data_8RKD
#
_model_server_result.job_id            PcvxVASa2Bnu9penRVbQ-Q 
_model_server_result.datetime_utc      '2024-10-13 19:16:52' 
_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          8rkd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":702}' 
#
_entry.id    8RKD 
#
_exptl.entry_id    8RKD 
_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    4 
_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            8RKD 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8RKD 
_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    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,Q,R 
_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
? 2 G N N 
? 2 J N N 
? 2 N N N 
? 2 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 B OG1 THR 209 F THR 288 1_555 K MG MG . F MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc2 J O2B ADP . F ADP 702 1_555 K MG MG . F MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? 
metalc ? metalc3 E OG1 THR 209 C THR 288 1_555 Q MG MG . C MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc4 P O2B ADP . C ADP 702 1_555 Q MG MG . C MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
#
_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                     8RKD 
_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
G 2 ADP E 1 601 601 ADP ADP . 
H 3 EPE E 1 602 701 EPE EPE . 
I 3 EPE F 1 701 701 EPE EPE . 
J 2 ADP F 1 702 601 ADP ADP . 
K 4 MG F 1 703 801 MG MG . 
L 5 ANP A 1 601 601 ANP ANP . 
M 3 EPE B 1 701 701 EPE EPE . 
N 2 ADP B 1 702 601 ADP ADP . 
O 3 EPE C 1 701 701 EPE EPE . 
P 2 ADP C 1 702 601 ADP ADP . 
Q 4 MG C 1 703 801 MG MG . 
R 5 ANP D 1 601 601 ANP ANP . 
#
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 . . . N 2 197.686 181.031 160.576 1 20 ? PB ADP 702 B 1 
HETATM 2 O O1B ADP . . . N 2 197.787 181.611 161.966 1 20 ? O1B ADP 702 B 1 
HETATM 3 O O2B ADP . . . N 2 196.426 181.419 159.839 1 20 ? O2B ADP 702 B 1 
HETATM 4 O O3B ADP . . . N 2 198.035 179.566 160.483 1 20 ? O3B ADP 702 B 1 
HETATM 5 P PA ADP . . . N 2 200.269 182.097 160.458 1 20 ? PA ADP 702 B 1 
HETATM 6 O O1A ADP . . . N 2 200.084 183.304 161.345 1 20 ? O1A ADP 702 B 1 
HETATM 7 O O2A ADP . . . N 2 200.825 180.823 161.046 1 20 ? O2A ADP 702 B 1 
HETATM 8 O O3A ADP . . . N 2 198.859 181.77 159.754 1 20 ? O3A ADP 702 B 1 
HETATM 9 O O5' ADP . . . N 2 201.222 182.521 159.231 1 20 ? O5' ADP 702 B 1 
HETATM 10 C C5' ADP . . . N 2 202.284 183.446 159.45 1 20 ? C5' ADP 702 B 1 
HETATM 11 C C4' ADP . . . N 2 203.619 182.8 159.093 1 20 ? C4' ADP 702 B 1 
HETATM 12 O O4' ADP . . . N 2 204.159 183.35 157.887 1 20 ? O4' ADP 702 B 1 
HETATM 13 C C3' ADP . . . N 2 204.679 183.007 160.172 1 20 ? C3' ADP 702 B 1 
HETATM 14 O O3' ADP . . . N 2 204.929 181.792 160.885 1 20 ? O3' ADP 702 B 1 
HETATM 15 C C2' ADP . . . N 2 205.925 183.462 159.44 1 20 ? C2' ADP 702 B 1 
HETATM 16 O O2' ADP . . . N 2 207.064 182.682 159.816 1 20 ? O2' ADP 702 B 1 
HETATM 17 C C1' ADP . . . N 2 205.586 183.292 157.963 1 20 ? C1' ADP 702 B 1 
HETATM 18 N N9 ADP . . . N 2 206.24 184.296 157.077 1 20 ? N9 ADP 702 B 1 
HETATM 19 C C8 ADP . . . N 2 207.2 185.183 157.419 1 20 ? C8 ADP 702 B 1 
HETATM 20 N N7 ADP . . . N 2 207.576 185.925 156.348 1 20 ? N7 ADP 702 B 1 
HETATM 21 C C5 ADP . . . N 2 206.862 185.508 155.291 1 20 ? C5 ADP 702 B 1 
HETATM 22 C C6 ADP . . . N 2 206.772 185.87 153.861 1 20 ? C6 ADP 702 B 1 
HETATM 23 N N6 ADP . . . N 2 207.549 186.855 153.353 1 20 ? N6 ADP 702 B 1 
HETATM 24 N N1 ADP . . . N 2 205.896 185.189 153.091 1 20 ? N1 ADP 702 B 1 
HETATM 25 C C2 ADP . . . N 2 205.122 184.208 153.593 1 20 ? C2 ADP 702 B 1 
HETATM 26 N N3 ADP . . . N 2 205.158 183.833 154.885 1 20 ? N3 ADP 702 B 1 
HETATM 27 C C4 ADP . . . N 2 205.993 184.428 155.77 1 20 ? C4 ADP 702 B 1 
HETATM 28 H "H5'1" ADP . . . N 2 202.281 183.764 160.494 1 20 ? "H5'1" ADP 702 B 1 
HETATM 29 H "H5'2" ADP . . . N 2 202.13 184.33 158.828 1 20 ? "H5'2" ADP 702 B 1 
HETATM 30 H H4' ADP . . . N 2 203.459 181.72 158.966 1 20 ? H4' ADP 702 B 1 
HETATM 31 H H3' ADP . . . N 2 204.364 183.801 160.862 1 20 ? H3' ADP 702 B 1 
HETATM 32 H HO3' ADP . . . N 2 205.504 181.973 161.64 1 20 ? HO3' ADP 702 B 1 
HETATM 33 H H2' ADP . . . N 2 206.082 184.521 159.68 1 20 ? H2' ADP 702 B 1 
HETATM 34 H HO2' ADP . . . N 2 207.317 182.898 160.725 1 20 ? HO2' ADP 702 B 1 
HETATM 35 H H1' ADP . . . N 2 205.915 182.288 157.661 1 20 ? H1' ADP 702 B 1 
HETATM 36 H H8 ADP . . . N 2 207.612 185.302 158.412 1 20 ? H8 ADP 702 B 1 
HETATM 37 H HN61 ADP . . . N 2 207.486 187.098 152.377 1 20 ? HN61 ADP 702 B 1 
HETATM 38 H HN62 ADP . . . N 2 208.194 187.346 153.954 1 20 ? HN62 ADP 702 B 1 
HETATM 39 H H2 ADP . . . N 2 204.438 183.698 152.926 1 20 ? H2 ADP 702 B 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    66 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           39 
#