data_8R9V
#
_model_server_result.job_id            J3ob6bEDF9l0PuruNKuo0Q 
_model_server_result.datetime_utc      '2025-04-01 13:38:41' 
_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          8r9v 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":401}' 
#
_entry.id    8R9V 
#
_exptl.entry_id    8R9V 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          5 
_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                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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
? 5 G N N 
? 5 H N N 
? 5 J N N 
? 5 L 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
covale ? covale1 B C ACE 1 B ACE 1 1_555 B N ASP 2 B ASP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
metalc ? metalc1 A OG1 THR 170 A THR 170 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
metalc ? metalc2 A OG SER 218 A SER 218 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc3 E O1 PO4 . A PO4 901 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.951 ? 
metalc ? metalc4 E O3 PO4 . A PO4 901 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.82 ? 
metalc ? metalc5 E O4 PO4 . A PO4 901 1_555 F MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.816 ? 
metalc ? metalc6 F MG MG . A MG 902 1_555 G O1B ADP . A ADP 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? 
metalc ? metalc7 H O2B ADP . B ADP 401 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? 
#
_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 7 n n 
PB O2B ADP sing 8 n n 
PB O3B ADP sing 9 n n 
PB O3A ADP sing 10 n n 
O2B HOB2 ADP sing 11 n n 
O3B HOB3 ADP sing 12 n n 
PA O1A ADP doub 13 n n 
PA O2A ADP sing 14 n n 
PA O3A ADP sing 15 n n 
PA O5' ADP sing 16 n n 
O2A HOA2 ADP sing 17 n n 
O5' C5' ADP sing 18 n n 
C5' C4' ADP sing 19 n n 
C5' "H5'1" ADP sing 20 n n 
C5' "H5'2" ADP sing 21 n n 
C4' O4' ADP sing 22 n n 
C4' C3' ADP sing 23 n n 
C4' H4' ADP sing 24 n n 
O4' C1' ADP sing 25 n n 
C3' O3' ADP sing 26 n n 
C3' C2' ADP sing 27 n n 
C3' H3' ADP sing 28 n n 
O3' HO3' ADP sing 29 n n 
C2' O2' ADP sing 30 n n 
C2' C1' ADP sing 31 n n 
C2' H2' ADP sing 32 n n 
O2' HO2' ADP sing 33 n n 
C1' N9 ADP sing 34 n n 
C1' H1' ADP sing 35 n n 
N9 C8 ADP sing 36 n y 
N9 C4 ADP sing 37 n y 
C8 N7 ADP doub 38 n y 
C8 H8 ADP sing 39 n n 
N7 C5 ADP sing 40 n y 
C5 C6 ADP sing 41 n y 
C5 C4 ADP doub 42 n y 
C6 N6 ADP sing 43 n n 
C6 N1 ADP doub 44 n y 
N6 HN61 ADP sing 45 n n 
N6 HN62 ADP sing 46 n n 
N1 C2 ADP sing 47 n y 
C2 N3 ADP doub 48 n y 
C2 H2 ADP sing 49 n n 
N3 C4 ADP sing 50 n y 
#
_atom_sites.entry_id                     8R9V 
_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
E 3 PO4 A 1 901 2003 PO4 PO4 . 
F 4 MG A 1 902 1901 MG MG . 
G 5 ADP A 1 903 1902 ADP ADP . 
H 5 ADP B 1 401 401 ADP ADP . 
I 4 MG B 1 402 402 MG MG . 
J 5 ADP C 1 401 401 ADP ADP . 
K 4 MG C 1 402 402 MG MG . 
L 5 ADP D 1 401 401 ADP ADP . 
M 4 MG D 1 402 402 MG MG . 
#
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 . . . L 5 194.678 210.791 220.03 1 177.6 ? PB ADP 401 D 1 
HETATM 2 O O1B ADP . . . L 5 194.215 210.497 218.63 1 177.6 ? O1B ADP 401 D 1 
HETATM 3 O O2B ADP . . . L 5 195.928 210.033 220.404 1 177.6 ? O2B ADP 401 D 1 
HETATM 4 O O3B ADP . . . L 5 193.581 210.656 221.056 1 177.6 ? O3B ADP 401 D 1 
HETATM 5 P PA ADP . . . L 5 196.475 213.05 219.7 1 177.6 ? PA ADP 401 D 1 
HETATM 6 O O1A ADP . . . L 5 197.077 212.42 218.488 1 177.6 ? O1A ADP 401 D 1 
HETATM 7 O O2A ADP . . . L 5 197.271 213.07 220.962 1 177.6 ? O2A ADP 401 D 1 
HETATM 8 O O3A ADP . . . L 5 195.075 212.344 220.012 1 177.6 ? O3A ADP 401 D 1 
HETATM 9 O O5' ADP . . . L 5 195.98 214.53 219.339 1 177.6 ? O5' ADP 401 D 1 
HETATM 10 C C5' ADP . . . L 5 196.065 214.927 217.95 1 177.6 ? C5' ADP 401 D 1 
HETATM 11 C C4' ADP . . . L 5 195.271 216.19 217.736 1 177.6 ? C4' ADP 401 D 1 
HETATM 12 O O4' ADP . . . L 5 196.116 217.335 218.002 1 177.6 ? O4' ADP 401 D 1 
HETATM 13 C C3' ADP . . . L 5 194.768 216.417 216.307 1 177.6 ? C3' ADP 401 D 1 
HETATM 14 O O3' ADP . . . L 5 193.66 217.306 216.269 1 177.6 ? O3' ADP 401 D 1 
HETATM 15 C C2' ADP . . . L 5 196.001 217.042 215.659 1 177.6 ? C2' ADP 401 D 1 
HETATM 16 O O2' ADP . . . L 5 195.677 217.777 214.5 1 177.6 ? O2' ADP 401 D 1 
HETATM 17 C C1' ADP . . . L 5 196.538 217.916 216.79 1 177.6 ? C1' ADP 401 D 1 
HETATM 18 N N9 ADP . . . L 5 197.992 217.993 216.797 1 177.6 ? N9 ADP 401 D 1 
HETATM 19 C C8 ADP . . . L 5 198.873 216.95 216.942 1 177.6 ? C8 ADP 401 D 1 
HETATM 20 N N7 ADP . . . L 5 200.127 217.318 216.879 1 177.6 ? N7 ADP 401 D 1 
HETATM 21 C C5 ADP . . . L 5 200.072 218.686 216.66 1 177.6 ? C5 ADP 401 D 1 
HETATM 22 C C6 ADP . . . L 5 201.075 219.657 216.485 1 177.6 ? C6 ADP 401 D 1 
HETATM 23 N N6 ADP . . . L 5 202.377 219.386 216.496 1 177.6 ? N6 ADP 401 D 1 
HETATM 24 N N1 ADP . . . L 5 200.677 220.931 216.272 1 177.6 ? N1 ADP 401 D 1 
HETATM 25 C C2 ADP . . . L 5 199.366 221.198 216.265 1 177.6 ? C2 ADP 401 D 1 
HETATM 26 N N3 ADP . . . L 5 198.336 220.372 216.412 1 177.6 ? N3 ADP 401 D 1 
HETATM 27 C C4 ADP . . . L 5 198.76 219.115 216.611 1 177.6 ? C4 ADP 401 D 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           274 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#