data_3SJD
#
_model_server_result.job_id            w76CKItBGpMPcQ5drRJJfQ 
_model_server_result.datetime_utc      '2024-12-21 12:37:27' 
_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          3sjd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":401}' 
#
_entry.id    3SJD 
#
_exptl.entry_id    3SJD 
_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    3 
_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            3SJD 
_cell.length_a            149.64 
_cell.length_b            209.75 
_cell.length_c            133.24 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3SJD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? trimeric 3 author_defined_assembly 1 
? tetrameric 4 author_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,E,F,G,H,I,J 1 1 
C,D,K,L,M 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' 4_555 x,-y,-z 1 0 0 0 -1 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 F N N 
? 3 H N N 
? 3 K 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 32 A THR 32 1_555 G MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
metalc ? metalc2 A SG CYS 285 A CYS 285 1_555 J ZN ZN . B ZN 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? 
metalc ? metalc3 A SG CYS 288 A CYS 288 1_555 J ZN ZN . B ZN 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? 
metalc ? metalc4 F O2B ADP . A ADP 401 1_555 G MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc5 B OG1 THR 32 B THR 32 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? 
metalc ? metalc6 B SG CYS 288 B CYS 288 1_555 J ZN ZN . B ZN 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
metalc ? metalc7 H O2B ADP . B ADP 401 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
metalc ? metalc8 C OG1 THR 32 C THR 32 1_555 L MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? 
metalc ? metalc9 C SG CYS 285 C CYS 285 1_555 M ZN ZN . C ZN 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? 
metalc ? metalc10 K O2B ADP . C ADP 401 1_555 L MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
#
_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                     3SJD 
_atom_sites.fract_transf_matrix[1][1]    0.006683 
_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]    0.004768 
_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]    0.007505 
_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
F 3 ADP A 1 401 401 ADP ADP . 
G 4 MG A 1 402 402 MG MG . 
H 3 ADP B 1 401 401 ADP ADP . 
I 4 MG B 1 402 402 MG MG . 
J 5 ZN B 1 363 363 ZN ZN . 
K 3 ADP C 1 401 401 ADP ADP . 
L 4 MG C 1 402 402 MG MG . 
M 5 ZN C 1 363 363 ZN ZN . 
#
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 . . . F 3 41.156 -48.706 -19.707 1 323.48 ? PB ADP 401 A 1 
HETATM 2 O O1B ADP . . . F 3 40.131 -47.979 -18.784 1 322.14 ? O1B ADP 401 A 1 
HETATM 3 O O2B ADP . . . F 3 40.973 -48.01 -21.099 1 324 ? O2B ADP 401 A 1 
HETATM 4 O O3B ADP . . . F 3 41.23 -50.148 -19.712 1 323.14 ? O3B ADP 401 A 1 
HETATM 5 P PA ADP . . . F 3 43.496 -46.809 -19.438 1 326.6 ? PA ADP 401 A 1 
HETATM 6 O O1A ADP . . . F 3 44.217 -47.133 -20.797 1 327.85 ? O1A ADP 401 A 1 
HETATM 7 O O2A ADP . . . F 3 42.657 -45.589 -19.425 1 326.15 ? O2A ADP 401 A 1 
HETATM 8 O O3A ADP . . . F 3 42.552 -48.062 -19.209 1 325.04 ? O3A ADP 401 A 1 
HETATM 9 O O5' ADP . . . F 3 44.658 -46.852 -18.344 1 327.25 ? O5' ADP 401 A 1 
HETATM 10 C C5' ADP . . . F 3 44.314 -46.598 -16.992 1 326.38 ? C5' ADP 401 A 1 
HETATM 11 C C4' ADP . . . F 3 45.375 -45.678 -16.389 1 327.41 ? C4' ADP 401 A 1 
HETATM 12 O O4' ADP . . . F 3 46.657 -46.334 -16.364 1 328.26 ? O4' ADP 401 A 1 
HETATM 13 C C3' ADP . . . F 3 45.565 -44.397 -17.274 1 328.57 ? C3' ADP 401 A 1 
HETATM 14 O O3' ADP . . . F 3 45.735 -43.261 -16.431 1 328.74 ? O3' ADP 401 A 1 
HETATM 15 C C2' ADP . . . F 3 46.824 -44.705 -18.117 1 330.07 ? C2' ADP 401 A 1 
HETATM 16 O O2' ADP . . . F 3 47.58 -43.581 -18.493 1 331.52 ? O2' ADP 401 A 1 
HETATM 17 C C1' ADP . . . F 3 47.639 -45.567 -17.138 1 329.8 ? C1' ADP 401 A 1 
HETATM 18 N N9 ADP . . . F 3 48.367 -46.619 -17.767 1 330.23 ? N9 ADP 401 A 1 
HETATM 19 C C8 ADP . . . F 3 47.931 -47.733 -18.494 1 329.77 ? C8 ADP 401 A 1 
HETATM 20 N N7 ADP . . . F 3 48.885 -48.668 -18.669 1 330.11 ? N7 ADP 401 A 1 
HETATM 21 C C5 ADP . . . F 3 49.98 -48.134 -17.976 1 330.71 ? C5 ADP 401 A 1 
HETATM 22 C C6 ADP . . . F 3 51.307 -48.558 -17.714 1 331.12 ? C6 ADP 401 A 1 
HETATM 23 N N6 ADP . . . F 3 51.686 -49.777 -18.169 1 330.93 ? N6 ADP 401 A 1 
HETATM 24 N N1 ADP . . . F 3 52.183 -47.796 -16.967 1 331.52 ? N1 ADP 401 A 1 
HETATM 25 C C2 ADP . . . F 3 51.742 -46.623 -16.517 1 331.65 ? C2 ADP 401 A 1 
HETATM 26 N N3 ADP . . . F 3 50.517 -46.084 -16.669 1 331.32 ? N3 ADP 401 A 1 
HETATM 27 C C4 ADP . . . F 3 49.68 -46.858 -17.39 1 330.83 ? C4 ADP 401 A 1 
#
_model_server_stats.io_time_ms              76 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           289 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#