data_4PL3
#
_model_server_result.job_id            c2xAoXf2M6k9B69HSi4aYA 
_model_server_result.datetime_utc      '2024-10-20 00:46:02' 
_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          4pl3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":1002}' 
#
_entry.id    4PL3 
#
_exptl.entry_id    4PL3 
_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          91.88 
_cell.angle_gamma         90 
_cell.entry_id            4PL3 
_cell.length_a            246.08 
_cell.length_b            90.5 
_cell.length_c            72.13 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4PL3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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    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
? 3 D N N 
? 3 G 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
covale ? covale1 A NZ LYS 365 A LYS 907 1_555 C C19 31J . A 31J 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.266 ? 
covale ? covale2 B NZ LYS 365 B LYS 907 1_555 F C19 31J . B 31J 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.241 ? 
metalc ? metalc1 A OD1 ASP 169 A ASP 711 1_555 E MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? 
metalc ? metalc2 A OD2 ASP 169 A ASP 711 1_555 E MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? 
metalc ? metalc3 D O1A ADP . A ADP 1002 1_555 E MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.87 ? 
metalc ? metalc4 D O3A ADP . A ADP 1002 1_555 E MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.551 ? 
metalc ? metalc5 B O HIS 150 B HIS 692 1_555 H MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.925 ? 
metalc ? metalc6 B OD1 ASN 151 B ASN 693 1_555 H MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc7 B OD2 ASP 169 B ASP 711 1_555 H MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? 
metalc ? metalc8 G O1B ADP . B ADP 1002 1_555 H MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.98 ? 
metalc ? metalc9 G O2A ADP . B ADP 1002 1_555 H MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? 
#
_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 47 n n 
PB O2B ADP sing 48 n n 
PB O3B ADP sing 49 n n 
PB O3A ADP sing 50 n n 
O2B HOB2 ADP sing 51 n n 
O3B HOB3 ADP sing 52 n n 
PA O1A ADP doub 53 n n 
PA O2A ADP sing 54 n n 
PA O3A ADP sing 55 n n 
PA O5' ADP sing 56 n n 
O2A HOA2 ADP sing 57 n n 
O5' C5' ADP sing 58 n n 
C5' C4' ADP sing 59 n n 
C5' "H5'1" ADP sing 60 n n 
C5' "H5'2" ADP sing 61 n n 
C4' O4' ADP sing 62 n n 
C4' C3' ADP sing 63 n n 
C4' H4' ADP sing 64 n n 
O4' C1' ADP sing 65 n n 
C3' O3' ADP sing 66 n n 
C3' C2' ADP sing 67 n n 
C3' H3' ADP sing 68 n n 
O3' HO3' ADP sing 69 n n 
C2' O2' ADP sing 70 n n 
C2' C1' ADP sing 71 n n 
C2' H2' ADP sing 72 n n 
O2' HO2' ADP sing 73 n n 
C1' N9 ADP sing 74 n n 
C1' H1' ADP sing 75 n n 
N9 C8 ADP sing 76 n y 
N9 C4 ADP sing 77 n y 
C8 N7 ADP doub 78 n y 
C8 H8 ADP sing 79 n n 
N7 C5 ADP sing 80 n y 
C5 C6 ADP sing 81 n y 
C5 C4 ADP doub 82 n y 
C6 N6 ADP sing 83 n n 
C6 N1 ADP doub 84 n y 
N6 HN61 ADP sing 85 n n 
N6 HN62 ADP sing 86 n n 
N1 C2 ADP sing 87 n y 
C2 N3 ADP doub 88 n y 
C2 H2 ADP sing 89 n n 
N3 C4 ADP sing 90 n y 
#
_atom_sites.entry_id                     4PL3 
_atom_sites.fract_transf_matrix[1][1]    0.004064 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000134 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01105 
_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]    0.013871 
_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 31J A 1 1001 401 31J 31J . 
D 3 ADP A 1 1002 1 ADP ADP . 
E 4 MG A 1 1003 1 MG MG . 
F 2 31J B 1 1001 401 31J 31J . 
G 3 ADP B 1 1002 1 ADP ADP . 
H 4 MG B 1 1003 1 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 . . . G 3 25.424 22.776 -9.33 1 47.18 ? PB ADP 1002 B 1 
HETATM 2 O O1B ADP . . . G 3 25.226 23.097 -7.882 1 40.95 ? O1B ADP 1002 B 1 
HETATM 3 O O2B ADP . . . G 3 26.4 23.707 -10.004 1 39.44 ? O2B ADP 1002 B 1 
HETATM 4 O O3B ADP . . . G 3 25.6 21.303 -9.614 1 57.17 ? O3B ADP 1002 B 1 
HETATM 5 P PA ADP . . . G 3 22.661 22.888 -9.14 1 34.7 ? PA ADP 1002 B 1 
HETATM 6 O O1A ADP . . . G 3 21.601 22.231 -9.998 1 24.7 ? O1A ADP 1002 B 1 
HETATM 7 O O2A ADP . . . G 3 23.109 22.231 -7.858 1 54.65 ? O2A ADP 1002 B 1 
HETATM 8 O O3A ADP . . . G 3 23.998 23.092 -10.01 1 67.74 ? O3A ADP 1002 B 1 
HETATM 9 O O5' ADP . . . G 3 22.253 24.406 -8.771 1 34.57 ? O5' ADP 1002 B 1 
HETATM 10 C C5' ADP . . . G 3 23.297 25.268 -8.297 1 35.2 ? C5' ADP 1002 B 1 
HETATM 11 C C4' ADP . . . G 3 22.99 26.045 -7.008 1 27.44 ? C4' ADP 1002 B 1 
HETATM 12 O O4' ADP . . . G 3 21.739 25.665 -6.442 1 13.8 ? O4' ADP 1002 B 1 
HETATM 13 C C3' ADP . . . G 3 24.026 25.84 -5.899 1 54.54 ? C3' ADP 1002 B 1 
HETATM 14 O O3' ADP . . . G 3 25.056 26.851 -5.898 1 74.92 ? O3' ADP 1002 B 1 
HETATM 15 C C2' ADP . . . G 3 23.207 25.866 -4.621 1 41.27 ? C2' ADP 1002 B 1 
HETATM 16 O O2' ADP . . . G 3 23.368 27.117 -3.952 1 46.77 ? O2' ADP 1002 B 1 
HETATM 17 C C1' ADP . . . G 3 21.748 25.731 -5.019 1 13.29 ? C1' ADP 1002 B 1 
HETATM 18 N N9 ADP . . . G 3 21.092 24.524 -4.431 1 30.16 ? N9 ADP 1002 B 1 
HETATM 19 C C8 ADP . . . G 3 21.07 23.265 -4.95 1 25.48 ? C8 ADP 1002 B 1 
HETATM 20 N N7 ADP . . . G 3 20.36 22.413 -4.151 1 10.94 ? N7 ADP 1002 B 1 
HETATM 21 C C5 ADP . . . G 3 19.923 23.135 -3.099 1 37.24 ? C5 ADP 1002 B 1 
HETATM 22 C C6 ADP . . . G 3 19.127 22.869 -1.884 1 50.42 ? C6 ADP 1002 B 1 
HETATM 23 N N6 ADP . . . G 3 18.658 21.625 -1.641 1 59.5 ? N6 ADP 1002 B 1 
HETATM 24 N N1 ADP . . . G 3 18.885 23.894 -1.036 1 33.4 ? N1 ADP 1002 B 1 
HETATM 25 C C2 ADP . . . G 3 19.344 25.131 -1.269 1 25.34 ? C2 ADP 1002 B 1 
HETATM 26 N N3 ADP . . . G 3 20.08 25.443 -2.353 1 21.26 ? N3 ADP 1002 B 1 
HETATM 27 C C4 ADP . . . G 3 20.397 24.516 -3.289 1 30.48 ? C4 ADP 1002 B 1 
HETATM 28 H "H5'1" ADP . . . G 3 24.193 24.666 -8.131 1 42.24 ? "H5'1" ADP 1002 B 1 
HETATM 29 H "H5'2" ADP . . . G 3 23.536 25.986 -9.084 1 42.24 ? "H5'2" ADP 1002 B 1 
HETATM 30 H H4' ADP . . . G 3 22.964 27.116 -7.255 1 32.93 ? H4' ADP 1002 B 1 
HETATM 31 H H3' ADP . . . G 3 24.476 24.844 -6.012 1 65.45 ? H3' ADP 1002 B 1 
HETATM 32 H HO3' ADP . . . G 3 25.681 26.675 -5.182 1 89.9 ? HO3' ADP 1002 B 1 
HETATM 33 H H2' ADP . . . G 3 23.497 25.028 -3.972 1 49.52 ? H2' ADP 1002 B 1 
HETATM 34 H HO2' ADP . . . G 3 24.297 27.236 -3.71 1 56.12 ? HO2' ADP 1002 B 1 
HETATM 35 H H1' ADP . . . G 3 21.215 26.635 -4.691 1 15.95 ? H1' ADP 1002 B 1 
HETATM 36 H H8 ADP . . . G 3 21.549 22.978 -5.878 1 30.58 ? H8 ADP 1002 B 1 
HETATM 37 H HN61 ADP . . . G 3 18.112 21.445 -0.811 1 71.4 ? HN61 ADP 1002 B 1 
HETATM 38 H HN62 ADP . . . G 3 18.851 20.876 -2.291 1 71.4 ? HN62 ADP 1002 B 1 
HETATM 39 H H2 ADP . . . G 3 19.12 25.911 -0.552 1 30.41 ? H2 ADP 1002 B 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           263 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           39 
#