data_1Y4S
#
_model_server_result.job_id            TD4DRyOmo9-BhXxz7udrqg 
_model_server_result.datetime_utc      '2024-11-05 01:19:49' 
_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          1y4s 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":702}' 
#
_entry.id    1Y4S 
#
_exptl.entry_id    1Y4S 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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    2 
_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            1Y4S 
_cell.length_a            72.5 
_cell.length_b            84.18 
_cell.length_c            212.886 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1Y4S 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 D N N 
? 3 F 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 A OE1 GLU 34 A GLU 34 1_555 C MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.145 ? 
metalc ? metalc2 A OD1 ASN 38 A ASN 38 1_555 C MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? 
metalc ? metalc3 D O1B ADP . A ADP 701 1_555 C MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? 
metalc ? metalc4 D O3B ADP . A ADP 701 1_555 C MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? 
metalc ? metalc5 D O1A ADP . A ADP 701 1_555 C MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? 
metalc ? metalc6 B OD1 ASN 38 B ASN 38 1_555 E MG MG . B MG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? 
metalc ? metalc7 F O1B ADP . B ADP 702 1_555 E MG MG . B MG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? 
metalc ? metalc8 F O3B ADP . B ADP 702 1_555 E MG MG . B MG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? 
metalc ? metalc9 F O1A ADP . B ADP 702 1_555 E MG MG . B MG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? 
#
_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                     1Y4S 
_atom_sites.fract_transf_matrix[1][1]    0.013793 
_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]    0.011879 
_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]    0.004697 
_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
C 2 MG A 1 703 701 MG MG . 
D 3 ADP A 1 701 702 ADP ADP . 
E 2 MG B 1 704 701 MG MG . 
F 3 ADP B 1 702 702 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 . . . F 3 51.03 20.248 88.824 1 37.81 ? PB ADP 702 B 1 
HETATM 2 O O1B ADP . . . F 3 50.07 20.311 89.956 1 39.33 ? O1B ADP 702 B 1 
HETATM 3 O O2B ADP . . . F 3 51.323 18.817 88.506 1 37.67 ? O2B ADP 702 B 1 
HETATM 4 O O3B ADP . . . F 3 50.443 20.926 87.639 1 38 ? O3B ADP 702 B 1 
HETATM 5 P PA ADP . . . F 3 52.378 21.48 90.761 1 38.67 ? PA ADP 702 B 1 
HETATM 6 O O1A ADP . . . F 3 51.227 22.41 90.99 1 38.22 ? O1A ADP 702 B 1 
HETATM 7 O O2A ADP . . . F 3 53.668 22.159 91.089 1 38.44 ? O2A ADP 702 B 1 
HETATM 8 O O3A ADP . . . F 3 52.407 20.999 89.216 1 38.27 ? O3A ADP 702 B 1 
HETATM 9 O O5' ADP . . . F 3 52.217 20.213 91.714 1 37.37 ? O5' ADP 702 B 1 
HETATM 10 C C5' ADP . . . F 3 52.782 18.969 91.337 1 36.87 ? C5' ADP 702 B 1 
HETATM 11 C C4' ADP . . . F 3 52.058 17.839 92.012 1 36.31 ? C4' ADP 702 B 1 
HETATM 12 O O4' ADP . . . F 3 51.877 18.139 93.411 1 34.71 ? O4' ADP 702 B 1 
HETATM 13 C C3' ADP . . . F 3 50.642 17.559 91.536 1 36.1 ? C3' ADP 702 B 1 
HETATM 14 O O3' ADP . . . F 3 50.68 16.766 90.354 1 36.82 ? O3' ADP 702 B 1 
HETATM 15 C C2' ADP . . . F 3 50.067 16.756 92.704 1 35.34 ? C2' ADP 702 B 1 
HETATM 16 O O2' ADP . . . F 3 50.383 15.378 92.616 1 36.9 ? O2' ADP 702 B 1 
HETATM 17 C C1' ADP . . . F 3 50.8 17.365 93.902 1 33.74 ? C1' ADP 702 B 1 
HETATM 18 N N9 ADP . . . F 3 49.97 18.216 94.742 1 31.47 ? N9 ADP 702 B 1 
HETATM 19 C C8 ADP . . . F 3 50.084 19.569 94.95 1 30.27 ? C8 ADP 702 B 1 
HETATM 20 N N7 ADP . . . F 3 49.199 20.051 95.787 1 29.16 ? N7 ADP 702 B 1 
HETATM 21 C C5 ADP . . . F 3 48.443 18.945 96.144 1 29.03 ? C5 ADP 702 B 1 
HETATM 22 C C6 ADP . . . F 3 47.341 18.792 96.997 1 28.12 ? C6 ADP 702 B 1 
HETATM 23 N N6 ADP . . . F 3 46.762 19.808 97.627 1 27.51 ? N6 ADP 702 B 1 
HETATM 24 N N1 ADP . . . F 3 46.836 17.547 97.17 1 29.98 ? N1 ADP 702 B 1 
HETATM 25 C C2 ADP . . . F 3 47.402 16.525 96.498 1 30.53 ? C2 ADP 702 B 1 
HETATM 26 N N3 ADP . . . F 3 48.433 16.55 95.642 1 31.55 ? N3 ADP 702 B 1 
HETATM 27 C C4 ADP . . . F 3 48.911 17.807 95.512 1 30.73 ? C4 ADP 702 B 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           265 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#