data_6Y1I
#
_model_server_result.job_id            tzDgVL3GS4AYqNppVfQtrQ 
_model_server_result.datetime_utc      '2024-11-14 19:08:55' 
_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          6y1i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    6Y1I 
#
_exptl.entry_id    6Y1I 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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    3 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          116.82 
_cell.angle_gamma         90 
_cell.entry_id            6Y1I 
_cell.length_a            87.428 
_cell.length_b            87.603 
_cell.length_c            95.065 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6Y1I 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E 1 1 
B,F,G 2 1 
C,H,I 3 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
? 2 D N N 
? 2 F N N 
? 2 H 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 112 A THR 112 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? 
metalc ? metalc2 D O1B ADP . A ADP 401 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
metalc ? metalc3 D O3B ADP . A ADP 401 1_555 E MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? 
metalc ? metalc4 B OG1 THR 112 B THR 112 1_555 G MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? 
metalc ? metalc5 F O3B ADP . B ADP 401 1_555 G MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc6 F O1A ADP . B ADP 401 1_555 G MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.991 ? 
metalc ? metalc7 C OG1 THR 112 C THR 112 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? 
metalc ? metalc8 H O2B ADP . C ADP 401 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? 
metalc ? metalc9 H O3B ADP . C ADP 401 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.993 ? 
#
_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                     6Y1I 
_atom_sites.fract_transf_matrix[1][1]    0.011438 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.005783 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011415 
_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]    0.011787 
_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
D 2 ADP A 1 401 1452 ADP ADP . 
E 3 MG A 1 402 701 MG MG . 
F 2 ADP B 1 401 1452 ADP ADP . 
G 3 MG B 1 402 701 MG MG . 
H 2 ADP C 1 401 1452 ADP ADP . 
I 3 MG C 1 402 701 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 . . . D 2 -37.511 -12.27 3.981 1 93.35 ? PB ADP 401 A 1 
HETATM 2 O O1B ADP . . . D 2 -38.951 -12.671 3.759 1 96.72 ? O1B ADP 401 A 1 
HETATM 3 O O2B ADP . . . D 2 -36.895 -12.892 5.214 1 62.63 ? O2B ADP 401 A 1 
HETATM 4 O O3B ADP . . . D 2 -37.262 -10.787 3.84 1 96.24 ? O3B ADP 401 A 1 
HETATM 5 P PA ADP . . . D 2 -37.448 -13.03 1.312 1 71.56 ? PA ADP 401 A 1 
HETATM 6 O O1A ADP . . . D 2 -37.942 -11.644 0.963 1 84.19 ? O1A ADP 401 A 1 
HETATM 7 O O2A ADP . . . D 2 -38.415 -14.189 1.376 1 77.95 ? O2A ADP 401 A 1 
HETATM 8 O O3A ADP . . . D 2 -36.707 -12.932 2.744 1 55.79 ? O3A ADP 401 A 1 
HETATM 9 O O5' ADP . . . D 2 -36.311 -13.452 0.251 1 62.41 ? O5' ADP 401 A 1 
HETATM 10 C C5' ADP . . . D 2 -36.654 -14.178 -0.938 1 69.78 ? C5' ADP 401 A 1 
HETATM 11 C C4' ADP . . . D 2 -35.59 -13.821 -1.963 1 107.44 ? C4' ADP 401 A 1 
HETATM 12 O O4' ADP . . . D 2 -34.513 -14.787 -1.953 1 140.37 ? O4' ADP 401 A 1 
HETATM 13 C C3' ADP . . . D 2 -36.018 -13.84 -3.419 1 124.07 ? C3' ADP 401 A 1 
HETATM 14 O O3' ADP . . . D 2 -35.044 -13.102 -4.158 1 145.94 ? O3' ADP 401 A 1 
HETATM 15 C C2' ADP . . . D 2 -35.962 -15.317 -3.757 1 119.19 ? C2' ADP 401 A 1 
HETATM 16 O O2' ADP . . . D 2 -35.589 -15.464 -5.12 1 113.16 ? O2' ADP 401 A 1 
HETATM 17 C C1' ADP . . . D 2 -34.806 -15.842 -2.908 1 137.51 ? C1' ADP 401 A 1 
HETATM 18 N N9 ADP . . . D 2 -34.895 -17.083 -2.105 1 122.41 ? N9 ADP 401 A 1 
HETATM 19 C C8 ADP . . . D 2 -34.945 -17.175 -0.76 1 123.64 ? C8 ADP 401 A 1 
HETATM 20 N N7 ADP . . . D 2 -34.972 -18.475 -0.367 1 140.36 ? N7 ADP 401 A 1 
HETATM 21 C C5 ADP . . . D 2 -34.899 -19.228 -1.48 1 128.95 ? C5 ADP 401 A 1 
HETATM 22 C C6 ADP . . . D 2 -34.872 -20.673 -1.805 1 104.2 ? C6 ADP 401 A 1 
HETATM 23 N N6 ADP . . . D 2 -34.933 -21.627 -0.844 1 85.89 ? N6 ADP 401 A 1 
HETATM 24 N N1 ADP . . . D 2 -34.79 -21.022 -3.11 1 116.6 ? N1 ADP 401 A 1 
HETATM 25 C C2 ADP . . . D 2 -34.728 -20.113 -4.102 1 126.42 ? C2 ADP 401 A 1 
HETATM 26 N N3 ADP . . . D 2 -34.746 -18.789 -3.876 1 118.48 ? N3 ADP 401 A 1 
HETATM 27 C C4 ADP . . . D 2 -34.827 -18.301 -2.617 1 124.86 ? C4 ADP 401 A 1 
HETATM 28 H "H5'1" ADP . . . D 2 -37.646 -13.892 -1.294 1 85.58 ? "H5'1" ADP 401 A 1 
HETATM 29 H "H5'2" ADP . . . D 2 -36.663 -15.253 -0.747 1 85.58 ? "H5'2" ADP 401 A 1 
HETATM 30 H H4' ADP . . . D 2 -35.321 -12.802 -1.651 1 130.78 ? H4' ADP 401 A 1 
HETATM 31 H H3' ADP . . . D 2 -37.001 -13.4 -3.637 1 150.73 ? H3' ADP 401 A 1 
HETATM 32 H HO3' ADP . . . D 2 -35.446 -12.755 -4.966 1 176.97 ? HO3' ADP 401 A 1 
HETATM 33 H H2' ADP . . . D 2 -36.919 -15.831 -3.586 1 144.87 ? H2' ADP 401 A 1 
HETATM 34 H HO2' ADP . . . D 2 -35.802 -14.653 -5.602 1 137.64 ? HO2' ADP 401 A 1 
HETATM 35 H H1' ADP . . . D 2 -34.082 -16.114 -3.689 1 166.86 ? H1' ADP 401 A 1 
HETATM 36 H H8 ADP . . . D 2 -34.962 -16.328 -0.085 1 150.22 ? H8 ADP 401 A 1 
HETATM 37 H HN61 ADP . . . D 2 -34.996 -21.371 0.131 1 104.91 ? HN61 ADP 401 A 1 
HETATM 38 H HN62 ADP . . . D 2 -34.913 -22.602 -1.109 1 104.91 ? HN62 ADP 401 A 1 
HETATM 39 H H2 ADP . . . D 2 -34.662 -20.464 -5.124 1 153.55 ? H2 ADP 401 A 1 
#
_model_server_stats.io_time_ms              32 
_model_server_stats.parse_time_ms           53 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           538 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           39 
#