data_3NBX
#
_model_server_result.job_id            Nf1OjNMp_qd-HBeB1oaIZw 
_model_server_result.datetime_utc      '2024-12-21 12:04:43' 
_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          3nbx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":800}' 
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_entry.id    3NBX 
#
_exptl.entry_id    3NBX 
_exptl.method      'X-RAY DIFFRACTION' 
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_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          2 
_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         120 
_cell.entry_id            3NBX 
_cell.length_a            162.232 
_cell.length_b            162.232 
_cell.length_c            55.316 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3NBX 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_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                     3NBX 
_atom_sites.fract_transf_matrix[1][1]    0.006164 
_atom_sites.fract_transf_matrix[1][2]    0.003559 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007118 
_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]    0.018078 
_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
B 2 ADP X 1 800 800 ADP ADP . 
C 3 SO4 X 1 499 1 SO4 SO4 . 
D 4 HOH X 1 500 18 HOH HOH . 
D 4 HOH X 2 501 27 HOH HOH . 
D 4 HOH X 3 502 31 HOH HOH . 
D 4 HOH X 4 503 35 HOH HOH . 
D 4 HOH X 5 504 36 HOH HOH . 
D 4 HOH X 6 505 40 HOH HOH . 
D 4 HOH X 7 506 42 HOH HOH . 
D 4 HOH X 8 507 43 HOH HOH . 
D 4 HOH X 9 508 49 HOH HOH . 
D 4 HOH X 10 509 53 HOH HOH . 
D 4 HOH X 11 510 60 HOH HOH . 
D 4 HOH X 12 511 61 HOH HOH . 
D 4 HOH X 13 512 67 HOH HOH . 
D 4 HOH X 14 513 68 HOH HOH . 
D 4 HOH X 15 514 71 HOH HOH . 
D 4 HOH X 16 515 73 HOH HOH . 
D 4 HOH X 17 516 84 HOH HOH . 
D 4 HOH X 18 517 85 HOH HOH . 
D 4 HOH X 19 518 96 HOH HOH . 
D 4 HOH X 20 519 102 HOH HOH . 
D 4 HOH X 21 520 103 HOH HOH . 
D 4 HOH X 22 521 105 HOH HOH . 
D 4 HOH X 23 522 110 HOH HOH . 
D 4 HOH X 24 523 115 HOH HOH . 
D 4 HOH X 25 524 116 HOH HOH . 
D 4 HOH X 26 525 118 HOH HOH . 
D 4 HOH X 27 526 119 HOH HOH . 
D 4 HOH X 28 527 120 HOH HOH . 
D 4 HOH X 29 528 121 HOH HOH . 
D 4 HOH X 30 529 122 HOH HOH . 
D 4 HOH X 31 530 123 HOH HOH . 
D 4 HOH X 32 531 124 HOH HOH . 
D 4 HOH X 33 532 125 HOH HOH . 
D 4 HOH X 34 533 126 HOH HOH . 
D 4 HOH X 35 534 127 HOH HOH . 
D 4 HOH X 36 535 128 HOH HOH . 
D 4 HOH X 37 536 129 HOH HOH . 
D 4 HOH X 38 537 130 HOH HOH . 
D 4 HOH X 39 538 131 HOH HOH . 
D 4 HOH X 40 539 132 HOH HOH . 
D 4 HOH X 41 540 133 HOH HOH . 
D 4 HOH X 42 541 134 HOH HOH . 
D 4 HOH X 43 542 135 HOH HOH . 
D 4 HOH X 44 543 136 HOH HOH . 
#
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 . . . B 2 22.724 20.604 49.81 1 56.39 ? PB ADP 800 X 1 
HETATM 2 O O1B ADP . . . B 2 21.621 20.947 50.778 1 58.31 ? O1B ADP 800 X 1 
HETATM 3 O O2B ADP . . . B 2 22.712 21.369 48.512 1 55.28 ? O2B ADP 800 X 1 
HETATM 4 O O3B ADP . . . B 2 22.978 19.135 49.61 1 56.46 ? O3B ADP 800 X 1 
HETATM 5 P PA ADP . . . B 2 24.325 20.816 52.119 1 60.61 ? PA ADP 800 X 1 
HETATM 6 O O1A ADP . . . B 2 23.63 21.828 52.995 1 54.17 ? O1A ADP 800 X 1 
HETATM 7 O O2A ADP . . . B 2 24.13 19.337 52.344 1 55.98 ? O2A ADP 800 X 1 
HETATM 8 O O3A ADP . . . B 2 24.022 21.142 50.576 1 58.55 ? O3A ADP 800 X 1 
HETATM 9 O O5' ADP . . . B 2 25.904 21.118 52.141 1 60.69 ? O5' ADP 800 X 1 
HETATM 10 C C5' ADP . . . B 2 26.47 21.919 53.169 1 55.88 ? C5' ADP 800 X 1 
HETATM 11 C C4' ADP . . . B 2 27.895 21.457 53.441 1 60.01 ? C4' ADP 800 X 1 
HETATM 12 O O4' ADP . . . B 2 28.703 21.646 52.277 1 61.34 ? O4' ADP 800 X 1 
HETATM 13 C C3' ADP . . . B 2 28.521 22.284 54.539 1 62.37 ? C3' ADP 800 X 1 
HETATM 14 O O3' ADP . . . B 2 29.407 21.447 55.284 1 57.09 ? O3' ADP 800 X 1 
HETATM 15 C C2' ADP . . . B 2 29.272 23.376 53.796 1 57.02 ? C2' ADP 800 X 1 
HETATM 16 O O2' ADP . . . B 2 30.462 23.783 54.489 1 55.62 ? O2' ADP 800 X 1 
HETATM 17 C C1' ADP . . . B 2 29.572 22.772 52.425 1 52.83 ? C1' ADP 800 X 1 
HETATM 18 N N9 ADP . . . B 2 29.338 23.707 51.287 1 53.88 ? N9 ADP 800 X 1 
HETATM 19 C C8 ADP . . . B 2 28.935 23.324 50.06 1 59.91 ? C8 ADP 800 X 1 
HETATM 20 N N7 ADP . . . B 2 28.808 24.381 49.219 1 57.53 ? N7 ADP 800 X 1 
HETATM 21 C C5 ADP . . . B 2 29.144 25.481 49.91 1 51.92 ? C5 ADP 800 X 1 
HETATM 22 C C6 ADP . . . B 2 29.233 26.933 49.624 1 53.22 ? C6 ADP 800 X 1 
HETATM 23 N N6 ADP . . . B 2 28.925 27.43 48.403 1 56.15 ? N6 ADP 800 X 1 
HETATM 24 N N1 ADP . . . B 2 29.632 27.751 50.627 1 56.06 ? N1 ADP 800 X 1 
HETATM 25 C C2 ADP . . . B 2 29.939 27.28 51.852 1 53.85 ? C2 ADP 800 X 1 
HETATM 26 N N3 ADP . . . B 2 29.88 25.974 52.176 1 53.17 ? N3 ADP 800 X 1 
HETATM 27 C C4 ADP . . . B 2 29.498 25.037 51.269 1 53.11 ? C4 ADP 800 X 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#