data_4JLV # _model_server_result.job_id ituNm1FdDRjszI1MtkJ-rg _model_server_result.datetime_utc '2024-12-01 12:11:26' _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 4jlv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1301}' # _entry.id 4JLV # _exptl.entry_id 4JLV _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 1 _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 4JLV _cell.length_a 41.03 _cell.length_b 64.63 _cell.length_c 88.28 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JLV _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 OG SER 97 A SER 1056 1_555 C MG MG . A MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? metalc ? metalc2 B O2B ADP . A ADP 1301 1_555 C MG MG . A MG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc3 C MG MG . A MG 1302 1_555 D O HOH . A HOH 1410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? # _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 4JLV _atom_sites.fract_transf_matrix[1][1] 0.024372 _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] 0.015473 _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] 0.011328 _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 B 2 ADP A 1 1301 300 ADP ADP . C 3 MG A 1 1302 301 MG MG . D 4 HOH A 1 1401 1 HOH HOH . D 4 HOH A 2 1402 2 HOH HOH . D 4 HOH A 3 1403 3 HOH HOH . D 4 HOH A 4 1404 4 HOH HOH . D 4 HOH A 5 1405 5 HOH HOH . D 4 HOH A 6 1406 6 HOH HOH . D 4 HOH A 7 1407 7 HOH HOH . D 4 HOH A 8 1408 8 HOH HOH . D 4 HOH A 9 1409 9 HOH HOH . D 4 HOH A 10 1410 10 HOH HOH . D 4 HOH A 11 1411 11 HOH HOH . D 4 HOH A 12 1412 12 HOH HOH . D 4 HOH A 13 1413 13 HOH HOH . D 4 HOH A 14 1414 14 HOH HOH . D 4 HOH A 15 1415 15 HOH HOH . D 4 HOH A 16 1416 16 HOH HOH . D 4 HOH A 17 1417 17 HOH HOH . D 4 HOH A 18 1418 18 HOH HOH . D 4 HOH A 19 1419 19 HOH HOH . D 4 HOH A 20 1420 20 HOH HOH . D 4 HOH A 21 1421 21 HOH HOH . D 4 HOH A 22 1422 22 HOH HOH . D 4 HOH A 23 1423 23 HOH HOH . # 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 . . . B 2 -0.417 -4.9 -16.38 1 63.66 ? PB ADP 1301 A 1 HETATM 2 O O1B ADP . . . B 2 0.899 -5.689 -16.505 1 66 ? O1B ADP 1301 A 1 HETATM 3 O O2B ADP . . . B 2 -0.271 -3.547 -15.708 1 55.15 ? O2B ADP 1301 A 1 HETATM 4 O O3B ADP . . . B 2 -1.58 -5.729 -15.85 1 59.47 ? O3B ADP 1301 A 1 HETATM 5 P PA ADP . . . B 2 -1.242 -3.255 -18.662 1 71.03 ? PA ADP 1301 A 1 HETATM 6 O O1A ADP . . . B 2 0.025 -2.49 -18.996 1 66.43 ? O1A ADP 1301 A 1 HETATM 7 O O2A ADP . . . B 2 -2.385 -2.539 -17.96 1 65.18 ? O2A ADP 1301 A 1 HETATM 8 O O3A ADP . . . B 2 -0.797 -4.637 -17.935 1 66.14 ? O3A ADP 1301 A 1 HETATM 9 O O5' ADP . . . B 2 -1.834 -3.871 -20.029 1 70.75 ? O5' ADP 1301 A 1 HETATM 10 C C5' ADP . . . B 2 -1.018 -4.737 -20.823 1 73.15 ? C5' ADP 1301 A 1 HETATM 11 C C4' ADP . . . B 2 -1.323 -4.465 -22.295 1 78.88 ? C4' ADP 1301 A 1 HETATM 12 O O4' ADP . . . B 2 -2.7 -4.795 -22.536 1 77.21 ? O4' ADP 1301 A 1 HETATM 13 C C3' ADP . . . B 2 -1.124 -2.994 -22.657 1 72.81 ? C3' ADP 1301 A 1 HETATM 14 O O3' ADP . . . B 2 -0.364 -2.888 -23.865 1 72.7 ? O3' ADP 1301 A 1 HETATM 15 C C2' ADP . . . B 2 -2.533 -2.443 -22.856 1 73.01 ? C2' ADP 1301 A 1 HETATM 16 O O2' ADP . . . B 2 -2.618 -1.484 -23.921 1 74.83 ? O2' ADP 1301 A 1 HETATM 17 C C1' ADP . . . B 2 -3.376 -3.683 -23.131 1 75.72 ? C1' ADP 1301 A 1 HETATM 18 N N9 ADP . . . B 2 -4.748 -3.575 -22.567 1 77.66 ? N9 ADP 1301 A 1 HETATM 19 C C8 ADP . . . B 2 -5.076 -3.339 -21.282 1 71.73 ? C8 ADP 1301 A 1 HETATM 20 N N7 ADP . . . B 2 -6.423 -3.304 -21.124 1 70.41 ? N7 ADP 1301 A 1 HETATM 21 C C5 ADP . . . B 2 -6.978 -3.518 -22.329 1 76.27 ? C5 ADP 1301 A 1 HETATM 22 C C6 ADP . . . B 2 -8.35 -3.613 -22.876 1 75.14 ? C6 ADP 1301 A 1 HETATM 23 N N6 ADP . . . B 2 -9.435 -3.466 -22.082 1 71.96 ? N6 ADP 1301 A 1 HETATM 24 N N1 ADP . . . B 2 -8.479 -3.849 -24.199 1 76.37 ? N1 ADP 1301 A 1 HETATM 25 C C2 ADP . . . B 2 -7.42 -4.004 -25.013 1 79.98 ? C2 ADP 1301 A 1 HETATM 26 N N3 ADP . . . B 2 -6.146 -3.931 -24.586 1 80.71 ? N3 ADP 1301 A 1 HETATM 27 C C4 ADP . . . B 2 -5.868 -3.695 -23.278 1 78.24 ? C4 ADP 1301 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #