data_5LJV
#
_model_server_result.job_id            YzQMWG96qctoxZMNnSvUqQ 
_model_server_result.datetime_utc      '2024-11-24 22:53:24' 
_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          5ljv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":402}' 
#
_entry.id    5LJV 
#
_exptl.entry_id    5LJV 
_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    6 
_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            5LJV 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5LJV 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_and_software_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 
_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 H N N 
? 3 J N N 
? 3 L N N 
? 3 N N N 
? 3 P N N 
? 3 R 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 OE1 GLU 143 A GLU 143 1_555 G MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? 
metalc ? metalc2 G MG MG . A MG 401 1_555 H O1B ADP . A ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.907 ? 
metalc ? metalc3 G MG MG . A MG 401 1_555 H O2B ADP . A ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? 
metalc ? metalc4 B OE1 GLU 143 B GLU 143 1_555 I MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? 
metalc ? metalc5 I MG MG . B MG 401 1_555 J O2B ADP . B ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? 
metalc ? metalc6 I MG MG . B MG 401 1_555 J O1B ADP . B ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? 
metalc ? metalc7 C OE1 GLU 143 C GLU 143 1_555 K MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? 
metalc ? metalc8 K MG MG . C MG 401 1_555 L O1B ADP . C ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? 
metalc ? metalc9 K MG MG . C MG 401 1_555 L O2B ADP . C ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc10 D OE1 GLU 143 D GLU 143 1_555 M MG MG . D MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.657 ? 
metalc ? metalc11 M MG MG . D MG 401 1_555 N O2B ADP . D ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? 
metalc ? metalc12 M MG MG . D MG 401 1_555 N O1B ADP . D ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.959 ? 
metalc ? metalc13 E OE1 GLU 143 E GLU 143 1_555 O MG MG . E MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? 
metalc ? metalc14 O MG MG . E MG 401 1_555 P O1B ADP . E ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc15 O MG MG . E MG 401 1_555 P O2B ADP . E ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.975 ? 
metalc ? metalc16 F OE1 GLU 143 F GLU 143 1_555 Q MG MG . F MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? 
metalc ? metalc17 Q MG MG . F MG 401 1_555 R O2B ADP . F ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc18 Q MG MG . F MG 401 1_555 R O1B ADP . F ADP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.932 ? 
#
_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                     5LJV 
_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 2 MG A 1 401 998 MG MG . 
H 3 ADP A 1 402 999 ADP ADP . 
I 2 MG B 1 401 998 MG MG . 
J 3 ADP B 1 402 999 ADP ADP . 
K 2 MG C 1 401 998 MG MG . 
L 3 ADP C 1 402 999 ADP ADP . 
M 2 MG D 1 401 998 MG MG . 
N 3 ADP D 1 402 999 ADP ADP . 
O 2 MG E 1 401 998 MG MG . 
P 3 ADP E 1 402 999 ADP ADP . 
Q 2 MG F 1 401 998 MG MG . 
R 3 ADP F 1 402 999 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 . . . R 3 172.765 187.679 190.302 1 66.19 ? PB ADP 402 F 1 
HETATM 2 O O1B ADP . . . R 3 174.118 187.715 189.481 1 65.25 ? O1B ADP 402 F 1 
HETATM 3 O O2B ADP . . . R 3 171.461 187.109 189.599 1 68.27 ? O2B ADP 402 F 1 
HETATM 4 O O3B ADP . . . R 3 172.809 186.933 191.618 1 64.5 ? O3B ADP 402 F 1 
HETATM 5 P PA ADP . . . R 3 170.869 189.66 190.537 1 57.26 ? PA ADP 402 F 1 
HETATM 6 O O1A ADP . . . R 3 170.114 189.664 189.191 1 57.16 ? O1A ADP 402 F 1 
HETATM 7 O O2A ADP . . . R 3 170.207 188.696 191.495 1 64.36 ? O2A ADP 402 F 1 
HETATM 8 O O3A ADP . . . R 3 172.434 189.249 190.604 1 58.49 ? O3A ADP 402 F 1 
HETATM 9 O O5' ADP . . . R 3 170.944 191.107 191.201 1 60.61 ? O5' ADP 402 F 1 
HETATM 10 C C5' ADP . . . R 3 171.274 191.243 192.572 1 67.03 ? C5' ADP 402 F 1 
HETATM 11 C C4' ADP . . . R 3 172.527 192.141 192.662 1 76.77 ? C4' ADP 402 F 1 
HETATM 12 O O4' ADP . . . R 3 172.152 193.44 192.242 1 78.97 ? O4' ADP 402 F 1 
HETATM 13 C C3' ADP . . . R 3 173.218 192.317 194.074 1 85.07 ? C3' ADP 402 F 1 
HETATM 14 O O3' ADP . . . R 3 174.65 192.621 194.077 1 78.09 ? O3' ADP 402 F 1 
HETATM 15 C C2' ADP . . . R 3 172.416 193.438 194.728 1 86.31 ? C2' ADP 402 F 1 
HETATM 16 O O2' ADP . . . R 3 173.019 194.21 195.824 1 84.08 ? O2' ADP 402 F 1 
HETATM 17 C C1' ADP . . . R 3 172.165 194.218 193.416 1 82.66 ? C1' ADP 402 F 1 
HETATM 18 N N9 ADP . . . R 3 170.848 194.726 193.594 1 84.08 ? N9 ADP 402 F 1 
HETATM 19 C C8 ADP . . . R 3 169.652 194.081 193.839 1 88.46 ? C8 ADP 402 F 1 
HETATM 20 N N7 ADP . . . R 3 168.672 195.037 193.945 1 92.17 ? N7 ADP 402 F 1 
HETATM 21 C C5 ADP . . . R 3 169.341 196.236 193.79 1 86.11 ? C5 ADP 402 F 1 
HETATM 22 C C6 ADP . . . R 3 168.934 197.623 193.777 1 83.39 ? C6 ADP 402 F 1 
HETATM 23 N N6 ADP . . . R 3 167.595 197.825 193.97 1 99.28 ? N6 ADP 402 F 1 
HETATM 24 N N1 ADP . . . R 3 169.881 198.549 193.564 1 72.32 ? N1 ADP 402 F 1 
HETATM 25 C C2 ADP . . . R 3 171.181 198.22 193.335 1 71.34 ? C2 ADP 402 F 1 
HETATM 26 N N3 ADP . . . R 3 171.663 196.986 193.293 1 69.85 ? N3 ADP 402 F 1 
HETATM 27 C C4 ADP . . . R 3 170.777 196.022 193.559 1 79.08 ? C4 ADP 402 F 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           292 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           27 
#