data_1T5T # _model_server_result.job_id Bx8BGGo_TBJ26OwgkjxK4w _model_server_result.datetime_utc '2024-11-24 05:44:39' _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 1t5t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1001}' # _entry.id 1T5T # _exptl.entry_id 1T5T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _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 108.82 _cell.angle_gamma 90 _cell.entry_id 1T5T _cell.length_a 162.477 _cell.length_b 75.617 _cell.length_c 151.651 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1T5T _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 6 _struct_asym.id H _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 O VAL 304 A VAL 304 1_555 C CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.678 ? metalc ? metalc2 A O ALA 305 A ALA 305 1_555 C CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc3 A O ILE 307 A ILE 307 1_555 C CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc4 A OE2 GLU 309 A GLU 309 1_555 C CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc5 A OE1 GLU 309 A GLU 309 1_555 C CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? metalc ? metalc6 A OD2 ASP 351 A ASP 351 1_555 B AL ALF . A ALF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.307 ? metalc ? metalc7 A OD1 ASP 351 A ASP 351 1_555 B AL ALF . A ALF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc8 A OD2 ASP 351 A ASP 351 1_555 E MG MG . A MG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc9 A O THR 353 A THR 353 1_555 E MG MG . A MG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc10 A NZ LYS 684 A LYS 684 1_555 B AL ALF . A ALF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.633 ? metalc ? metalc11 A OD1 ASP 703 A ASP 703 1_555 E MG MG . A MG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? metalc ? metalc12 A OD2 ASP 703 A ASP 703 1_555 E MG MG . A MG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc13 A O LEU 711 A LEU 711 1_555 F K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.837 ? metalc ? metalc14 A O LYS 712 A LYS 712 1_555 F K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.98 ? metalc ? metalc15 A O ALA 714 A ALA 714 1_555 F K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.688 ? metalc ? metalc16 A OE2 GLU 732 A GLU 732 1_555 F K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.178 ? metalc ? metalc17 A OE1 GLU 732 A GLU 732 1_555 F K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc18 A OD1 ASN 768 A ASN 768 1_555 D CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc19 A OE2 GLU 771 A GLU 771 1_555 D CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc20 A OD1 ASN 796 A ASN 796 1_555 C CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc21 A OG1 THR 799 A THR 799 1_555 D CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc22 A OD2 ASP 800 A ASP 800 1_555 C CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc23 A OD2 ASP 800 A ASP 800 1_555 D CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.344 ? metalc ? metalc24 A OD1 ASP 800 A ASP 800 1_555 D CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc25 A OE2 GLU 908 A GLU 908 1_555 D CA CA . A CA 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? metalc ? metalc26 H O3B ADP . A ADP 1001 1_555 B AL ALF . A ALF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc27 H O3A ADP . A ADP 1001 1_555 B AL ALF . A ALF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.506 ? metalc ? metalc28 H O1A ADP . A ADP 1001 1_555 G MG MG . A MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc29 H O2B ADP . A ADP 1001 1_555 G MG MG . A MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc30 B AL ALF . A ALF 1002 1_555 E MG MG . A MG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.378 ? metalc ? metalc31 B F3 ALF . A ALF 1002 1_555 E MG MG . A MG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.861 ? metalc ? metalc32 B F1 ALF . A ALF 1002 1_555 G MG MG . A MG 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? metalc ? metalc33 B AL ALF . A ALF 1002 1_555 I O HOH . A HOH 1047 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.704 ? metalc ? metalc34 D CA CA . A CA 1004 1_555 I O HOH . A HOH 1046 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc35 E MG MG . A MG 1005 1_555 I O HOH . A HOH 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.819 ? metalc ? metalc36 E MG MG . A MG 1005 1_555 I O HOH . A HOH 1047 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc37 G MG MG . A MG 1007 1_555 I O HOH . A HOH 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc38 G MG MG . A MG 1007 1_555 I O HOH . A HOH 1049 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc39 G MG MG . A MG 1007 1_555 I O HOH . A HOH 1050 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.651 ? # _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 1T5T _atom_sites.fract_transf_matrix[1][1] 0.006155 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002097 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013225 _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] 0.006966 _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 ALF A 1 1002 1002 ALF ALF . C 3 CA A 1 1003 1003 CA CA . D 3 CA A 1 1004 1004 CA CA . E 4 MG A 1 1005 1005 MG MG . F 5 K A 1 1006 1006 K K . G 4 MG A 1 1007 1007 MG MG . H 6 ADP A 1 1001 1001 ADP ADP . I 7 HOH A 1 1008 5 HOH HOH . I 7 HOH A 2 1009 6 HOH HOH . I 7 HOH A 3 1010 7 HOH HOH . I 7 HOH A 4 1011 8 HOH HOH . I 7 HOH A 5 1012 9 HOH HOH . I 7 HOH A 6 1013 10 HOH HOH . I 7 HOH A 7 1014 11 HOH HOH . I 7 HOH A 8 1015 12 HOH HOH . I 7 HOH A 9 1016 13 HOH HOH . I 7 HOH A 10 1017 14 HOH HOH . I 7 HOH A 11 1018 15 HOH HOH . I 7 HOH A 12 1019 16 HOH HOH . I 7 HOH A 13 1020 17 HOH HOH . I 7 HOH A 14 1021 18 HOH HOH . I 7 HOH A 15 1022 19 HOH HOH . I 7 HOH A 16 1023 21 HOH HOH . I 7 HOH A 17 1024 22 HOH HOH . I 7 HOH A 18 1025 23 HOH HOH . I 7 HOH A 19 1026 24 HOH HOH . I 7 HOH A 20 1027 25 HOH HOH . I 7 HOH A 21 1028 26 HOH HOH . I 7 HOH A 22 1029 27 HOH HOH . I 7 HOH A 23 1030 28 HOH HOH . I 7 HOH A 24 1031 29 HOH HOH . I 7 HOH A 25 1032 30 HOH HOH . I 7 HOH A 26 1033 31 HOH HOH . I 7 HOH A 27 1034 32 HOH HOH . I 7 HOH A 28 1035 33 HOH HOH . I 7 HOH A 29 1036 34 HOH HOH . I 7 HOH A 30 1037 35 HOH HOH . I 7 HOH A 31 1038 36 HOH HOH . I 7 HOH A 32 1039 37 HOH HOH . I 7 HOH A 33 1040 38 HOH HOH . I 7 HOH A 34 1041 39 HOH HOH . I 7 HOH A 35 1042 40 HOH HOH . I 7 HOH A 36 1043 41 HOH HOH . I 7 HOH A 37 1044 42 HOH HOH . I 7 HOH A 38 1045 44 HOH HOH . I 7 HOH A 39 1046 45 HOH HOH . I 7 HOH A 40 1047 61 HOH HOH . I 7 HOH A 41 1048 70 HOH HOH . I 7 HOH A 42 1049 71 HOH HOH . I 7 HOH A 43 1050 72 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 . . . H 6 -16.306 2.511 13.049 1 47.8 ? PB ADP 1001 A 1 HETATM 2 O O1B ADP . . . H 6 -16.24 3.483 11.895 1 45.43 ? O1B ADP 1001 A 1 HETATM 3 O O2B ADP . . . H 6 -17.403 1.48 13.001 1 47.44 ? O2B ADP 1001 A 1 HETATM 4 O O3B ADP . . . H 6 -16.306 3.155 14.42 1 45.82 ? O3B ADP 1001 A 1 HETATM 5 P PA ADP . . . H 6 -14.829 0.222 12.172 1 46.69 ? PA ADP 1001 A 1 HETATM 6 O O1A ADP . . . H 6 -15.639 -0.838 12.887 1 42.1 ? O1A ADP 1001 A 1 HETATM 7 O O2A ADP . . . H 6 -13.347 -0.056 11.945 1 47.91 ? O2A ADP 1001 A 1 HETATM 8 O O3A ADP . . . H 6 -14.929 1.693 12.847 1 44.68 ? O3A ADP 1001 A 1 HETATM 9 O O5' ADP . . . H 6 -15.433 0.565 10.722 1 43.31 ? O5' ADP 1001 A 1 HETATM 10 C C5' ADP . . . H 6 -14.555 1.032 9.692 1 38.47 ? C5' ADP 1001 A 1 HETATM 11 C C4' ADP . . . H 6 -15.35 1.704 8.589 1 38.39 ? C4' ADP 1001 A 1 HETATM 12 O O4' ADP . . . H 6 -15.901 0.7 7.746 1 37.55 ? O4' ADP 1001 A 1 HETATM 13 C C3' ADP . . . H 6 -16.553 2.572 9.023 1 38.9 ? C3' ADP 1001 A 1 HETATM 14 O O3' ADP . . . H 6 -16.202 3.925 9.342 1 38.02 ? O3' ADP 1001 A 1 HETATM 15 C C2' ADP . . . H 6 -17.517 2.493 7.852 1 36.88 ? C2' ADP 1001 A 1 HETATM 16 O O2' ADP . . . H 6 -17.187 3.459 6.857 1 32.19 ? O2' ADP 1001 A 1 HETATM 17 C C1' ADP . . . H 6 -17.174 1.153 7.241 1 39.83 ? C1' ADP 1001 A 1 HETATM 18 N N9 ADP . . . H 6 -18.101 0.08 7.586 1 39.61 ? N9 ADP 1001 A 1 HETATM 19 C C8 ADP . . . H 6 -18.539 -0.183 8.805 1 41.57 ? C8 ADP 1001 A 1 HETATM 20 N N7 ADP . . . H 6 -19.352 -1.258 8.766 1 43.74 ? N7 ADP 1001 A 1 HETATM 21 C C5 ADP . . . H 6 -19.417 -1.715 7.506 1 42.47 ? C5 ADP 1001 A 1 HETATM 22 C C6 ADP . . . H 6 -20.077 -2.836 6.801 1 43.02 ? C6 ADP 1001 A 1 HETATM 23 N N6 ADP . . . H 6 -20.865 -3.69 7.481 1 44.17 ? N6 ADP 1001 A 1 HETATM 24 N N1 ADP . . . H 6 -19.922 -2.976 5.478 1 42.49 ? N1 ADP 1001 A 1 HETATM 25 C C2 ADP . . . H 6 -19.143 -2.093 4.828 1 45.04 ? C2 ADP 1001 A 1 HETATM 26 N N3 ADP . . . H 6 -18.496 -1.049 5.401 1 44.34 ? N3 ADP 1001 A 1 HETATM 27 C C4 ADP . . . H 6 -18.587 -0.809 6.727 1 41.82 ? C4 ADP 1001 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 349 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #