data_1NLK
#
_model_server_result.job_id            -CZHER02bBt22-BtI6OPxg 
_model_server_result.datetime_utc      '2024-10-16 16:22:48' 
_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          1nlk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1}' 
#
_entry.id    1NLK 
#
_exptl.entry_id    1NLK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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    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            1NLK 
_cell.length_a            63.5 
_cell.length_b            63.5 
_cell.length_c            159.5 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1NLK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 43 21 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 tetrameric 4 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,E,F 1 1 
A,B,C,D,E,F 2 1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 F 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 D O2A ADP . R ADP 1 1_555 C MG MG . R MG 146 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.714 ? 
metalc ? metalc2 F O3B ADP . L ADP 1 1_555 E MG MG . L MG 146 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.822 ? 
metalc ? metalc3 F O3A ADP . L ADP 1 1_555 E MG MG . L MG 146 1_555 ? D ? ? ? ? ? ? ? ? ? ? 2.888 ? 
metalc ? metalc4 F O1A ADP . L ADP 1 1_555 E MG MG . L MG 146 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.488 ? 
metalc ? metalc5 F O3A ADP . L ADP 1 1_555 E MG MG . L MG 146 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.966 ? 
#
_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                     1NLK 
_atom_sites.fract_transf_matrix[1][1]    0.015748 
_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]    0.015748 
_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]    0.00627 
_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
C 2 MG R 1 146 2 MG MG . 
D 3 ADP R 1 1 1 ADP ADP . 
E 2 MG L 1 146 2 MG MG . 
F 3 ADP L 1 1 1 ADP ADP . 
#
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 . A . D 3 11.237 32.683 -16.843 0.21 36.29 ? PB ADP 1 R 1 
HETATM 2 P PB ADP . C . D 3 13.9 33.549 -15.215 0.53 23.95 ? PB ADP 1 R 1 
HETATM 3 O O1B ADP . A . D 3 10.644 32.693 -18.193 0.21 33.37 ? O1B ADP 1 R 1 
HETATM 4 O O1B ADP . C . D 3 13.673 33.638 -13.742 0.53 18.93 ? O1B ADP 1 R 1 
HETATM 5 O O2B ADP . A . D 3 11.928 33.912 -16.406 0.21 34.79 ? O2B ADP 1 R 1 
HETATM 6 O O2B ADP . C . D 3 13.04 34.43 -16.019 0.53 26.22 ? O2B ADP 1 R 1 
HETATM 7 O O3B ADP . A . D 3 9.986 32.677 -15.837 0.21 32.92 ? O3B ADP 1 R 1 
HETATM 8 O O3B ADP . C . D 3 15.368 34.163 -15.365 0.53 20.55 ? O3B ADP 1 R 1 
HETATM 9 P PA ADP . A . D 3 13.262 30.981 -16.768 0.21 33.1 ? PA ADP 1 R 1 
HETATM 10 P PA ADP . C . D 3 13.641 31.251 -16.789 0.53 25.37 ? PA ADP 1 R 1 
HETATM 11 O O1A ADP . A . D 3 14.238 31.348 -15.71 0.21 38.48 ? O1A ADP 1 R 1 
HETATM 12 O O1A ADP . C . D 3 14.207 29.877 -16.712 0.53 29.16 ? O1A ADP 1 R 1 
HETATM 13 O O2A ADP . A . D 3 13.354 29.564 -17.168 0.21 32.49 ? O2A ADP 1 R 1 
HETATM 14 O O2A ADP . C . D 3 12.184 31.267 -17.063 0.53 26.96 ? O2A ADP 1 R 1 
HETATM 15 O O3A ADP . A . D 3 11.879 31.409 -16.505 0.21 33.72 ? O3A ADP 1 R 1 
HETATM 16 O O3A ADP . C . D 3 14.183 32.172 -15.727 0.53 25.97 ? O3A ADP 1 R 1 
HETATM 17 O O5' ADP . A . D 3 13.833 31.681 -18.114 0.21 33.32 ? O5' ADP 1 R 1 
HETATM 18 O O5' ADP . C . D 3 14.307 31.685 -18.181 0.53 30.2 ? O5' ADP 1 R 1 
HETATM 19 C C5' ADP . A . D 3 15.146 32.277 -18.125 0.21 31.68 ? C5' ADP 1 R 1 
HETATM 20 C C5' ADP . C . D 3 15.53 32.404 -18.209 0.53 26.33 ? C5' ADP 1 R 1 
HETATM 21 C C4' ADP . A . D 3 15.37 33.289 -19.245 0.21 31.95 ? C4' ADP 1 R 1 
HETATM 22 C C4' ADP . C . D 3 15.51 33.462 -19.292 0.53 25.96 ? C4' ADP 1 R 1 
HETATM 23 O O4' ADP . A . D 3 15.367 32.707 -20.552 0.21 32.77 ? O4' ADP 1 R 1 
HETATM 24 O O4' ADP . C . D 3 15.473 32.92 -20.612 0.53 26.43 ? O4' ADP 1 R 1 
HETATM 25 C C3' ADP . A . D 3 14.257 34.307 -19.29 0.21 29.88 ? C3' ADP 1 R 1 
HETATM 26 C C3' ADP . C . D 3 14.271 34.31 -19.199 0.53 27.37 ? C3' ADP 1 R 1 
HETATM 27 O O3' ADP . A . D 3 14.267 35.182 -18.165 0.21 35.17 ? O3' ADP 1 R 1 
HETATM 28 O O3' ADP . C . D 3 14.304 35.146 -18.048 0.53 25.17 ? O3' ADP 1 R 1 
HETATM 29 C C2' ADP . A . D 3 14.43 34.924 -20.663 0.21 30.26 ? C2' ADP 1 R 1 
HETATM 30 C C2' ADP . C . D 3 14.26 34.988 -20.544 0.53 27.61 ? C2' ADP 1 R 1 
HETATM 31 O O2' ADP . A . D 3 15.53 35.826 -20.766 0.21 31.74 ? O2' ADP 1 R 1 
HETATM 32 O O2' ADP . C . D 3 15.253 35.994 -20.647 0.53 26.58 ? O2' ADP 1 R 1 
HETATM 33 C C1' ADP . A . D 3 14.774 33.668 -21.458 0.21 28.24 ? C1' ADP 1 R 1 
HETATM 34 C C1' ADP . C . D 3 14.709 33.831 -21.427 0.53 22.25 ? C1' ADP 1 R 1 
HETATM 35 N N9 ADP . A . D 3 13.583 33.09 -22.117 0.31 31.52 ? N9 ADP 1 R 1 
HETATM 36 N N9 ADP . C . D 3 13.564 33.138 -22.048 0.39 27.07 ? N9 ADP 1 R 1 
HETATM 37 C C8 ADP . A . D 3 12.589 32.315 -21.561 0.31 28.62 ? C8 ADP 1 R 1 
HETATM 38 C C8 ADP . C . D 3 12.584 32.373 -21.448 0.39 26.1 ? C8 ADP 1 R 1 
HETATM 39 N N7 ADP . A . D 3 11.645 31.981 -22.394 0.31 35.09 ? N7 ADP 1 R 1 
HETATM 40 N N7 ADP . C . D 3 11.621 32.021 -22.253 0.39 29.78 ? N7 ADP 1 R 1 
HETATM 41 C C5 ADP . A . D 3 12.038 32.578 -23.587 0.31 30.16 ? C5 ADP 1 R 1 
HETATM 42 C C5 ADP . C . D 3 11.998 32.573 -23.474 0.39 23.8 ? C5 ADP 1 R 1 
HETATM 43 C C6 ADP . A . D 3 11.478 32.546 -24.87 0.31 34.12 ? C6 ADP 1 R 1 
HETATM 44 C C6 ADP . C . D 3 11.433 32.481 -24.751 0.39 24.15 ? C6 ADP 1 R 1 
HETATM 45 N N6 ADP . A . D 3 10.333 31.913 -25.125 0.31 29.83 ? N6 ADP 1 R 1 
HETATM 46 N N6 ADP . C . D 3 10.303 31.813 -24.978 0.39 24.61 ? N6 ADP 1 R 1 
HETATM 47 N N1 ADP . A . D 3 12.131 33.198 -25.841 0.31 32.27 ? N1 ADP 1 R 1 
HETATM 48 N N1 ADP . C . D 3 12.078 33.101 -25.751 0.39 29.16 ? N1 ADP 1 R 1 
HETATM 49 C C2 ADP . A . D 3 13.258 33.843 -25.548 0.31 28.77 ? C2 ADP 1 R 1 
HETATM 50 C C2 ADP . C . D 3 13.201 33.767 -25.492 0.39 27.9 ? C2 ADP 1 R 1 
HETATM 51 N N3 ADP . A . D 3 13.902 33.928 -24.393 0.31 27.83 ? N3 ADP 1 R 1 
HETATM 52 N N3 ADP . C . D 3 13.855 33.895 -24.349 0.39 28.37 ? N3 ADP 1 R 1 
HETATM 53 C C4 ADP . A . D 3 13.215 33.264 -23.433 0.31 32.18 ? C4 ADP 1 R 1 
HETATM 54 C C4 ADP . C . D 3 13.178 33.263 -23.362 0.39 25.98 ? C4 ADP 1 R 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           262 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           54 
#