data_6Y1I
#
_model_server_result.job_id            NqwwAZ-cokgMammhL_p5uA 
_model_server_result.datetime_utc      '2024-11-22 22:21:06' 
_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":"F","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 . . . F 2 -93.403 -3.305 4.344 1 113.25 ? PB ADP 401 B 1 
HETATM 2 O O1B ADP . . . F 2 -93.85 -4.665 3.854 1 144.55 ? O1B ADP 401 B 1 
HETATM 3 O O2B ADP . . . F 2 -94.095 -2.77 5.572 1 54.3 ? O2B ADP 401 B 1 
HETATM 4 O O3B ADP . . . F 2 -91.897 -3.133 4.359 1 102.83 ? O3B ADP 401 B 1 
HETATM 5 P PA ADP . . . F 2 -93.363 -2.585 1.692 1 95.13 ? PA ADP 401 B 1 
HETATM 6 O O1A ADP . . . F 2 -92.879 -4.002 1.422 1 73.72 ? O1A ADP 401 B 1 
HETATM 7 O O2A ADP . . . F 2 -92.393 -1.43 1.617 1 54.69 ? O2A ADP 401 B 1 
HETATM 8 O O3A ADP . . . F 2 -94.023 -2.457 3.145 1 66.93 ? O3A ADP 401 B 1 
HETATM 9 O O5' ADP . . . F 2 -94.554 -2.269 0.664 1 118.59 ? O5' ADP 401 B 1 
HETATM 10 C C5' ADP . . . F 2 -94.173 -2.087 -0.683 1 145.25 ? C5' ADP 401 B 1 
HETATM 11 C C4' ADP . . . F 2 -95.384 -1.839 -1.557 1 143.52 ? C4' ADP 401 B 1 
HETATM 12 O O4' ADP . . . F 2 -96.154 -0.728 -1.074 1 151.26 ? O4' ADP 401 B 1 
HETATM 13 C C3' ADP . . . F 2 -94.964 -1.518 -2.989 1 143.21 ? C3' ADP 401 B 1 
HETATM 14 O O3' ADP . . . F 2 -95.818 -2.188 -3.916 1 155.94 ? O3' ADP 401 B 1 
HETATM 15 C C2' ADP . . . F 2 -95.117 -0.008 -3.08 1 154.27 ? C2' ADP 401 B 1 
HETATM 16 O O2' ADP . . . F 2 -95.677 0.315 -4.344 1 170.93 ? O2' ADP 401 B 1 
HETATM 17 C C1' ADP . . . F 2 -96.157 0.354 -2.026 1 164.49 ? C1' ADP 401 B 1 
HETATM 18 N N9 ADP . . . F 2 -96.089 1.619 -1.261 1 155.99 ? N9 ADP 401 B 1 
HETATM 19 C C8 ADP . . . F 2 -96.114 1.773 0.079 1 148.16 ? C8 ADP 401 B 1 
HETATM 20 N N7 ADP . . . F 2 -96.093 3.093 0.409 1 151.34 ? N7 ADP 401 B 1 
HETATM 21 C C5 ADP . . . F 2 -96.091 3.791 -0.745 1 153.57 ? C5 ADP 401 B 1 
HETATM 22 C C6 ADP . . . F 2 -96.09 5.213 -1.16 1 158.82 ? C6 ADP 401 B 1 
HETATM 23 N N6 ADP . . . F 2 -96.056 6.22 -0.255 1 155.03 ? N6 ADP 401 B 1 
HETATM 24 N N1 ADP . . . F 2 -96.072 5.485 -2.486 1 164.63 ? N1 ADP 401 B 1 
HETATM 25 C C2 ADP . . . F 2 -96.088 4.521 -3.425 1 157.84 ? C2 ADP 401 B 1 
HETATM 26 N N3 ADP . . . F 2 -96.106 3.216 -3.118 1 152.44 ? N3 ADP 401 B 1 
HETATM 27 C C4 ADP . . . F 2 -96.109 2.806 -1.833 1 150.06 ? C4 ADP 401 B 1 
HETATM 28 H "H5'1" ADP . . . F 2 -93.643 -2.974 -1.035 1 176.15 ? "H5'1" ADP 401 B 1 
HETATM 29 H "H5'2" ADP . . . F 2 -93.49 -1.238 -0.757 1 176.15 ? "H5'2" ADP 401 B 1 
HETATM 30 H H4' ADP . . . F 2 -95.99 -2.756 -1.527 1 174.07 ? H4' ADP 401 B 1 
HETATM 31 H H3' ADP . . . F 2 -93.945 -1.85 -3.233 1 173.69 ? H3' ADP 401 B 1 
HETATM 32 H HO3' ADP . . . F 2 -95.495 -2.042 -4.816 1 188.97 ? HO3' ADP 401 B 1 
HETATM 33 H H2' ADP . . . F 2 -94.158 0.512 -2.947 1 186.97 ? H2' ADP 401 B 1 
HETATM 34 H HO2' ADP . . . F 2 -95.076 0.029 -5.045 1 206.96 ? HO2' ADP 401 B 1 
HETATM 35 H H1' ADP . . . F 2 -97.052 0.517 -2.642 1 199.23 ? H1' ADP 401 B 1 
HETATM 36 H H8 ADP . . . F 2 -96.146 0.959 0.793 1 179.63 ? H8 ADP 401 B 1 
HETATM 37 H HN61 ADP . . . F 2 -96.049 6.013 0.735 1 187.88 ? HN61 ADP 401 B 1 
HETATM 38 H HN62 ADP . . . F 2 -96.038 7.179 -0.578 1 187.88 ? HN62 ADP 401 B 1 
HETATM 39 H H2 ADP . . . F 2 -96.087 4.81 -4.469 1 191.25 ? H2 ADP 401 B 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           244 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           39 
#