data_5W3D
#
_model_server_result.job_id            Q4qO_hFUMaCx-XtXT4wd2Q 
_model_server_result.datetime_utc      '2024-11-04 20:16:45' 
_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          5w3d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":802}' 
#
_entry.id    5W3D 
#
_exptl.entry_id    5W3D 
_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          97.92 
_cell.angle_gamma         90 
_cell.entry_id            5W3D 
_cell.length_a            163.271 
_cell.length_b            67.249 
_cell.length_c            94.421 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5W3D 
_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 
_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 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 A OG1 THR 153 A THR 441 1_555 C MG MG . A MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? 
metalc ? metalc2 C MG MG . A MG 801 1_555 D O2B ADP . A ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? 
metalc ? metalc3 B OG1 THR 153 B THR 441 1_555 E MG MG . B MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
metalc ? metalc4 E MG MG . B MG 801 1_555 F O1B ADP . B ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? 
#
_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                     5W3D 
_atom_sites.fract_transf_matrix[1][1]    0.006125 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000852 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01487 
_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]    0.010693 
_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 A 1 801 996 MG MG . 
D 3 ADP A 1 802 998 ADP ADP . 
E 2 MG B 1 801 996 MG MG . 
F 3 ADP B 1 802 998 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 . . . D 3 6.576 -9.343 15.828 1 73.23 ? PB ADP 802 A 1 
HETATM 2 O O1B ADP . . . D 3 7.194 -8.962 14.523 1 86.29 ? O1B ADP 802 A 1 
HETATM 3 O O2B ADP . . . D 3 7.358 -8.896 17.05 1 81.59 ? O2B ADP 802 A 1 
HETATM 4 O O3B ADP . . . D 3 6.21 -10.801 15.848 1 72.21 ? O3B ADP 802 A 1 
HETATM 5 P PA ADP . . . D 3 4.346 -8.232 14.488 1 65.53 ? PA ADP 802 A 1 
HETATM 6 O O1A ADP . . . D 3 4.265 -9.613 13.956 1 77.06 ? O1A ADP 802 A 1 
HETATM 7 O O2A ADP . . . D 3 3.069 -7.473 14.716 1 80.17 ? O2A ADP 802 A 1 
HETATM 8 O O3A ADP . . . D 3 5.254 -8.397 15.814 1 72.31 ? O3A ADP 802 A 1 
HETATM 9 O O5' ADP . . . D 3 5.109 -7.325 13.422 1 75.77 ? O5' ADP 802 A 1 
HETATM 10 C C5' ADP . . . D 3 5.166 -7.715 12.045 1 74.29 ? C5' ADP 802 A 1 
HETATM 11 C C4' ADP . . . D 3 4.388 -6.774 11.135 1 72.65 ? C4' ADP 802 A 1 
HETATM 12 O O4' ADP . . . D 3 3.711 -7.533 10.144 1 70.49 ? O4' ADP 802 A 1 
HETATM 13 C C3' ADP . . . D 3 3.331 -5.925 11.806 1 74.43 ? C3' ADP 802 A 1 
HETATM 14 O O3' ADP . . . D 3 3.576 -4.58 11.424 1 81.2 ? O3' ADP 802 A 1 
HETATM 15 C C2' ADP . . . D 3 1.995 -6.348 11.252 1 75.94 ? C2' ADP 802 A 1 
HETATM 16 O O2' ADP . . . D 3 1.276 -5.203 10.786 1 76.72 ? O2' ADP 802 A 1 
HETATM 17 C C1' ADP . . . D 3 2.316 -7.237 10.078 1 72.51 ? C1' ADP 802 A 1 
HETATM 18 N N9 ADP . . . D 3 1.627 -8.545 10.043 1 68.72 ? N9 ADP 802 A 1 
HETATM 19 C C8 ADP . . . D 3 2.002 -9.618 10.75 1 71.86 ? C8 ADP 802 A 1 
HETATM 20 N N7 ADP . . . D 3 1.211 -10.684 10.471 1 75.44 ? N7 ADP 802 A 1 
HETATM 21 C C5 ADP . . . D 3 0.322 -10.287 9.554 1 74.53 ? C5 ADP 802 A 1 
HETATM 22 C C6 ADP . . . D 3 -0.803 -10.925 8.826 1 77.63 ? C6 ADP 802 A 1 
HETATM 23 N N6 ADP . . . D 3 -1.098 -12.223 9.07 1 80.91 ? N6 ADP 802 A 1 
HETATM 24 N N1 ADP . . . D 3 -1.51 -10.172 7.943 1 73.97 ? N1 ADP 802 A 1 
HETATM 25 C C2 ADP . . . D 3 -1.2 -8.874 7.721 1 72 ? C2 ADP 802 A 1 
HETATM 26 N N3 ADP . . . D 3 -0.187 -8.236 8.364 1 72.14 ? N3 ADP 802 A 1 
HETATM 27 C C4 ADP . . . D 3 0.598 -8.873 9.272 1 69.5 ? C4 ADP 802 A 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           27 
#