data_8VAP
#
_model_server_result.job_id            fR2GduHGtRjBtI264tYe9w 
_model_server_result.datetime_utc      '2025-04-12 06:09:10' 
_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          8vap 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":401}' 
#
_entry.id    8VAP 
#
_exptl.entry_id    8VAP 
_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    3 
_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            8VAP 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8VAP 
_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    heptameric 
_pdbx_struct_assembly.oligomeric_count      7 
_pdbx_struct_assembly.details               author_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,S,T 
_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    ? 
_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 H N N 
? 5 L N N 
? 5 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 SG CYS 67 B CYS 64 1_555 K ZN ZN . B ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? 
metalc ? metalc2 B SG CYS 76 B CYS 73 1_555 K ZN ZN . B ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? 
metalc ? metalc3 B SG CYS 79 B CYS 76 1_555 K ZN ZN . B ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc4 B SG CYS 82 B CYS 79 1_555 K ZN ZN . B ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? 
metalc ? metalc5 H O3B ADP . B ADP 401 1_555 I BE BEF . B BEF 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.651 ? 
metalc ? metalc6 H O1B ADP . B ADP 401 1_555 J MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? 
metalc ? metalc7 C OG1 THR 55 C THR 52 1_555 M MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.842 ? 
metalc ? metalc8 C SG CYS 79 C CYS 76 1_555 N ZN ZN . C ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc9 C SG CYS 82 C CYS 79 1_555 N ZN ZN . C ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? 
metalc ? metalc10 L O3B ADP . C ADP 401 1_555 O BE BEF . D BEF 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.645 ? 
metalc ? metalc11 D OG1 THR 55 D THR 52 1_555 R MG MG . D MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.736 ? 
metalc ? metalc12 D SG CYS 67 D CYS 64 1_555 S ZN ZN . D ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc13 D SG CYS 76 D CYS 73 1_555 S ZN ZN . D ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc14 D SG CYS 79 D CYS 76 1_555 S ZN ZN . D ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? 
metalc ? metalc15 D SG CYS 82 D CYS 79 1_555 S ZN ZN . D ZN 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc16 P O3B ADP . D ADP 402 1_555 Q BE BEF . D BEF 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.64 ? 
metalc ? metalc17 P O1B ADP . D ADP 402 1_555 R MG MG . D MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? 
metalc ? metalc18 E SG CYS 53 E CYS 50 1_555 T ZN ZN . E ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc19 E SG CYS 62 E CYS 59 1_555 T ZN ZN . E ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc20 E SG CYS 65 E CYS 62 1_555 T ZN ZN . E ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc21 E SG CYS 68 E CYS 65 1_555 T ZN ZN . E ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
#
_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                     8VAP 
_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
H 5 ADP B 1 401 400 ADP ADP . 
I 6 BEF B 1 402 401 BEF BEF . 
J 7 MG B 1 403 412 MG MG . 
K 8 ZN B 1 404 418 ZN ZN . 
L 5 ADP C 1 401 402 ADP ADP . 
M 7 MG C 1 402 413 MG MG . 
N 8 ZN C 1 403 419 ZN ZN . 
O 6 BEF D 1 401 403 BEF BEF . 
P 5 ADP D 1 402 404 ADP ADP . 
Q 6 BEF D 1 403 405 BEF BEF . 
R 7 MG D 1 404 414 MG MG . 
S 8 ZN D 1 405 420 ZN ZN . 
T 8 ZN E 1 401 421 ZN ZN . 
#
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 . . . H 5 125.272 156.901 126.86 1 86.47 ? PB ADP 401 B 1 
HETATM 2 O O1B ADP . . . H 5 126.249 155.94 126.121 1 63.94 ? O1B ADP 401 B 1 
HETATM 3 O O2B ADP . . . H 5 125.406 158.392 126.699 1 65.54 ? O2B ADP 401 B 1 
HETATM 4 O O3B ADP . . . H 5 125.51 156.777 128.449 1 74.76 ? O3B ADP 401 B 1 
HETATM 5 P PA ADP . . . H 5 123.151 155.684 125.384 1 55.48 ? PA ADP 401 B 1 
HETATM 6 O O1A ADP . . . H 5 123.026 156.666 124.246 1 56.85 ? O1A ADP 401 B 1 
HETATM 7 O O2A ADP . . . H 5 123.966 154.419 125.248 1 60.92 ? O2A ADP 401 B 1 
HETATM 8 O O3A ADP . . . H 5 123.713 156.497 126.676 1 64.02 ? O3A ADP 401 B 1 
HETATM 9 O O5' ADP . . . H 5 121.617 155.298 125.618 1 43.42 ? O5' ADP 401 B 1 
HETATM 10 C C5' ADP . . . H 5 121.21 154.059 126.172 1 54.02 ? C5' ADP 401 B 1 
HETATM 11 C C4' ADP . . . H 5 119.7 154.067 126.087 1 50.18 ? C4' ADP 401 B 1 
HETATM 12 O O4' ADP . . . H 5 119.175 155.226 126.704 1 62.04 ? O4' ADP 401 B 1 
HETATM 13 C C3' ADP . . . H 5 119.3 154.195 124.653 1 52.22 ? C3' ADP 401 B 1 
HETATM 14 O O3' ADP . . . H 5 119.019 152.883 124.22 1 63.89 ? O3' ADP 401 B 1 
HETATM 15 C C2' ADP . . . H 5 118.053 155.023 124.649 1 61.08 ? C2' ADP 401 B 1 
HETATM 16 O O2' ADP . . . H 5 116.964 154.173 124.944 1 61.86 ? O2' ADP 401 B 1 
HETATM 17 C C1' ADP . . . H 5 118.174 155.836 125.888 1 61.63 ? C1' ADP 401 B 1 
HETATM 18 N N9 ADP . . . H 5 118.512 157.227 125.488 1 65.21 ? N9 ADP 401 B 1 
HETATM 19 C C8 ADP . . . H 5 119.498 158.014 125.99 1 68.32 ? C8 ADP 401 B 1 
HETATM 20 N N7 ADP . . . H 5 119.507 159.243 125.409 1 51.57 ? N7 ADP 401 B 1 
HETATM 21 C C5 ADP . . . H 5 118.499 159.256 124.523 1 46.89 ? C5 ADP 401 B 1 
HETATM 22 C C6 ADP . . . H 5 117.956 160.249 123.585 1 62.47 ? C6 ADP 401 B 1 
HETATM 23 N N6 ADP . . . H 5 118.501 161.481 123.481 1 64.29 ? N6 ADP 401 B 1 
HETATM 24 N N1 ADP . . . H 5 116.902 159.857 122.84 1 70.92 ? N1 ADP 401 B 1 
HETATM 25 C C2 ADP . . . H 5 116.367 158.616 122.949 1 61.26 ? C2 ADP 401 B 1 
HETATM 26 N N3 ADP . . . H 5 116.796 157.656 123.781 1 61.24 ? N3 ADP 401 B 1 
HETATM 27 C C4 ADP . . . H 5 117.847 157.929 124.577 1 56.52 ? C4 ADP 401 B 1 
#
_model_server_stats.io_time_ms              29 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           297 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           27 
#