chem_comp.formula           'C11 H18 N5 O12 P3' 
_chem_comp.formula_weight    505.208 
_chem_comp.id                ACP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" 
#
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 ACP doub 1 n n 
PG O2G ACP sing 2 n n 
PG O3G ACP sing 3 n n 
PG C3B ACP sing 4 n n 
O2G HOG2 ACP sing 5 n n 
O3G HOG3 ACP sing 6 n n 
PB O1B ACP doub 7 n n 
PB O2B ACP sing 8 n n 
PB C3B ACP sing 9 n n 
PB O3A ACP sing 10 n n 
O2B HOB2 ACP sing 11 n n 
C3B H3B1 ACP sing 12 n n 
C3B H3B2 ACP sing 13 n n 
PA O1A ACP doub 14 n n 
PA O2A ACP sing 15 n n 
PA O3A ACP sing 16 n n 
PA O5' ACP sing 17 n n 
O2A HOA2 ACP sing 18 n n 
O5' C5' ACP sing 19 n n 
C5' C4' ACP sing 20 n n 
C5' "H5'1" ACP sing 21 n n 
C5' "H5'2" ACP sing 22 n n 
C4' O4' ACP sing 23 n n 
C4' C3' ACP sing 24 n n 
C4' H4' ACP sing 25 n n 
O4' C1' ACP sing 26 n n 
C3' O3' ACP sing 27 n n 
C3' C2' ACP sing 28 n n 
C3' H3' ACP sing 29 n n 
O3' HO3' ACP sing 30 n n 
C2' O2' ACP sing 31 n n 
C2' C1' ACP sing 32 n n 
C2' H2' ACP sing 33 n n 
O2' HO2' ACP sing 34 n n 
C1' N9 ACP sing 35 n n 
C1' H1' ACP sing 36 n n 
N9 C8 ACP sing 37 n y 
N9 C4 ACP sing 38 n y 
C8 N7 ACP doub 39 n y 
C8 H8 ACP sing 40 n n 
N7 C5 ACP sing 41 n y 
C5 C6 ACP sing 42 n y 
C5 C4 ACP doub 43 n y 
C6 N6 ACP sing 44 n n 
C6 N1 ACP doub 45 n y 
N6 HN61 ACP sing 46 n n 
N6 HN62 ACP sing 47 n n 
N1 C2 ACP sing 48 n y 
C2 N3 ACP doub 49 n y 
C2 H2 ACP sing 50 n n 
N3 C4 ACP sing 51 n y 
#
_atom_sites.entry_id                     8D3W 
_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 
#
_pdbx_nonpoly_scheme.asym_id          D 
_pdbx_nonpoly_scheme.entity_id        4 
_pdbx_nonpoly_scheme.mon_id           ACP 
_pdbx_nonpoly_scheme.pdb_strand_id    A 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      2001 
_pdbx_nonpoly_scheme.auth_seq_num     2001 
_pdbx_nonpoly_scheme.pdb_mon_id       ACP 
_pdbx_nonpoly_scheme.auth_mon_id      ACP 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 ACP . . . D 4 84.3 94.145 147.717 1 44.14 ? PG ACP 2001 A 1 
HETATM 2 O O1G ACP . . . D 4 84.81 92.74 147.322 1 44.14 ? O1G ACP 2001 A 1 
HETATM 3 O O2G ACP . . . D 4 84.201 94.975 146.526 1 44.14 ? O2G ACP 2001 A 1 
HETATM 4 O O3G ACP . . . D 4 85.285 94.79 148.701 1 44.14 ? O3G ACP 2001 A 1 
HETATM 5 P PB ACP . . . D 4 82.738 93.059 150.064 1 44.14 ? PB ACP 2001 A 1 
HETATM 6 O O1B ACP . . . D 4 81.66 93.535 151.044 1 44.14 ? O1B ACP 2001 A 1 
HETATM 7 O O2B ACP . . . D 4 84.096 93.269 150.685 1 44.14 ? O2B ACP 2001 A 1 
HETATM 8 C C3B ACP . . . D 4 82.613 94.004 148.501 1 44.14 ? C3B ACP 2001 A 1 
HETATM 9 P PA ACP . . . D 4 83.331 90.226 150.477 1 44.14 ? PA ACP 2001 A 1 
HETATM 10 O O1A ACP . . . D 4 83.919 90.718 151.747 1 44.14 -1 O1A ACP 2001 A 1 
HETATM 11 O O2A ACP . . . D 4 84.388 89.699 149.609 1 44.14 ? O2A ACP 2001 A 1 
HETATM 12 O O3A ACP . . . D 4 82.522 91.472 149.721 1 44.14 ? O3A ACP 2001 A 1 
HETATM 13 O O5' ACP . . . D 4 82.202 89.006 150.818 1 44.14 ? O5' ACP 2001 A 1 
HETATM 14 C C5' ACP . . . D 4 81.567 89.076 152.042 1 44.14 ? C5' ACP 2001 A 1 
HETATM 15 C C4' ACP . . . D 4 79.984 88.977 151.852 1 44.14 ? C4' ACP 2001 A 1 
HETATM 16 O O4' ACP . . . D 4 79.411 88.777 152.995 1 44.14 ? O4' ACP 2001 A 1 
HETATM 17 C C3' ACP . . . D 4 79.393 90.314 151.358 1 44.14 ? C3' ACP 2001 A 1 
HETATM 18 O O3' ACP . . . D 4 78.207 90.082 150.712 1 44.14 ? O3' ACP 2001 A 1 
HETATM 19 C C2' ACP . . . D 4 79.139 91.116 152.648 1 44.14 ? C2' ACP 2001 A 1 
HETATM 20 O O2' ACP . . . D 4 77.801 91.79 152.566 1 44.14 ? O2' ACP 2001 A 1 
HETATM 21 C C1' ACP . . . D 4 79.138 90.252 153.628 1 44.14 ? C1' ACP 2001 A 1 
HETATM 22 N N9 ACP . . . D 4 80.141 90.579 154.594 1 44.14 ? N9 ACP 2001 A 1 
HETATM 23 C C8 ACP . . . D 4 81.111 91.483 154.449 1 44.14 ? C8 ACP 2001 A 1 
HETATM 24 N N7 ACP . . . D 4 81.841 91.499 155.567 1 44.14 ? N7 ACP 2001 A 1 
HETATM 25 C C5 ACP . . . D 4 81.316 90.594 156.417 1 44.14 ? C5 ACP 2001 A 1 
HETATM 26 C C6 ACP . . . D 4 81.675 90.208 157.702 1 44.14 ? C6 ACP 2001 A 1 
HETATM 27 N N6 ACP . . . D 4 82.73 90.663 158.519 1 44.14 ? N6 ACP 2001 A 1 
HETATM 28 N N1 ACP . . . D 4 80.972 89.267 158.341 1 44.14 ? N1 ACP 2001 A 1 
HETATM 29 C C2 ACP . . . D 4 79.902 88.688 157.727 1 44.14 ? C2 ACP 2001 A 1 
HETATM 30 N N3 ACP . . . D 4 79.549 89.061 156.479 1 44.14 ? N3 ACP 2001 A 1 
HETATM 31 C C4 ACP . . . D 4 80.271 90.029 155.82 1 44.14 ? C4 ACP 2001 A 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    44 
_model_server_stats.query_time_ms           374 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           31 
#