data_2I5B # _model_server_result.job_id WsmEppqOEBmAIdbjkMiaiA _model_server_result.datetime_utc '2024-11-24 16:35:28' _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 2i5b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":501}' # _entry.id 2I5B # _exptl.entry_id 2I5B _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 5 _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 90 _cell.entry_id 2I5B _cell.length_a 102.499 _cell.length_b 102.499 _cell.length_c 251.36 _cell.Z_PDB 40 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2I5B _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 ? dimeric 2 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,F,I 1 1 B,C,G,H 2 1 E,J 3 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 8_554 -y,-x,-z-1/2 0 -1 0 -1 0 0 0 0 -1 0 0 -125.68 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 F N N ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 112 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 112 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 112 _struct_conn.ptnr2_auth_asym_id C _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 112 _struct_conn.ptnr2_symmetry 1_555 _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 2.009 _struct_conn.pdbx_value_order ? # _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 2I5B _atom_sites.fract_transf_matrix[1][1] 0.009756 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009756 _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] 0.003978 _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 F 2 ADP A 1 301 301 ADP ADP . G 2 ADP C 1 401 401 ADP ADP . H 2 ADP D 1 501 501 ADP ADP . I 2 ADP B 1 601 601 ADP ADP . J 2 ADP E 1 701 701 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 . . . H 2 19.131 -37.903 -45.246 1 40.33 ? PB ADP 501 D 1 HETATM 2 O O1B ADP . . . H 2 18.779 -37.253 -46.561 1 40.24 ? O1B ADP 501 D 1 HETATM 3 O O2B ADP . . . H 2 18.019 -38.71 -44.606 1 39.65 ? O2B ADP 501 D 1 HETATM 4 O O3B ADP . . . H 2 19.856 -36.992 -44.286 1 40.69 ? O3B ADP 501 D 1 HETATM 5 P PA ADP . . . H 2 20.004 -40.178 -46.765 1 37.59 ? PA ADP 501 D 1 HETATM 6 O O1A ADP . . . H 2 18.539 -40.556 -46.773 1 35.03 ? O1A ADP 501 D 1 HETATM 7 O O2A ADP . . . H 2 20.696 -39.653 -48.01 1 38.43 ? O2A ADP 501 D 1 HETATM 8 O O3A ADP . . . H 2 20.247 -39.016 -45.647 1 40.06 ? O3A ADP 501 D 1 HETATM 9 O O5' ADP . . . H 2 20.903 -41.445 -46.334 1 35.73 ? O5' ADP 501 D 1 HETATM 10 C C5' ADP . . . H 2 20.963 -41.989 -45.022 1 34.84 ? C5' ADP 501 D 1 HETATM 11 C C4' ADP . . . H 2 21.277 -43.476 -45.148 1 35.09 ? C4' ADP 501 D 1 HETATM 12 O O4' ADP . . . H 2 20.092 -44.278 -45.21 1 35.25 ? O4' ADP 501 D 1 HETATM 13 C C3' ADP . . . H 2 22.049 -43.768 -46.404 1 34.91 ? C3' ADP 501 D 1 HETATM 14 O O3' ADP . . . H 2 23.012 -44.757 -46.074 1 35.1 ? O3' ADP 501 D 1 HETATM 15 C C2' ADP . . . H 2 21.053 -44.398 -47.342 1 36.16 ? C2' ADP 501 D 1 HETATM 16 O O2' ADP . . . H 2 21.715 -45.298 -48.243 1 36.87 ? O2' ADP 501 D 1 HETATM 17 C C1' ADP . . . H 2 20.071 -45.06 -46.391 1 36.82 ? C1' ADP 501 D 1 HETATM 18 N N9 ADP . . . H 2 18.682 -45.067 -46.896 1 37.53 ? N9 ADP 501 D 1 HETATM 19 C C8 ADP . . . H 2 17.863 -44.009 -47.106 1 38.28 ? C8 ADP 501 D 1 HETATM 20 N N7 ADP . . . H 2 16.644 -44.402 -47.568 1 37.82 ? N7 ADP 501 D 1 HETATM 21 C C5 ADP . . . H 2 16.682 -45.74 -47.645 1 36.84 ? C5 ADP 501 D 1 HETATM 22 C C6 ADP . . . H 2 15.748 -46.799 -48.053 1 37.09 ? C6 ADP 501 D 1 HETATM 23 N N6 ADP . . . H 2 14.501 -46.502 -48.471 1 37.53 ? N6 ADP 501 D 1 HETATM 24 N N1 ADP . . . H 2 16.174 -48.078 -47.99 1 38.23 ? N1 ADP 501 D 1 HETATM 25 C C2 ADP . . . H 2 17.42 -48.39 -47.567 1 38.63 ? C2 ADP 501 D 1 HETATM 26 N N3 ADP . . . H 2 18.336 -47.479 -47.177 1 37.53 ? N3 ADP 501 D 1 HETATM 27 C C4 ADP . . . H 2 18.019 -46.169 -47.203 1 37.12 ? C4 ADP 501 D 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #