data_6NYB
#
_model_server_result.job_id            TDEiTadAoD3O9cGUCsjytA 
_model_server_result.datetime_utc      '2024-11-12 22:50:55' 
_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          6nyb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":601}' 
#
_entry.id    6NYB 
#
_exptl.entry_id    6NYB 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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            6NYB 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6NYB 
_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    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      6 
_struct_asym.id                             H 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 A C SER 391 A SER 364 1_555 A N SEP 392 A SEP 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? 
covale ? covale2 A C SEP 392 A SEP 365 1_555 A N ALA 393 A ALA 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? 
covale ? covale3 A C ALA 755 A ALA 728 1_555 A N SEP 756 A SEP 729 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? 
covale ? covale4 A C SEP 756 A SEP 729 1_555 A N GLU 757 A GLU 730 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? 
metalc ? metalc1 A NE2 HIS 262 A HIS 235 1_555 G ZN ZN . A ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? 
metalc ? metalc2 A SG CYS 275 A CYS 248 1_555 F ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? 
metalc ? metalc3 A SG CYS 278 A CYS 251 1_555 F ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? 
metalc ? metalc4 A SG CYS 288 A CYS 261 1_555 G ZN ZN . A ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.892 ? 
metalc ? metalc5 A SG CYS 291 A CYS 264 1_555 G ZN ZN . A ZN 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? 
metalc ? metalc6 B OD1 ASN 217 B ASN 195 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? 
metalc ? metalc7 B OD2 ASP 230 B ASP 208 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? 
metalc ? metalc8 H O2B ADP . B ADP 601 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? 
metalc ? metalc9 H O1A ADP . B ADP 601 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? 
#
_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                     6NYB 
_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 4 AGS A 1 801 801 AGS AGS . 
F 5 ZN A 1 901 901 ZN ZN . 
G 5 ZN A 1 902 902 ZN ZN . 
H 6 ADP B 1 601 601 ADP ADP . 
I 7 MG B 1 602 602 MG MG . 
J 8 LCJ B 1 901 901 LCJ GDC . 
#
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 6 87.398 119.545 134.783 1 176.64 ? PB ADP 601 B 1 
HETATM 2 O O1B ADP . . . H 6 87.172 118.333 133.914 1 176.64 ? O1B ADP 601 B 1 
HETATM 3 O O2B ADP . . . H 6 86.111 120.208 135.206 1 176.64 ? O2B ADP 601 B 1 
HETATM 4 O O3B ADP . . . H 6 88.321 119.267 135.944 1 176.64 ? O3B ADP 601 B 1 
HETATM 5 P PA ADP . . . H 6 88.247 122.226 133.899 1 176.64 ? PA ADP 601 B 1 
HETATM 6 O O1A ADP . . . H 6 87.092 122.784 133.137 1 176.64 ? O1A ADP 601 B 1 
HETATM 7 O O2A ADP . . . H 6 89.624 122.638 133.493 1 176.64 ? O2A ADP 601 B 1 
HETATM 8 O O3A ADP . . . H 6 88.162 120.624 133.859 1 176.64 ? O3A ADP 601 B 1 
HETATM 9 O O5' ADP . . . H 6 88.04 122.517 135.465 1 176.64 ? O5' ADP 601 B 1 
HETATM 10 C C5' ADP . . . H 6 89.212 122.747 136.289 1 176.64 ? C5' ADP 601 B 1 
HETATM 11 C C4' ADP . . . H 6 88.814 122.887 137.739 1 176.64 ? C4' ADP 601 B 1 
HETATM 12 O O4' ADP . . . H 6 88.291 124.22 137.958 1 176.64 ? O4' ADP 601 B 1 
HETATM 13 C C3' ADP . . . H 6 87.738 121.917 138.255 1 176.64 ? C3' ADP 601 B 1 
HETATM 14 O O3' ADP . . . H 6 88.279 121.069 139.261 1 176.64 ? O3' ADP 601 B 1 
HETATM 15 C C2' ADP . . . H 6 86.623 122.81 138.818 1 176.64 ? C2' ADP 601 B 1 
HETATM 16 O O2' ADP . . . H 6 86.167 122.371 140.079 1 176.64 ? O2' ADP 601 B 1 
HETATM 17 C C1' ADP . . . H 6 87.283 124.181 138.938 1 176.64 ? C1' ADP 601 B 1 
HETATM 18 N N9 ADP . . . H 6 86.369 125.29 138.685 1 176.64 ? N9 ADP 601 B 1 
HETATM 19 C C8 ADP . . . H 6 86.031 125.782 137.449 1 176.64 ? C8 ADP 601 B 1 
HETATM 20 N N7 ADP . . . H 6 85.194 126.786 137.497 1 176.64 ? N7 ADP 601 B 1 
HETATM 21 C C5 ADP . . . H 6 84.953 126.966 138.85 1 176.64 ? C5 ADP 601 B 1 
HETATM 22 C C6 ADP . . . H 6 84.142 127.88 139.549 1 176.64 ? C6 ADP 601 B 1 
HETATM 23 N N6 ADP . . . H 6 83.4 128.812 138.957 1 176.64 ? N6 ADP 601 B 1 
HETATM 24 N N1 ADP . . . H 6 84.121 127.792 140.901 1 176.64 ? N1 ADP 601 B 1 
HETATM 25 C C2 ADP . . . H 6 84.868 126.848 141.49 1 176.64 ? C2 ADP 601 B 1 
HETATM 26 N N3 ADP . . . H 6 85.672 125.942 140.937 1 176.64 ? N3 ADP 601 B 1 
HETATM 27 C C4 ADP . . . H 6 85.672 126.049 139.597 1 176.64 ? C4 ADP 601 B 1 
#
_model_server_stats.io_time_ms              69 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    41 
_model_server_stats.query_time_ms           366 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           27 
#