data_3DIN
#
_model_server_result.job_id            rSfWwDiO29qCx2hGW8cpiQ 
_model_server_result.datetime_utc      '2024-11-23 10:00:15' 
_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          3din 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":873}' 
#
_entry.id    3DIN 
#
_exptl.entry_id    3DIN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          6 
_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            3DIN 
_cell.length_a            101.616 
_cell.length_b            156.003 
_cell.length_c            358.155 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3DIN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,I,J,K 1 1 
E,F,G,H,L,M,N 2 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
? 6 J N N 
? 6 M 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 J O2B ADP . A ADP 873 1_555 K BE BEF . A BEF 874 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.823 ? 
metalc ? metalc2 M O2B ADP . B ADP 873 1_555 N BE BEF . B BEF 874 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.823 ? 
#
_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                     3DIN 
_atom_sites.fract_transf_matrix[1][1]    0.009841 
_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]    0.00641 
_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]    0.002792 
_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
I 5 MG A 1 872 1 MG MG . 
J 6 ADP A 1 873 1 ADP ADP . 
K 7 BEF A 1 874 1 BEF BEF . 
L 5 MG B 1 872 2 MG MG . 
M 6 ADP B 1 873 2 ADP ADP . 
N 7 BEF B 1 874 2 BEF BEF . 
#
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 . . . M 6 26.124 22.782 28.205 1 183.45 ? PB ADP 873 B 1 
HETATM 2 O O1B ADP . . . M 6 27.13 22.939 29.405 1 181.45 ? O1B ADP 873 B 1 
HETATM 3 O O2B ADP . . . M 6 25.35 21.422 28.181 1 184.42 ? O2B ADP 873 B 1 
HETATM 4 O O3B ADP . . . M 6 26.611 23.349 26.834 1 184.5 ? O3B ADP 873 B 1 
HETATM 5 P PA ADP . . . M 6 24.369 24.156 30.156 1 186.82 ? PA ADP 873 B 1 
HETATM 6 O O1A ADP . . . M 6 22.948 24.819 30.034 1 183.51 ? O1A ADP 873 B 1 
HETATM 7 O O2A ADP . . . M 6 24.511 22.845 31.053 1 180.06 ? O2A ADP 873 B 1 
HETATM 8 O O3A ADP . . . M 6 25.002 23.888 28.657 1 186.76 ? O3A ADP 873 B 1 
HETATM 9 O O5' ADP . . . M 6 25.345 25.313 30.738 1 186.46 ? O5' ADP 873 B 1 
HETATM 10 C C5' ADP . . . M 6 26.697 25.013 31.071 1 186.67 ? C5' ADP 873 B 1 
HETATM 11 C C4' ADP . . . M 6 27.168 25.918 32.2 1 188.35 ? C4' ADP 873 B 1 
HETATM 12 O O4' ADP . . . M 6 27.219 27.276 31.739 1 190.54 ? O4' ADP 873 B 1 
HETATM 13 C C3' ADP . . . M 6 26.273 25.954 33.428 1 192.89 ? C3' ADP 873 B 1 
HETATM 14 O O3' ADP . . . M 6 26.506 24.852 34.312 1 191.77 ? O3' ADP 873 B 1 
HETATM 15 C C2' ADP . . . M 6 26.625 27.313 33.994 1 195.28 ? C2' ADP 873 B 1 
HETATM 16 O O2' ADP . . . M 6 27.83 27.236 34.758 1 188.67 ? O2' ADP 873 B 1 
HETATM 17 C C1' ADP . . . M 6 26.796 28.189 32.755 1 187.81 ? C1' ADP 873 B 1 
HETATM 18 N N9 ADP . . . M 6 25.466 28.745 32.451 1 189.05 ? N9 ADP 873 B 1 
HETATM 19 C C8 ADP . . . M 6 24.789 28.566 31.156 1 185.94 ? C8 ADP 873 B 1 
HETATM 20 N N7 ADP . . . M 6 23.739 29.554 31.177 1 188.99 ? N7 ADP 873 B 1 
HETATM 21 C C5 ADP . . . M 6 23.967 30.407 32.262 1 191.78 ? C5 ADP 873 B 1 
HETATM 22 C C6 ADP . . . M 6 23.305 31.575 32.586 1 181.73 ? C6 ADP 873 B 1 
HETATM 23 N N6 ADP . . . M 6 22.229 32.059 31.826 1 186.4 ? N6 ADP 873 B 1 
HETATM 24 N N1 ADP . . . M 6 23.727 32.215 33.686 1 185.82 ? N1 ADP 873 B 1 
HETATM 25 C C2 ADP . . . M 6 24.768 31.752 34.422 1 187.47 ? C2 ADP 873 B 1 
HETATM 26 N N3 ADP . . . M 6 25.43 30.619 34.097 1 134.73 ? N3 ADP 873 B 1 
HETATM 27 C C4 ADP . . . M 6 25.019 29.953 33.013 1 399.04 ? C4 ADP 873 B 1 
#
_model_server_stats.io_time_ms              34 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           324 
_model_server_stats.encode_time_ms          17 
_model_server_stats.element_count           27 
#