data_4JSV # _model_server_result.job_id bV1Yf-uA8Mg3hxnlrxjfrA _model_server_result.datetime_utc '2024-11-20 04:31:24' _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 4jsv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":2601}' # _entry.id 4JSV # _exptl.entry_id 4JSV _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 90 _cell.angle_gamma 90 _cell.entry_id 4JSV _cell.length_a 139.4 _cell.length_b 163.2 _cell.length_c 207.8 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JSV _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H 1 1 C,D,I,J,K,L 2 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 E N N ? 3 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 OD1 ASN 968 B ASN 2343 1_555 F MG MG . B MG 2602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc2 A OD1 ASP 982 B ASP 2357 1_555 G MG MG . B MG 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc3 A OD2 ASP 982 B ASP 2357 1_555 G MG MG . B MG 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc4 E O1A ADP . B ADP 2601 1_555 F MG MG . B MG 2602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc5 E O3B ADP . B ADP 2601 1_555 F MG MG . B MG 2602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc6 E O3B ADP . B ADP 2601 1_555 H MG MGF . B MGF 2604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? metalc ? metalc7 C OD1 ASN 968 A ASN 2343 1_555 J MG MG . A MG 2602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc8 C OD1 ASP 982 A ASP 2357 1_555 K MG MG . A MG 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc9 C OD2 ASP 982 A ASP 2357 1_555 K MG MG . A MG 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.967 ? metalc ? metalc10 I O1A ADP . A ADP 2601 1_555 J MG MG . A MG 2602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc11 I O3B ADP . A ADP 2601 1_555 J MG MG . A MG 2602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc12 I O3B ADP . A ADP 2601 1_555 L MG MGF . A MGF 2604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? # _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 4JSV _atom_sites.fract_transf_matrix[1][1] 0.007174 _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] 0.006127 _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] 0.004812 _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 E 3 ADP B 1 2601 297 ADP ADP . F 4 MG B 1 2602 298 MG MG . G 4 MG B 1 2603 299 MG MG . H 5 MGF B 1 2604 300 MGF MGF . I 3 ADP A 1 2601 297 ADP ADP . J 4 MG A 1 2602 298 MG MG . K 4 MG A 1 2603 299 MG MG . L 5 MGF A 1 2604 300 MGF MGF . # 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 . . . E 3 -17.534 -30.951 -63.634 1 62.13 ? PB ADP 2601 B 1 HETATM 2 O O1B ADP . . . E 3 -17.125 -31.895 -64.75 1 60.24 ? O1B ADP 2601 B 1 HETATM 3 O O2B ADP . . . E 3 -18.983 -30.491 -63.7 1 62.1 ? O2B ADP 2601 B 1 HETATM 4 O O3B ADP . . . E 3 -16.526 -29.836 -63.474 1 59.93 ? O3B ADP 2601 B 1 HETATM 5 P PA ADP . . . E 3 -17.604 -31.415 -60.708 1 62.25 ? PA ADP 2601 B 1 HETATM 6 O O1A ADP . . . E 3 -17.435 -29.902 -60.609 1 60.79 ? O1A ADP 2601 B 1 HETATM 7 O O2A ADP . . . E 3 -16.699 -32.308 -59.879 1 60.8 ? O2A ADP 2601 B 1 HETATM 8 O O3A ADP . . . E 3 -17.426 -31.863 -62.275 1 62.67 ? O3A ADP 2601 B 1 HETATM 9 O O5' ADP . . . E 3 -19.134 -31.842 -60.315 1 60.52 ? O5' ADP 2601 B 1 HETATM 10 C C5' ADP . . . E 3 -20.296 -31.035 -60.564 1 58.02 ? C5' ADP 2601 B 1 HETATM 11 C C4' ADP . . . E 3 -21.172 -30.949 -59.315 1 56.22 ? C4' ADP 2601 B 1 HETATM 12 O O4' ADP . . . E 3 -21.205 -32.204 -58.622 1 55.22 ? O4' ADP 2601 B 1 HETATM 13 C C3' ADP . . . E 3 -20.682 -29.924 -58.286 1 55.31 ? C3' ADP 2601 B 1 HETATM 14 O O3' ADP . . . E 3 -21.199 -28.606 -58.51 1 54.83 ? O3' ADP 2601 B 1 HETATM 15 C C2' ADP . . . E 3 -21.083 -30.504 -56.93 1 54.43 ? C2' ADP 2601 B 1 HETATM 16 O O2' ADP . . . E 3 -22.371 -30.096 -56.446 1 52.96 ? O2' ADP 2601 B 1 HETATM 17 C C1' ADP . . . E 3 -21.154 -31.999 -57.19 1 54.33 ? C1' ADP 2601 B 1 HETATM 18 N N9 ADP . . . E 3 -19.984 -32.682 -56.551 1 53.15 ? N9 ADP 2601 B 1 HETATM 19 C C8 ADP . . . E 3 -18.912 -33.185 -57.203 1 52.54 ? C8 ADP 2601 B 1 HETATM 20 N N7 ADP . . . E 3 -18.029 -33.754 -56.342 1 51.79 ? N7 ADP 2601 B 1 HETATM 21 C C5 ADP . . . E 3 -18.534 -33.621 -55.103 1 51.33 ? C5 ADP 2601 B 1 HETATM 22 C C6 ADP . . . E 3 -18.105 -34.002 -53.738 1 50.77 ? C6 ADP 2601 B 1 HETATM 23 N N6 ADP . . . E 3 -16.93 -34.651 -53.554 1 50.44 ? N6 ADP 2601 B 1 HETATM 24 N N1 ADP . . . E 3 -18.918 -33.681 -52.702 1 50.46 ? N1 ADP 2601 B 1 HETATM 25 C C2 ADP . . . E 3 -20.084 -33.033 -52.895 1 50.61 ? C2 ADP 2601 B 1 HETATM 26 N N3 ADP . . . E 3 -20.535 -32.653 -54.109 1 51.07 ? N3 ADP 2601 B 1 HETATM 27 C C4 ADP . . . E 3 -19.821 -32.915 -55.237 1 51.85 ? C4 ADP 2601 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 46 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #