data_8RKD
#
_model_server_result.job_id            0M_keEe6ToYcxfxmMgZzQQ 
_model_server_result.datetime_utc      '2024-10-13 19:16:13' 
_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":"J","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 . . . J 2 137.306 184.954 165.135 1 64.29 ? PB ADP 702 F 1 
HETATM 2 O O1B ADP . . . J 2 138.233 186.101 165.45 1 64.29 ? O1B ADP 702 F 1 
HETATM 3 O O2B ADP . . . J 2 137.356 183.81 166.117 1 64.29 ? O2B ADP 702 F 1 
HETATM 4 O O3B ADP . . . J 2 137.321 184.536 163.687 1 64.29 ? O3B ADP 702 F 1 
HETATM 5 P PA ADP . . . J 2 135.038 186.154 164.056 1 64.29 ? PA ADP 702 F 1 
HETATM 6 O O1A ADP . . . J 2 136.003 186.972 163.237 1 64.29 ? O1A ADP 702 F 1 
HETATM 7 O O2A ADP . . . J 2 134.307 185 163.418 1 64.29 ? O2A ADP 702 F 1 
HETATM 8 O O3A ADP . . . J 2 135.837 185.58 165.328 1 64.29 ? O3A ADP 702 F 1 
HETATM 9 O O5' ADP . . . J 2 133.961 187.158 164.708 1 64.29 ? O5' ADP 702 F 1 
HETATM 10 C C5' ADP . . . J 2 132.646 187.27 164.169 1 64.29 ? C5' ADP 702 F 1 
HETATM 11 C C4' ADP . . . J 2 132.354 188.726 163.812 1 64.29 ? C4' ADP 702 F 1 
HETATM 12 O O4' ADP . . . J 2 132.408 188.891 162.391 1 64.29 ? O4' ADP 702 F 1 
HETATM 13 C C3' ADP . . . J 2 130.977 189.205 164.259 1 64.29 ? C3' ADP 702 F 1 
HETATM 14 O O3' ADP . . . J 2 131.114 190.273 165.2 1 64.29 ? O3' ADP 702 F 1 
HETATM 15 C C2' ADP . . . J 2 130.277 189.692 163.005 1 64.29 ? C2' ADP 702 F 1 
HETATM 16 O O2' ADP . . . J 2 129.662 190.968 163.203 1 64.29 ? O2' ADP 702 F 1 
HETATM 17 C C1' ADP . . . J 2 131.367 189.767 161.95 1 64.29 ? C1' ADP 702 F 1 
HETATM 18 N N9 ADP . . . J 2 130.859 189.363 160.613 1 64.29 ? N9 ADP 702 F 1 
HETATM 19 C C8 ADP . . . J 2 130.943 188.134 160.071 1 64.29 ? C8 ADP 702 F 1 
HETATM 20 N N7 ADP . . . J 2 130.386 188.114 158.832 1 64.29 ? N7 ADP 702 F 1 
HETATM 21 C C5 ADP . . . J 2 129.936 189.352 158.566 1 64.29 ? C5 ADP 702 F 1 
HETATM 22 C C6 ADP . . . J 2 129.247 190.026 157.442 1 64.29 ? C6 ADP 702 F 1 
HETATM 23 N N6 ADP . . . J 2 128.914 189.354 156.315 1 64.29 ? N6 ADP 702 F 1 
HETATM 24 N N1 ADP . . . J 2 128.959 191.339 157.578 1 64.29 ? N1 ADP 702 F 1 
HETATM 25 C C2 ADP . . . J 2 129.278 192.032 158.686 1 64.29 ? C2 ADP 702 F 1 
HETATM 26 N N3 ADP . . . J 2 129.903 191.478 159.74 1 64.29 ? N3 ADP 702 F 1 
HETATM 27 C C4 ADP . . . J 2 130.253 190.171 159.742 1 64.29 ? C4 ADP 702 F 1 
HETATM 28 H "H5'1" ADP . . . J 2 131.924 186.907 164.902 1 64.29 ? "H5'1" ADP 702 F 1 
HETATM 29 H "H5'2" ADP . . . J 2 132.557 186.648 163.278 1 64.29 ? "H5'2" ADP 702 F 1 
HETATM 30 H H4' ADP . . . J 2 133.117 189.36 164.285 1 64.29 ? H4' ADP 702 F 1 
HETATM 31 H H3' ADP . . . J 2 130.405 188.374 164.695 1 64.29 ? H3' ADP 702 F 1 
HETATM 32 H HO3' ADP . . . J 2 130.245 190.519 165.545 1 64.29 ? HO3' ADP 702 F 1 
HETATM 33 H H2' ADP . . . J 2 129.529 188.948 162.699 1 64.29 ? H2' ADP 702 F 1 
HETATM 34 H HO2' ADP . . . J 2 128.892 190.867 163.779 1 64.29 ? HO2' ADP 702 F 1 
HETATM 35 H H1' ADP . . . J 2 131.747 190.797 161.905 1 64.29 ? H1' ADP 702 F 1 
HETATM 36 H H8 ADP . . . J 2 131.391 187.279 160.558 1 64.29 ? H8 ADP 702 F 1 
HETATM 37 H HN61 ADP . . . J 2 128.444 189.835 155.562 1 64.29 ? HN61 ADP 702 F 1 
HETATM 38 H HN62 ADP . . . J 2 129.136 188.372 156.228 1 64.29 ? HN62 ADP 702 F 1 
HETATM 39 H H2 ADP . . . J 2 129.02 193.082 158.732 1 64.29 ? H2 ADP 702 F 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    43 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           39 
#