data_6PDW
#
_model_server_result.job_id            brjXboL0Z59-17zuv0SDcA 
_model_server_result.datetime_utc      '2025-07-07 09:07:55' 
_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          6pdw 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":501}' 
#
_entry.id    6PDW 
#
_exptl.entry_id    6PDW 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          3 
_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            6PDW 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PDW 
_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_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 
_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
? 3 G N N 
? 3 J N N 
? 3 M N N 
? 3 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 A OG1 THR 133 B THR 161 1_555 I MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? 
metalc ? metalc2 G O2B ADP . B ADP 501 1_555 I MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? 
metalc ? metalc3 H F1 BEF . B BEF 502 1_555 I MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc4 B OG1 THR 133 C THR 161 1_555 K MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? 
metalc ? metalc5 J O2B ADP . C ADP 501 1_555 K MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? 
metalc ? metalc6 K MG MG . C MG 502 1_555 L F1 BEF . C BEF 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
metalc ? metalc7 C OG1 THR 133 D THR 161 1_555 O MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
metalc ? metalc8 C OD2 ASP 185 D ASP 213 1_555 O MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.837 ? 
metalc ? metalc9 M O2B ADP . D ADP 501 1_555 O MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? 
metalc ? metalc10 N F3 BEF . D BEF 502 1_555 O MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
metalc ? metalc11 D OG1 THR 133 E THR 161 1_555 Q MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.62 ? 
metalc ? metalc12 P O3B ADP . E ADP 501 1_555 Q MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? 
#
_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                     6PDW 
_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 3 ADP B 1 501 501 ADP ADP . 
H 4 BEF B 1 502 502 BEF BEF . 
I 5 MG B 1 503 601 MG MG . 
J 3 ADP C 1 501 501 ADP ADP . 
K 5 MG C 1 502 601 MG MG . 
L 4 BEF C 1 503 502 BEF BEF . 
M 3 ADP D 1 501 501 ADP ADP . 
N 4 BEF D 1 502 502 BEF BEF . 
O 5 MG D 1 503 601 MG MG . 
P 3 ADP E 1 501 501 ADP ADP . 
Q 5 MG E 1 502 601 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 . . . P 3 143.732 133.818 167.338 1 62.65 ? PB ADP 501 E 1 
HETATM 2 O O1B ADP . . . P 3 144.678 133.145 166.374 1 62.65 -1 O1B ADP 501 E 1 
HETATM 3 O O2B ADP . . . P 3 144.401 134.688 168.37 1 62.65 ? O2B ADP 501 E 1 
HETATM 4 O O3B ADP . . . P 3 142.512 134.428 166.696 1 62.65 ? O3B ADP 501 E 1 
HETATM 5 P PA ADP . . . P 3 142.415 132.951 169.607 1 62.65 ? PA ADP 501 E 1 
HETATM 6 O O1A ADP . . . P 3 141.122 133.653 169.305 1 62.65 ? O1A ADP 501 E 1 
HETATM 7 O O2A ADP . . . P 3 143.42 133.591 170.527 1 62.65 -1 O2A ADP 501 E 1 
HETATM 8 O O3A ADP . . . P 3 143.145 132.614 168.219 1 62.65 ? O3A ADP 501 E 1 
HETATM 9 O O5' ADP . . . P 3 142.034 131.506 170.183 1 62.65 ? O5' ADP 501 E 1 
HETATM 10 C C5' ADP . . . P 3 140.845 131.401 170.947 1 62.65 ? C5' ADP 501 E 1 
HETATM 11 C C4' ADP . . . P 3 140.919 130.205 171.883 1 62.65 ? C4' ADP 501 E 1 
HETATM 12 O O4' ADP . . . P 3 142.097 130.296 172.68 1 62.65 ? O4' ADP 501 E 1 
HETATM 13 C C3' ADP . . . P 3 139.726 130.153 172.816 1 62.65 ? C3' ADP 501 E 1 
HETATM 14 O O3' ADP . . . P 3 138.853 129.071 172.478 1 62.65 ? O3' ADP 501 E 1 
HETATM 15 C C2' ADP . . . P 3 140.3 130.033 174.215 1 62.65 ? C2' ADP 501 E 1 
HETATM 16 O O2' ADP . . . P 3 140.08 128.748 174.805 1 62.65 ? O2' ADP 501 E 1 
HETATM 17 C C1' ADP . . . P 3 141.806 130.234 174.078 1 62.65 ? C1' ADP 501 E 1 
HETATM 18 N N9 ADP . . . P 3 142.331 131.48 174.703 1 62.65 ? N9 ADP 501 E 1 
HETATM 19 C C8 ADP . . . P 3 143.2 132.322 174.112 1 62.65 ? C8 ADP 501 E 1 
HETATM 20 N N7 ADP . . . P 3 143.512 133.357 174.928 1 62.65 ? N7 ADP 501 E 1 
HETATM 21 C C5 ADP . . . P 3 142.844 133.18 176.074 1 62.65 ? C5 ADP 501 E 1 
HETATM 22 C C6 ADP . . . P 3 142.716 133.899 177.354 1 62.65 ? C6 ADP 501 E 1 
HETATM 23 N N6 ADP . . . P 3 143.391 135.047 177.573 1 62.65 ? N6 ADP 501 E 1 
HETATM 24 N N1 ADP . . . P 3 141.907 133.374 178.295 1 62.65 ? N1 ADP 501 E 1 
HETATM 25 C C2 ADP . . . P 3 141.227 132.231 178.096 1 62.65 ? C2 ADP 501 E 1 
HETATM 26 N N3 ADP . . . P 3 141.3 131.53 176.954 1 62.65 ? N3 ADP 501 E 1 
HETATM 27 C C4 ADP . . . P 3 142.08 131.938 175.93 1 62.65 ? C4 ADP 501 E 1 
HETATM 28 H "H5'1" ADP . . . P 3 140.724 132.318 171.521 1 62.65 ? "H5'1" ADP 501 E 1 
HETATM 29 H "H5'2" ADP . . . P 3 139.99 131.302 170.28 1 62.65 ? "H5'2" ADP 501 E 1 
HETATM 30 H H4' ADP . . . P 3 140.939 129.284 171.288 1 62.65 ? H4' ADP 501 E 1 
HETATM 31 H H3' ADP . . . P 3 139.177 131.101 172.745 1 62.65 ? H3' ADP 501 E 1 
HETATM 32 H HO3' ADP . . . P 3 138.13 129.037 173.118 1 62.65 ? HO3' ADP 501 E 1 
HETATM 33 H H2' ADP . . . P 3 139.84 130.801 174.838 1 62.65 ? H2' ADP 501 E 1 
HETATM 34 H HO2' ADP . . . P 3 140.248 128.045 174.165 1 62.65 ? HO2' ADP 501 E 1 
HETATM 35 H H1' ADP . . . P 3 142.307 129.367 174.523 1 62.65 ? H1' ADP 501 E 1 
HETATM 36 H H8 ADP . . . P 3 143.596 132.2 173.113 1 62.65 ? H8 ADP 501 E 1 
HETATM 37 H HN61 ADP . . . P 3 143.293 135.524 178.454 1 62.65 ? HN61 ADP 501 E 1 
HETATM 38 H HN62 ADP . . . P 3 143.991 135.423 176.855 1 62.65 ? HN62 ADP 501 E 1 
HETATM 39 H H2 ADP . . . P 3 140.595 131.858 178.891 1 62.65 ? H2 ADP 501 E 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           39 
#