data_7NPE
#
_model_server_result.job_id            YdhPSh_9H8yAxntAcVQE7w 
_model_server_result.datetime_utc      '2025-03-24 16:44:02' 
_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          7npe 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":450}' 
#
_entry.id    7NPE 
#
_exptl.entry_id    7NPE 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          2 
_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         120 
_cell.entry_id            7NPE 
_cell.length_a            199.205 
_cell.length_b            199.205 
_cell.length_c            260.066 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7NPE 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 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,E,F,G,H,I,J 1 1 
C,D,K,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
? 2 E N N 
? 2 H N N 
? 2 K N N 
? 2 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 A OG SER 125 A SER 125 1_555 F MG MG . A MG 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
metalc ? metalc2 E O2B ADP . A ADP 450 1_555 F MG MG . A MG 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? 
metalc ? metalc3 E O3B ADP . A ADP 450 1_555 F MG MG . A MG 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? 
metalc ? metalc4 B OG SER 125 B SER 125 1_555 I MG MG . B MG 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? 
metalc ? metalc5 H O1B ADP . B ADP 450 1_555 I MG MG . B MG 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc6 C OG SER 125 C SER 125 1_555 L MG MG . C MG 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? 
metalc ? metalc7 K O2B ADP . C ADP 450 1_555 L MG MG . C MG 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? 
metalc ? metalc8 K O3B ADP . C ADP 450 1_555 L MG MG . C MG 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc9 D OG SER 125 D SER 125 1_555 N MG MG . D MG 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? 
metalc ? metalc10 M O1B ADP . D ADP 450 1_555 N MG MG . D MG 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? 
#
_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                     7NPE 
_atom_sites.fract_transf_matrix[1][1]    0.00502 
_atom_sites.fract_transf_matrix[1][2]    0.002898 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.005797 
_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]    0.003845 
_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 2 ADP A 1 450 450 ADP ADP . 
F 3 MG A 1 451 451 MG MG . 
G 4 GOL A 1 501 501 GOL GOL . 
H 2 ADP B 1 450 450 ADP ADP . 
I 3 MG B 1 451 451 MG MG . 
J 4 GOL B 1 500 500 GOL GOL . 
K 2 ADP C 1 450 450 ADP ADP . 
L 3 MG C 1 451 451 MG MG . 
M 2 ADP D 1 450 450 ADP ADP . 
N 3 MG D 1 451 451 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 . . . H 2 -21.159 69.527 -13.343 1 122.67 ? PB ADP 450 B 1 
HETATM 2 O O1B ADP . . . H 2 -21.064 70.03 -14.764 1 113.39 ? O1B ADP 450 B 1 
HETATM 3 O O2B ADP . . . H 2 -19.837 69.439 -12.623 1 100.89 ? O2B ADP 450 B 1 
HETATM 4 O O3B ADP . . . H 2 -22.044 68.317 -13.175 1 144.97 ? O3B ADP 450 B 1 
HETATM 5 P PA ADP . . . H 2 -21.524 72.235 -12.765 1 186.39 ? PA ADP 450 B 1 
HETATM 6 O O1A ADP . . . H 2 -22.409 72.808 -13.847 1 155.69 ? O1A ADP 450 B 1 
HETATM 7 O O2A ADP . . . H 2 -20.024 72.302 -12.917 1 83.61 ? O2A ADP 450 B 1 
HETATM 8 O O3A ADP . . . H 2 -21.961 70.696 -12.581 1 114.57 ? O3A ADP 450 B 1 
HETATM 9 O O5' ADP . . . H 2 -21.929 72.93 -11.371 1 105.46 ? O5' ADP 450 B 1 
HETATM 10 C C5' ADP . . . H 2 -21.284 72.558 -10.157 1 100.96 ? C5' ADP 450 B 1 
HETATM 11 C C4' ADP . . . H 2 -21.833 73.402 -9.014 1 107.49 ? C4' ADP 450 B 1 
HETATM 12 O O4' ADP . . . H 2 -20.989 73.26 -7.871 1 100.12 ? O4' ADP 450 B 1 
HETATM 13 C C3' ADP . . . H 2 -21.874 74.88 -9.371 1 107.55 ? C3' ADP 450 B 1 
HETATM 14 O O3' ADP . . . H 2 -23.23 75.329 -9.441 1 119.69 ? O3' ADP 450 B 1 
HETATM 15 C C2' ADP . . . H 2 -21.151 75.605 -8.255 1 90.02 ? C2' ADP 450 B 1 
HETATM 16 O O2' ADP . . . H 2 -22.052 76.488 -7.583 1 102.99 ? O2' ADP 450 B 1 
HETATM 17 C C1' ADP . . . H 2 -20.684 74.529 -7.29 1 83.31 ? C1' ADP 450 B 1 
HETATM 18 N N9 ADP . . . H 2 -19.218 74.634 -7.096 1 101.21 ? N9 ADP 450 B 1 
HETATM 19 C C8 ADP . . . H 2 -18.282 74.144 -7.931 1 90.97 ? C8 ADP 450 B 1 
HETATM 20 N N7 ADP . . . H 2 -17.032 74.402 -7.471 1 100.32 ? N7 ADP 450 B 1 
HETATM 21 C C5 ADP . . . H 2 -17.163 75.074 -6.313 1 99.36 ? C5 ADP 450 B 1 
HETATM 22 C C6 ADP . . . H 2 -16.241 75.65 -5.309 1 92.05 ? C6 ADP 450 B 1 
HETATM 23 N N6 ADP . . . H 2 -14.899 75.55 -5.464 1 101.11 ? N6 ADP 450 B 1 
HETATM 24 N N1 ADP . . . H 2 -16.784 76.273 -4.24 1 105.81 ? N1 ADP 450 B 1 
HETATM 25 C C2 ADP . . . H 2 -18.117 76.374 -4.081 1 111.36 ? C2 ADP 450 B 1 
HETATM 26 N N3 ADP . . . H 2 -19.012 75.875 -4.953 1 102.26 ? N3 ADP 450 B 1 
HETATM 27 C C4 ADP . . . H 2 -18.604 75.226 -6.069 1 104.52 ? C4 ADP 450 B 1 
#
_model_server_stats.io_time_ms              52 
_model_server_stats.parse_time_ms           36 
_model_server_stats.create_model_time_ms    41 
_model_server_stats.query_time_ms           515 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           27 
#