data_8GRD
#
_model_server_result.job_id            nCfHLB3-LBo2_SKeWNXEhg 
_model_server_result.datetime_utc      '2025-02-17 06:41:49' 
_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          8grd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    8GRD 
#
_exptl.entry_id    8GRD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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            8GRD 
_cell.length_a            165.897 
_cell.length_b            165.897 
_cell.length_c            129.583 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8GRD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        97 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 
#
_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
metalc ? metalc1 A OD1 ASP 230 A ASP 230 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? 
metalc ? metalc2 A OD1 ASP 234 A ASP 234 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? 
metalc ? metalc3 C MG MG . A MG 401 1_555 B OD2 ASP 217 B ASP 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
#
_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                     8GRD 
_atom_sites.fract_transf_matrix[1][1]    0.006028 
_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]    0.006028 
_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]    0.007717 
_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 3 MG A 1 401 1 MG MG . 
D 4 ADP B 1 401 1 ADP ADP . 
E 5 HOH A 1 501 23 HOH HOH . 
E 5 HOH A 2 502 49 HOH HOH . 
E 5 HOH A 3 503 40 HOH HOH . 
E 5 HOH A 4 504 19 HOH HOH . 
E 5 HOH A 5 505 43 HOH HOH . 
E 5 HOH A 6 506 29 HOH HOH . 
E 5 HOH A 7 507 52 HOH HOH . 
E 5 HOH A 8 508 11 HOH HOH . 
E 5 HOH A 9 509 22 HOH HOH . 
E 5 HOH A 10 510 36 HOH HOH . 
E 5 HOH A 11 511 28 HOH HOH . 
E 5 HOH A 12 512 27 HOH HOH . 
E 5 HOH A 13 513 3 HOH HOH . 
E 5 HOH A 14 514 26 HOH HOH . 
E 5 HOH A 15 515 6 HOH HOH . 
E 5 HOH A 16 516 45 HOH HOH . 
E 5 HOH A 17 517 10 HOH HOH . 
E 5 HOH A 18 518 12 HOH HOH . 
E 5 HOH A 19 519 41 HOH HOH . 
E 5 HOH A 20 520 21 HOH HOH . 
E 5 HOH A 21 521 13 HOH HOH . 
E 5 HOH A 22 522 18 HOH HOH . 
E 5 HOH A 23 523 31 HOH HOH . 
E 5 HOH A 24 524 35 HOH HOH . 
E 5 HOH A 25 525 33 HOH HOH . 
E 5 HOH A 26 526 20 HOH HOH . 
E 5 HOH A 27 527 38 HOH HOH . 
E 5 HOH A 28 528 32 HOH HOH . 
E 5 HOH A 29 529 50 HOH HOH . 
F 5 HOH B 1 501 5 HOH HOH . 
F 5 HOH B 2 502 25 HOH HOH . 
F 5 HOH B 3 503 46 HOH HOH . 
F 5 HOH B 4 504 9 HOH HOH . 
F 5 HOH B 5 505 47 HOH HOH . 
F 5 HOH B 6 506 44 HOH HOH . 
F 5 HOH B 7 507 17 HOH HOH . 
F 5 HOH B 8 508 37 HOH HOH . 
F 5 HOH B 9 509 15 HOH HOH . 
F 5 HOH B 10 510 34 HOH HOH . 
F 5 HOH B 11 511 14 HOH HOH . 
F 5 HOH B 12 512 24 HOH HOH . 
F 5 HOH B 13 513 16 HOH HOH . 
F 5 HOH B 14 514 2 HOH HOH . 
F 5 HOH B 15 515 42 HOH HOH . 
F 5 HOH B 16 516 4 HOH HOH . 
F 5 HOH B 17 517 30 HOH HOH . 
F 5 HOH B 18 518 8 HOH HOH . 
F 5 HOH B 19 519 51 HOH HOH . 
F 5 HOH B 20 520 39 HOH HOH . 
F 5 HOH B 21 521 7 HOH HOH . 
F 5 HOH B 22 522 1 HOH HOH . 
F 5 HOH B 23 523 48 HOH HOH . 
F 5 HOH B 24 524 54 HOH HOH . 
F 5 HOH B 25 525 53 HOH HOH . 
#
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 . . . D 4 45.071 -1.303 46.869 1 38.38 ? PB ADP 401 B 1 
HETATM 2 O O1B ADP . . . D 4 44.967 -0.158 45.911 1 50.53 ? O1B ADP 401 B 1 
HETATM 3 O O2B ADP . . . D 4 46.3 -1.204 47.756 1 47.09 ? O2B ADP 401 B 1 
HETATM 4 O O3B ADP . . . D 4 44.761 -2.652 46.262 1 42.73 ? O3B ADP 401 B 1 
HETATM 5 P PA ADP . . . D 4 42.744 -0.196 48.235 1 48.46 ? PA ADP 401 B 1 
HETATM 6 O O1A ADP . . . D 4 43.352 1.162 48.51 1 50.33 ? O1A ADP 401 B 1 
HETATM 7 O O2A ADP . . . D 4 41.958 -0.973 49.265 1 40.2 ? O2A ADP 401 B 1 
HETATM 8 O O3A ADP . . . D 4 43.916 -1.254 47.974 1 45.43 ? O3A ADP 401 B 1 
HETATM 9 O O5' ADP . . . D 4 41.871 -0.084 46.88 1 46.49 ? O5' ADP 401 B 1 
HETATM 10 C C5' ADP . . . D 4 40.472 -0.271 47.004 1 42.5 ? C5' ADP 401 B 1 
HETATM 11 C C4' ADP . . . D 4 39.746 1.017 46.723 1 44.37 ? C4' ADP 401 B 1 
HETATM 12 O O4' ADP . . . D 4 38.43 0.638 46.355 1 46.89 ? O4' ADP 401 B 1 
HETATM 13 C C3' ADP . . . D 4 39.638 1.886 47.962 1 45.43 ? C3' ADP 401 B 1 
HETATM 14 O O3' ADP . . . D 4 40.517 3.017 47.875 1 43.22 ? O3' ADP 401 B 1 
HETATM 15 C C2' ADP . . . D 4 38.183 2.326 47.98 1 45.58 ? C2' ADP 401 B 1 
HETATM 16 O O2' ADP . . . D 4 38.027 3.606 47.35 1 50.49 ? O2' ADP 401 B 1 
HETATM 17 C C1' ADP . . . D 4 37.455 1.316 47.124 1 41.86 ? C1' ADP 401 B 1 
HETATM 18 N N9 ADP . . . D 4 36.834 0.286 47.969 1 44.11 ? N9 ADP 401 B 1 
HETATM 19 C C8 ADP . . . D 4 37.303 -0.96 48.188 1 42.32 ? C8 ADP 401 B 1 
HETATM 20 N N7 ADP . . . D 4 36.467 -1.649 49.008 1 40.48 ? N7 ADP 401 B 1 
HETATM 21 C C5 ADP . . . D 4 35.456 -0.832 49.316 1 39.95 ? C5 ADP 401 B 1 
HETATM 22 C C6 ADP . . . D 4 34.248 -0.937 50.154 1 46.14 ? C6 ADP 401 B 1 
HETATM 23 N N6 ADP . . . D 4 33.972 -2.095 50.806 1 37.72 ? N6 ADP 401 B 1 
HETATM 24 N N1 ADP . . . D 4 33.448 0.162 50.219 1 45.74 ? N1 ADP 401 B 1 
HETATM 25 C C2 ADP . . . D 4 33.742 1.301 49.54 1 42.09 ? C2 ADP 401 B 1 
HETATM 26 N N3 ADP . . . D 4 34.828 1.471 48.758 1 36.94 ? N3 ADP 401 B 1 
HETATM 27 C C4 ADP . . . D 4 35.696 0.444 48.626 1 41.64 ? C4 ADP 401 B 1 
#
_model_server_stats.io_time_ms              69 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           313 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#