data_6GFG # _model_server_result.job_id V404rZ4M2qR9aPlJgPJMQg _model_server_result.datetime_utc '2024-11-13 04:02:29' _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 6gfg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 6GFG # _exptl.entry_id 6GFG _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 89.5 _cell.angle_beta 88.34 _cell.angle_gamma 62.54 _cell.entry_id 6GFG _cell.length_a 59.566 _cell.length_b 60.82 _cell.length_c 82.439 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6GFG _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 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,C,D,E,F,G 1 1 B,H,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 D 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 ND1 HIS 339 B HIS 320 1_555 G ZN ZN . B ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc2 A SG CYS 349 B CYS 330 1_555 G ZN ZN . B ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc3 A SG CYS 352 B CYS 333 1_555 G ZN ZN . B ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc4 A NE2 HIS 365 B HIS 346 1_555 G ZN ZN . B ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc5 A OD1 ASP 426 B ASP 407 1_555 E MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc6 A OD2 ASP 426 B ASP 407 1_555 F MG MG . B MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.588 ? metalc ? metalc7 D O1B ADP . B ADP 502 1_555 E MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc8 D O2B ADP . B ADP 502 1_555 F MG MG . B MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc9 D O1A ADP . B ADP 502 1_555 F MG MG . B MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? metalc ? metalc10 B ND1 HIS 339 A HIS 320 1_555 L ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc11 B SG CYS 349 A CYS 330 1_555 L ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc12 B SG CYS 352 A CYS 333 1_555 L ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc13 B NE2 HIS 365 A HIS 346 1_555 L ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.863 ? metalc ? metalc14 B OD2 ASP 426 A ASP 407 1_555 J MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc15 B OD1 ASP 426 A ASP 407 1_555 K MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc16 B OD2 ASP 426 A ASP 407 1_555 K MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc17 I O3B ADP . A ADP 502 1_555 J MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.97 ? metalc ? metalc18 I O3A ADP . A ADP 502 1_555 J MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc19 I O2B ADP . A ADP 502 1_555 K MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? # _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 6GFG _atom_sites.fract_transf_matrix[1][1] 0.016788 _atom_sites.fract_transf_matrix[1][2] -0.008726 _atom_sites.fract_transf_matrix[1][3] -0.000532 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01853 _atom_sites.fract_transf_matrix[2][3] 0.000096 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.012135 _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 KGN B 1 501 2 KGN KGN . D 3 ADP B 1 502 4 ADP ADP . E 4 MG B 1 503 7 MG MG . F 4 MG B 1 504 8 MG MG . G 5 ZN B 1 505 10 ZN ZN . H 2 KGN A 1 501 1 KGN KGN . I 3 ADP A 1 502 3 ADP ADP . J 4 MG A 1 503 5 MG MG . K 4 MG A 1 504 6 MG MG . L 5 ZN A 1 505 9 ZN ZN . # 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 -9.617 -35.254 34.68 0.87 44.38 ? PB ADP 502 B 1 HETATM 2 O O1B ADP . . . D 3 -8.408 -35.325 33.783 0.87 52.17 ? O1B ADP 502 B 1 HETATM 3 O O2B ADP . . . D 3 -10.479 -34.069 34.263 0.87 45.65 ? O2B ADP 502 B 1 HETATM 4 O O3B ADP . . . D 3 -10.284 -36.582 34.912 0.87 41.98 ? O3B ADP 502 B 1 HETATM 5 P PA ADP . . . D 3 -9.268 -33.688 37.089 0.87 46.32 ? PA ADP 502 B 1 HETATM 6 O O1A ADP . . . D 3 -9.269 -32.412 36.279 0.87 38.55 ? O1A ADP 502 B 1 HETATM 7 O O2A ADP . . . D 3 -8.385 -33.769 38.313 0.87 48.61 ? O2A ADP 502 B 1 HETATM 8 O O3A ADP . . . D 3 -9.034 -35.005 36.168 0.87 44.33 ? O3A ADP 502 B 1 HETATM 9 O O5' ADP . . . D 3 -10.792 -33.878 37.55 0.87 49.48 ? O5' ADP 502 B 1 HETATM 10 C C5' ADP . . . D 3 -11.186 -34.365 38.823 0.87 48.25 ? C5' ADP 502 B 1 HETATM 11 C C4' ADP . . . D 3 -12.179 -33.421 39.52 0.87 44.81 ? C4' ADP 502 B 1 HETATM 12 O O4' ADP . . . D 3 -11.931 -33.501 40.93 0.87 46.11 ? O4' ADP 502 B 1 HETATM 13 C C3' ADP . . . D 3 -12.058 -31.955 39.109 0.87 43.14 ? C3' ADP 502 B 1 HETATM 14 O O3' ADP . . . D 3 -13.055 -31.568 38.146 0.87 36.83 ? O3' ADP 502 B 1 HETATM 15 C C2' ADP . . . D 3 -12.082 -31.188 40.434 0.87 47.63 ? C2' ADP 502 B 1 HETATM 16 O O2' ADP . . . D 3 -13.321 -30.584 40.789 0.87 44.64 ? O2' ADP 502 B 1 HETATM 17 C C1' ADP . . . D 3 -11.751 -32.212 41.497 0.87 45.62 ? C1' ADP 502 B 1 HETATM 18 N N9 ADP . . . D 3 -10.333 -31.979 41.822 0.87 40.88 ? N9 ADP 502 B 1 HETATM 19 C C8 ADP . . . D 3 -9.276 -32.377 41.096 0.87 42.82 ? C8 ADP 502 B 1 HETATM 20 N N7 ADP . . . D 3 -8.124 -31.964 41.669 0.87 45.12 ? N7 ADP 502 B 1 HETATM 21 C C5 ADP . . . D 3 -8.455 -31.286 42.772 0.87 44.33 ? C5 ADP 502 B 1 HETATM 22 C C6 ADP . . . D 3 -7.728 -30.58 43.821 0.87 44.55 ? C6 ADP 502 B 1 HETATM 23 N N6 ADP . . . D 3 -6.38 -30.556 43.758 0.87 48.01 ? N6 ADP 502 B 1 HETATM 24 N N1 ADP . . . D 3 -8.443 -29.985 44.801 0.87 43.41 ? N1 ADP 502 B 1 HETATM 25 C C2 ADP . . . D 3 -9.778 -30.024 44.839 0.87 42.6 ? C2 ADP 502 B 1 HETATM 26 N N3 ADP . . . D 3 -10.504 -30.647 43.903 0.87 51.32 ? N3 ADP 502 B 1 HETATM 27 C C4 ADP . . . D 3 -9.909 -31.282 42.867 0.87 46.23 ? C4 ADP 502 B 1 HETATM 28 H "H5'1" ADP . . . D 3 -10.301 -34.485 39.452 0.87 57.89 ? "H5'1" ADP 502 B 1 HETATM 29 H "H5'2" ADP . . . D 3 -11.646 -35.348 38.706 0.87 57.89 ? "H5'2" ADP 502 B 1 HETATM 30 H H4' ADP . . . D 3 -13.2 -33.764 39.303 0.87 53.77 ? H4' ADP 502 B 1 HETATM 31 H H3' ADP . . . D 3 -11.064 -31.815 38.662 0.87 51.77 ? H3' ADP 502 B 1 HETATM 32 H HO3' ADP . . . D 3 -12.937 -30.635 37.918 0.87 44.2 ? HO3' ADP 502 B 1 HETATM 33 H H2' ADP . . . D 3 -11.288 -30.429 40.417 0.87 57.16 ? H2' ADP 502 B 1 HETATM 34 H HO2' ADP . . . D 3 -13.565 -29.931 40.119 0.87 53.57 ? HO2' ADP 502 B 1 HETATM 35 H H1' ADP . . . D 3 -12.393 -32.066 42.377 0.87 54.74 ? H1' ADP 502 B 1 HETATM 36 H H8 ADP . . . D 3 -9.337 -32.959 40.185 0.87 51.38 ? H8 ADP 502 B 1 HETATM 37 H HN61 ADP . . . D 3 -5.849 -30.082 44.475 0.87 57.62 ? HN61 ADP 502 B 1 HETATM 38 H HN62 ADP . . . D 3 -5.901 -31.022 43 0.87 57.62 ? HN62 ADP 502 B 1 HETATM 39 H H2 ADP . . . D 3 -10.291 -29.526 45.652 0.87 51.12 ? H2 ADP 502 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #