data_6IXW
#
_model_server_result.job_id            8gI7BftY5DVSpNYFZYBzCA 
_model_server_result.datetime_utc      '2024-10-19 12:22:30' 
_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          6ixw 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":401}' 
#
_entry.id    6IXW 
#
_exptl.entry_id    6IXW 
_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          131.55 
_cell.angle_gamma         90 
_cell.entry_id            6IXW 
_cell.length_a            164.153 
_cell.length_b            93.922 
_cell.length_c            114.699 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6IXW 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 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
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_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,F 1 1 
B,G,H 2 1 
C,I,J,K 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 G N N 
? 2 I 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 OE1 GLU 127 C GLU 125 1_555 F MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? 
metalc ? metalc2 D O1B ADP . C ADP 401 1_555 E MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
metalc ? metalc3 G O1B ADP . B ADP 401 1_555 H MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? 
metalc ? metalc4 C OD1 ASP 227 A ASP 225 1_555 K MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? 
metalc ? metalc5 C OD2 ASP 227 A ASP 225 1_555 K MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.823 ? 
metalc ? metalc6 I O1B ADP . A ADP 401 1_555 J MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? 
#
_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                     6IXW 
_atom_sites.fract_transf_matrix[1][1]    0.006092 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.005399 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010647 
_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]    0.011649 
_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 C 1 401 380 ADP ADP . 
E 3 MG C 1 402 401 MG MG . 
F 3 MG C 1 403 1 MG MG . 
G 2 ADP B 1 401 380 ADP ADP . 
H 3 MG B 1 402 401 MG MG . 
I 2 ADP A 1 401 380 ADP ADP . 
J 3 MG A 1 402 401 MG MG . 
K 3 MG A 1 403 2 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 -24.294 19.478 23.528 1 47.58 ? PB ADP 401 C 1 
HETATM 2 O O1B ADP . . . D 2 -24.861 18.887 22.245 1 112.7 ? O1B ADP 401 C 1 
HETATM 3 O O2B ADP . . . D 2 -24.282 20.984 23.561 1 47.04 ? O2B ADP 401 C 1 
HETATM 4 O O3B ADP . . . D 2 -24.812 18.826 24.786 1 85.14 ? O3B ADP 401 C 1 
HETATM 5 P PA ADP . . . D 2 -21.645 19.718 22.567 1 57.18 ? PA ADP 401 C 1 
HETATM 6 O O1A ADP . . . D 2 -20.989 18.683 21.679 1 59.42 ? O1A ADP 401 C 1 
HETATM 7 O O2A ADP . . . D 2 -22.24 20.963 21.973 1 72.81 ? O2A ADP 401 C 1 
HETATM 8 O O3A ADP . . . D 2 -22.772 18.97 23.441 1 110.69 ? O3A ADP 401 C 1 
HETATM 9 O O5' ADP . . . D 2 -20.619 20.145 23.725 1 43.97 ? O5' ADP 401 C 1 
HETATM 10 C C5' ADP . . . D 2 -19.877 21.358 23.637 1 53.1 ? C5' ADP 401 C 1 
HETATM 11 C C4' ADP . . . D 2 -19.114 21.585 24.937 1 48.54 ? C4' ADP 401 C 1 
HETATM 12 O O4' ADP . . . D 2 -17.819 21.019 24.783 1 39.64 ? O4' ADP 401 C 1 
HETATM 13 C C3' ADP . . . D 2 -18.897 23.063 25.262 1 43.53 ? C3' ADP 401 C 1 
HETATM 14 O O3' ADP . . . D 2 -19.872 23.582 26.178 1 50.12 ? O3' ADP 401 C 1 
HETATM 15 C C2' ADP . . . D 2 -17.524 23.114 25.895 1 99.69 ? C2' ADP 401 C 1 
HETATM 16 O O2' ADP . . . D 2 -17.582 23.024 27.329 1 96.43 ? O2' ADP 401 C 1 
HETATM 17 C C1' ADP . . . D 2 -16.846 21.86 25.396 1 47.86 ? C1' ADP 401 C 1 
HETATM 18 N N9 ADP . . . D 2 -15.824 22.251 24.401 1 70.44 ? N9 ADP 401 C 1 
HETATM 19 C C8 ADP . . . D 2 -15.97 22.353 23.064 1 54.53 ? C8 ADP 401 C 1 
HETATM 20 N N7 ADP . . . D 2 -14.798 22.722 22.477 1 71.33 ? N7 ADP 401 C 1 
HETATM 21 C C5 ADP . . . D 2 -13.883 22.862 23.463 1 81.72 ? C5 ADP 401 C 1 
HETATM 22 C C6 ADP . . . D 2 -12.449 23.233 23.565 1 68.22 ? C6 ADP 401 C 1 
HETATM 23 N N6 ADP . . . D 2 -11.719 23.549 22.457 1 56.93 ? N6 ADP 401 C 1 
HETATM 24 N N1 ADP . . . D 2 -11.896 23.25 24.808 1 87.45 ? N1 ADP 401 C 1 
HETATM 25 C C2 ADP . . . D 2 -12.592 22.947 25.922 1 49.95 ? C2 ADP 401 C 1 
HETATM 26 N N3 ADP . . . D 2 -13.89 22.608 25.904 1 61.31 ? N3 ADP 401 C 1 
HETATM 27 C C4 ADP . . . D 2 -14.569 22.55 24.728 1 91.69 ? C4 ADP 401 C 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          13 
_model_server_stats.element_count           27 
#