data_2I8C
#
_model_server_result.job_id            TgGk34EHSvwzje5izVWc4A 
_model_server_result.datetime_utc      '2024-11-05 23:58:27' 
_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          2i8c 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":400}' 
#
_entry.id    2I8C 
#
_exptl.entry_id    2I8C 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          96.05 
_cell.angle_gamma         90 
_cell.entry_id            2I8C 
_cell.length_a            67.802 
_cell.length_b            66.972 
_cell.length_c            78.992 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2I8C 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 G 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 B OE2 GLU 306 B GLU 306 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? 
metalc ? metalc2 G O2A ADP . B ADP 400 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? 
metalc ? metalc3 G O2B ADP . B ADP 400 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
#
_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                     2I8C 
_atom_sites.fract_transf_matrix[1][1]    0.014749 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001563 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014932 
_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]    0.01273 
_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
C 2 SO4 A 1 401 401 SO4 SO4 . 
D 3 ADP A 1 400 400 ADP ADP . 
E 2 SO4 B 1 401 401 SO4 SO4 . 
F 4 MG B 1 402 402 MG MG . 
G 3 ADP B 1 400 400 ADP ADP . 
#
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 3 10.795 -13.847 8.564 1 94.5 ? PB ADP 400 A 1 
HETATM 2 O O1B ADP . . . D 3 11.694 -12.724 9.037 1 93.63 ? O1B ADP 400 A 1 
HETATM 3 O O2B ADP . . . D 3 9.845 -13.499 7.422 1 94.13 ? O2B ADP 400 A 1 
HETATM 4 O O3B ADP . . . D 3 11.515 -15.16 8.376 1 93.83 ? O3B ADP 400 A 1 
HETATM 5 P PA ADP . . . D 3 8.245 -14.12 9.951 1 90.5 ? PA ADP 400 A 1 
HETATM 6 O O1A ADP . . . D 3 7.914 -13.617 11.332 1 89.4 ? O1A ADP 400 A 1 
HETATM 7 O O2A ADP . . . D 3 7.554 -13.5 8.754 1 89.25 ? O2A ADP 400 A 1 
HETATM 8 O O3A ADP . . . D 3 9.862 -14.115 9.87 1 93.01 ? O3A ADP 400 A 1 
HETATM 9 O O5' ADP . . . D 3 8.004 -15.712 9.831 1 91.1 ? O5' ADP 400 A 1 
HETATM 10 C C5' ADP . . . D 3 8.271 -16.44 8.623 1 90.48 ? C5' ADP 400 A 1 
HETATM 11 C C4' ADP . . . D 3 7.002 -17.105 8.081 1 90.47 ? C4' ADP 400 A 1 
HETATM 12 O O4' ADP . . . D 3 6.56 -18.11 8.994 1 90.06 ? O4' ADP 400 A 1 
HETATM 13 C C3' ADP . . . D 3 5.827 -16.142 7.875 1 90.66 ? C3' ADP 400 A 1 
HETATM 14 O O3' ADP . . . D 3 5.64 -15.753 6.505 1 91.42 ? O3' ADP 400 A 1 
HETATM 15 C C2' ADP . . . D 3 4.605 -16.868 8.4 1 90.08 ? C2' ADP 400 A 1 
HETATM 16 O O2' ADP . . . D 3 3.765 -17.41 7.387 1 89.54 ? O2' ADP 400 A 1 
HETATM 17 C C1' ADP . . . D 3 5.15 -18.002 9.246 1 89.65 ? C1' ADP 400 A 1 
HETATM 18 N N9 ADP . . . D 3 4.804 -17.577 10.619 1 89.54 ? N9 ADP 400 A 1 
HETATM 19 C C8 ADP . . . D 3 5.622 -16.965 11.492 1 89.43 ? C8 ADP 400 A 1 
HETATM 20 N N7 ADP . . . D 3 4.956 -16.68 12.637 1 90.15 ? N7 ADP 400 A 1 
HETATM 21 C C5 ADP . . . D 3 3.686 -17.096 12.498 1 89.74 ? C5 ADP 400 A 1 
HETATM 22 C C6 ADP . . . D 3 2.477 -17.101 13.341 1 89.11 ? C6 ADP 400 A 1 
HETATM 23 N N6 ADP . . . D 3 2.521 -16.583 14.586 1 88.9 ? N6 ADP 400 A 1 
HETATM 24 N N1 ADP . . . D 3 1.357 -17.634 12.81 1 89.14 ? N1 ADP 400 A 1 
HETATM 25 C C2 ADP . . . D 3 1.335 -18.148 11.563 1 89.09 ? C2 ADP 400 A 1 
HETATM 26 N N3 ADP . . . D 3 2.401 -18.181 10.751 1 88.65 ? N3 ADP 400 A 1 
HETATM 27 C C4 ADP . . . D 3 3.585 -17.679 11.156 1 89.45 ? C4 ADP 400 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           274 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           27 
#